The DOI matches its Crossref record; 62 of the 64 references it cites were found in a registry or an index; 22 of the 49 sources its claims cite were checked for support.
Assembly requirements of PU.1–Pip (IRF‐4) activator complexes: inhibiting function in vivo using fused dimers
Open accessAbstract
Gene expression in higher eukaryotes appears to be regulated by specific combinations of transcription factors binding to regulatory sequences. The Ets factor PU.1 and the IRF protein Pip (IRF-4) represent a pair of interacting transcription factors implicated in regulating B cell-specific gene expression. Pip is recruited to its binding site on DNA by phosphorylated PU.1. PU.1-Pip interaction is shown to be template directed and involves two distinct protein-protein interaction surfaces: (i) the ets and IRF DNA-binding domains; and (ii) the phosphorylated PEST region of PU.1 and a lysine-requiring putative alpha-helix in Pip. Thus, a coordinated set of protein-protein and protein-DNA contacts are essential for PU.1-Pip ternary complex assembly. To analyze the function of these factors in vivo, we engineered chimeric repressors containing the ets and IRF DNA-binding domains connected by a flexible POU domain linker. When stably expressed, the wild-type fused dimer strongly repressed the expression of a rearranged immunoglobulin lambda gene, thereby establishing the functional importance of PU.1-Pip complexes in B cell gene expression. Comparative analysis of the wild-type dimer with a series of mutant dimers distinguished a gene regulated by PU.1 and Pip from one regulated by PU.1 alone. This strategy should prove generally useful in analyzing the function of interacting transcription factors in vivo, and for identifying novel genes regulated by such complexes.
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Claims the paper makes
96 Own result · 71 Own interpretation · 18 Own method · 15 No full text of the sources · 10 Supported · 8 Partly supported · 4 No basis given · 3 Sources not found · 3 Not checked yet · 2 Couldn’t confirm · 1 Supported so far · accuracy not yet measured
Every source the paper cites for this claim was checked and supports it.
In the paper
“When co-expressed ectopically, PU.1 and Pip synergistically activate transcription of a reporter gene containing multiple copies of the composite element from the IgL λ enhancer, E λ2-4 (Eisenbeis et al., 1995).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Introduction
What the sources say
- Supportedcites Eisenbeis et al., 1995 source
The section “In conjunction with PU.1, Pip functions as a transcriptional activator” reports that neither protein alone activated the reporter, whereas co-expression in NIH-3T3 cells did. Figure 6 identifies the reporter as containing a tetramer of composite elements from the Eλ2-4 enhancer. (LLM, conf=0.93)
plaindirect- Asserted: passes — The authors put it forward as true.
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- Supported
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In the paper
“A C-terminal regulatory domain within Pip itself is also required for ternary complex assembly (Brass et al., 1996).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Introduction
What the sources say
- Partly supportedcites Brass et al., 1996 sourceExperimental — accuracy not yet measured
The deletion analysis reports that Pip amino acids 410–439 are necessary for high-affinity ternary complex formation with PU.1. However, mutants lacking that segment still formed weak ternary complexes, so the paper does not show that the C-terminal domain is required for assembly altogether. The relevant passages are in the section on Pip repression of IFN-inducible transcription; page numbers are unavailable in our copy. (LLM, conf=0.88)
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- Partly supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“In addition, this regulatory domain autoinhibits binding of Pip to DNA in the absence of PU.1.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Introduction
What the sources say
- Supportedcites Brass et al., 1996 source
The 'Structural basis for PU.1-dependent DNA-binding of Pip' section identifies amino acids 138–450 as a regulatory domain responsible for autoinhibition of DNA binding. The deletion-analysis section reports that full-length Pip did not bind DNA independently but formed a ternary complex with PU.1. Page numbers are not provided in the supplied passages. (LLM, conf=0.94)
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- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“Previously, using deletion analysis and secondary structure predictions, we suggested that a putative α-helical region (amino acids 399-413) in Pip's C-terminus is important for ternary complex formation with PU.1 (Figure 1A and B; Brass et al., 1996).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
What the sources say
- Supportedcites Brass et al., 1996 source
In “Structural basis for PU.1-dependent DNA-binding of Pip,” the authors predict an α-helical region in Pip’s C-terminus and postulate that it may play a key role in ternary complex formation. The “Model of PU.1/Pip ternary complex formation” identifies that putative helix as amino acids 399–413. The citing sentence preserves the paper’s tentative framing. (LLM, conf=0.94)
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“PU.1 and Pip represent the major components of the ternary complex formed with nuclear extract from these cells”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
What the sources say
- Supportedcites Brass et al., 1996 source
In the “Pip is NF-EM5” section (page not provided), anti-PU.1 and anti-Pip antisera each supershift the JB2 complex formed with J558L nuclear extract. The authors conclude that Pip is the predominant factor associating with PU.1 on these enhancer segments in J558L cells. (LLM, conf=0.93)
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Supported
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In the paper
“On lower affinity sites, however, the chelating effect provided by the linker may lower the overall entropic cost associated with binding, allowing PipPU to bind as efficiently as the wildtype proteins”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
What the sources say
- Partly supportedcites Klemm and Pabo, 1996 sourceExperimental — accuracy not yet measured
The “Contribution of the linker to cooperative binding” section (page unavailable) says the linker produces a chelate effect and reduces the entropic cost of complex formation. The paper studies Oct-1 POU-domain binding; it does not establish that PipPU binds lower-affinity sites as efficiently as wild-type proteins. (LLM, conf=0.87)
hedgedconditional- Asserted: passes — The authors put it forward as true.
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- Partly supported
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In the paper
“it appears that other, as yet uncharacterized helices within this region may pack together with Pip's helix amino acids 395-413 to form a tertiary fold which is competent for PU.1 association.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
What the sources say
- Partly supportedcites Brass et al., 1996 sourceExperimental — accuracy not yet measured
In the deletion-analysis passage (page not available), removing Pip residues 150–340 weakened ternary complex formation with PU.1; the authors suggest that region may position the carboxy-terminal domain or contain another required region. In “Structural basis for PU.1-dependent DNA-binding of Pip” (page not available), they propose a role for a putative helix near residues 399–413. Our copy does not say that uncharacterized helices in residues 150–340 pack with it to form a tertiary fold. (LLM, conf=0.84)
hedgedconditional- Asserted: passes — The authors put it forward as true.
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- Partly supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“This is presumably due to displacement of endogenous PU.1 from an isolated Ets site in the J chain promoter”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Fused dimers as a general tool for analysis of combinatorial control of transcription in vivo
What the sources say
- Supportedcites Shin and Koshland, 1993 source
In “A PU.1 dominant negative mutant blocks PU.1 regulation of the J-chain gene promoter” (Fig. 10; page not provided), the paper reports that the N133 mutant suppressed J-chain promoter activity by competitively binding its single PU.1 site. It interprets this as preventing endogenous PU.1 from binding the JB element, supporting the proposed displacement mechanism. (LLM, conf=0.94)
hedgedconditional- Asserted: passes — The authors put it forward as true.
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- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“This is consistent with increased expression of Pip in plasma cell lines such as J558L”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
What the sources say
- Supportedcites Brass et al., 1996 source
The “Pip is NF-EM5” section reports Western blot detection of Pip in B-cell lines, including the plasmacyte line J558L, with expression increasing in later-stage cells (Fig. 1B). This supports the claim of increased Pip expression in a plasma-cell line such as J558L. (LLM, conf=0.93)
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Supported
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“Each enhancer contains an essential composite site (λB) bound by PU.1 and Pip”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
What the sources say
- Could not verifycites Hagman et al., 1990 sourceExperimental — accuracy not yet measured
The Abstract identifies two lambda enhancers, and “Cloning of a second enhancer and comparison with” discusses conserved sequence motifs. Neither passage identifies an essential λB composite site or reports binding by PU.1 and Pip; searches for those terms found no supporting passage in our copy. (LLM, conf=0.76)
- Not matchedcites Rudin and Storb 1992
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Not checked — no full text of the sourcecites Eisenbeis et al., 1993 source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Could not verify
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, the affinity of full-length Pip for the PU.1-DNA complex is Ͼ800-fold greater than that observed for the Pip DBD (2.6 nM versus 2.1 µM).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Unlike full-length Pip, the isolated Pip DBD possessed intrinsic, albeit weak, DNA affinity (K d ~96 µM, compare Figures 3B and 4A), consistent with removal of the autoinhibitory domain.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
plain- Asserted: passes — The authors put it forward as true.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“PU.1-Pip interaction is shown to be template directed and involves two distinct protein-protein interaction surfaces: (i) the ets and IRF DNA-binding domains; and (ii) the phosphorylated PEST region of PU.1 and a lysine-requiring putative α-helix in Pip.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Abstract
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“PU.1-Pip interaction is shown to be template directed and involves two distinct protein-protein interaction surfaces: (i) the ets and IRF DNA-binding domains; and (ii) the phosphorylated PEST region of PU.1 and a lysine-requiring putative α-helix in Pip.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Abstract
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“A glutaraldehyde-dependent adduct containing Pip was detected, with a molecular mass of ~80-85 kDa, in excellent agreement with the predicted size of a crosslinked species comprising a heterodimer of Pip and PU.1 983 (Figure 5B, compare lanes 1 and 2).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > PU.1 and the DNA-binding domain of IRF-1 compete for binding to λB DNA
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Chimeric proteins containing either two or three copies of the linker bound to the λB site with highest affinity.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
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In the paper
“The alanine substitution of amino acids 397-400 (PipAS397) and 401-404 (PipAS401) within the predicted helix impaired ternary complex formation, resulting in ~1 or 26% binding, respectively, as compared with wild-type Pip (Figure 1D, compare lane 3 with lanes 6 and 7).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“A substantial retention of wild-type binding (40%) was seen after substitution of an arginine for lysine at that position (Figure 1E, compare lanes 9 and 3).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“We observed that the DNA-binding activity of Pip was completely dependent on the presence of PU.1 at all protein concentrations tested (Figure 3B and C).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Formation of the PU.1-Pip protein adduct was dependent on: (i) phosphorylation of Ser148 in PU.1; (ii) Lys399 in Pip's interaction helix; and (iii) λB DNA containing intact PU.1-and Pip-binding sites (Figure 5B, lanes 3-8, probes designated B1 and B2 contain severe mutations in either the PU.1-or Pip-binding sites; detailed in Figure 6B).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > PU.1 and the DNA-binding domain of IRF-1 compete for binding to λB DNA
plaindirect- Asserted: passes — The authors put it forward as true.
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Furthermore, the region immediately preceding the helix, amino acids 389-392 (PipAS389), was also important for complex formation (17% of wild-type Pip binding; Figure 1D, lanes 3 and 4).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“(ii) the IRF-1 DBD bound the λB site as both a monomer and a dimer;”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > PU.1 and the DNA-binding domain of IRF-1 compete for binding to λB DNA
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The increasing ability of the PipAS401, 405 and 409 proteins to stimulate transcription correlated with increasing propensity for ternary complex formation (Figure 1D; Table I).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Consistent with the biochemical analysis, PipAS397 was least effective in stimulating transcription (Table I).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The alanine substitution of amino acids 397-400 (PipAS397) and 401-404 (PipAS401) within the predicted helix impaired ternary complex formation, resulting in ~1 or 26% binding, respectively, as compared with wild-type Pip (Figure 1D, compare lane 3 with lanes 6 and 7).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Furthermore, similar experiments revealed that the isolated ets domain of PU.1 (amino acids 160-272) recruited the Pip DBD to the λB site comparably with the PU.1 protein containing the PEST region (amino acids 119-272, Figure 4C).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
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In the paper
“Western blotting using anti-PU.1 antisera showed that this protein adduct also contained PU.1 (data not shown).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > PU.1 and the DNA-binding domain of IRF-1 compete for binding to λB DNA
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“Formation of the PU.1-Pip protein adduct was dependent on: (i) phosphorylation of Ser148 in PU.1; (ii) Lys399 in Pip's interaction helix; and (iii) λB DNA containing intact PU.1-and Pip-binding sites (Figure 5B, lanes 3-8, probes designated B1 and B2 contain severe mutations in either the PU.1-or Pip-binding sites; detailed in Figure 6B).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > PU.1 and the DNA-binding domain of IRF-1 compete for binding to λB DNA
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Consistent with previous data, PU.1 and Pip (FLPip) synergistically activated transcription (17-fold).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“No changes in the rate or pattern of proteolysis were detected when Pip was recruited by PU.1 on λB DNA (Figure 3A, compare lanes 1-6 with lanes 7-12).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip contains two major structural domains, a DNAbinding domain and a regulatory domain, separated by a linker
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In the paper
“Formation of the PU.1-Pip protein adduct was dependent on: (i) phosphorylation of Ser148 in PU.1; (ii) Lys399 in Pip's interaction helix; and (iii) λB DNA containing intact PU.1-and Pip-binding sites (Figure 5B, lanes 3-8, probes designated B1 and B2 contain severe mutations in either the PU.1-or Pip-binding sites; detailed in Figure 6B).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > PU.1 and the DNA-binding domain of IRF-1 compete for binding to λB DNA
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“These data demonstrated: (i) the high DNA affinity of IRF-1's DBD compared with that of the Pip DBD (compare Figure 4D with A, taking note of protein concentrations);”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > PU.1 and the DNA-binding domain of IRF-1 compete for binding to λB DNA
boostedcorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“PU.1-Pip interaction is shown to be template directed and involves two distinct protein-protein interaction surfaces: (i) the ets and IRF DNA-binding domains; and (ii) the phosphorylated PEST region of PU.1 and a lysine-requiring putative α-helix in Pip.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Abstract
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In the paper
“PipE406P showed severely reduced interaction with PU.1 (2% of wild-type levels; Figure 1E, compare lane 10 with lane 3).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“Alanine substitution mutagenesis of residues 389-420 showed that amino acids 401-408 were specifically required for autoinhibition (Figure 2A, compare lane 2 with lanes 7 and 8).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“(iii) increasing concentrations of the IRF-1 DBD displaced either PU.1 or PU.1 DBD from the λB site.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > PU.1 and the DNA-binding domain of IRF-1 compete for binding to λB DNA
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In the paper
“Mutation of E406 to proline also generated a protein which bound DNA independently (32-fold above background), suggesting that overall helix integrity is necessary for both autoinhibition and ternary complex formation (Figure 2A, compare lanes 2 and 12).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“In addition, gel shift assays using the phosphorylation-defective PU.1 mutant, PU.1S148A, showed that the binding of Pip was dependent on the presence of pSer148 (data not shown).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
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In the paper
“We note that the interaction between the isolated DBD of Pip and PU.1 is not dependent on phosphorylation of Ser148 since the phosphorylation-deficient PU.1S148A interacted with the Pip DBD equivalently to PU.1 (data not shown).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
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In the paper
“This experiment showed that Lys399 was important for ternary complex formation, as its substitution by alanine resulted in 8% of wild-type complex assembly (Figure 1E, lane 7).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“The data from gel shift assays allowed us to calculate the equilibrium dissociation constant (K d ) of Pip in the presence of PU.1 to be ~2.6 nM (Figure 3D).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
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In the paper
“Pip DBD bound the λB template with higher affinity in the presence of PU.1, K d ~2.1 µM (Figure 4A and B).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
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In the paper
“Importantly, mutation of this Glu406 to an alanine had no effect on ternary complex formation, indicating that the nature of the side chain was not critical (data not shown).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“Alanine subsitutions of Arg398 and Leu400 also diminished complexation (45 or 31% of wild-type binding levels; Figure 1E, compare lane 3 with lanes 6 and 8).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“Comparative analysis of the wild-type dimer with a series of mutant dimers distinguished a gene regulated by PU.1 and Pip from one regulated by PU.1 alone.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Abstract
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In the paper
“When stably expressed, the wild-type fused dimer strongly repressed the expression of a rearranged immunoglobulin λ gene, thereby establishing the functional importance of PU.1-Pip complexes in B cell gene expression.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Abstract
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In the paper
“On the CD20 element, PipPU bound with comparable affinity to PU.1 and Pip”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
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In the paper
“Substitution of Lys399 by arginine partially restored complex formation, showing that a positively charged residue at this site is an important structural component of the complex.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
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In the paper
“the double mutant (DM) fused dimer did not interact detectably with the composite sites”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
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“PU.1 bound with lower affinity to the CD20 site as compared with λB”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
What the sources say
- Not matchedcites Himmelman et al., 1997
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
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- Not matched
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In the paper
“the binding of PU.1 and Pip to λB was greater than that of the chimera (4-fold)”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
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In the paper
“the wild-type chimera (PipPU) potently repressed endogenous IgL λ gene expression (17-fold).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
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In the paper
“the Pipmut or PUmut mutant chimeras inhibited less effectively (5.5-and 1.8-fold repression, respectively).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
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In the paper
“the J chain gene was repressed equivalently by the wild-type and Pipmut repressors.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
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In the paper
“the binding of PUmut to the composite element was strictly dependent on the Pip binding site”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
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In the paper
“the presence of E λ2-4 stimulated transcription 12-fold.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Wild-type, Pipmut and PUmut chimeras repress λ enhancer function in transient assays
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In the paper
“The alanine substitution study demonstrated that Arg398, Lys399 and Leu400, located within this predicted helix and conserved between Pip and ICSBP, are critical for PU.1-Pip interaction in vitro and in vivo”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
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In the paper
“the PipPU fused dimer bound the wild-type CD20 site with an 8-fold higher affinity than the C2 mutant site”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
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- Rests on an assumption: The CD20 composite element contains a lower-affinity PU.1-binding site (AAAGAA).
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In the paper
“The PipPU protein was somewhat more effective at blocking reporter gene activity as compared with the PUmut or Pipmut proteins.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Wild-type, Pipmut and PUmut chimeras repress λ enhancer function in transient assays
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In the paper
“the PU.1 mutant (PUmut) bound the λB and CD20 sites with affinity similar to the wild-type fused dimer”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
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In the paper
“PipPU preferred the composite element to one containing only a PU.1 site by a factor of 3”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
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In the paper
“the half-life of the PU.1-Pip ternary complex was nearly identical to that of PU.1 alone”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
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In the paper
“Although the DNA affinity of PUmut was comparable with that of PipPU, its DNA specificity was quite different.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
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In the paper
“Transcription of the J chain gene was inhibited 3.5-fold by the wild-type PipPU chimera.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
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In the paper
“Here we undertake a series of biochemical studies to elucidate this mechanism, and find that interdependent protein-protein and protein-DNA contacts regulate PU.1-Pip ternary complex assembly.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Introduction
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In the paper
“J chain gene transcription was not inhibited by the PUmut chimera.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
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In the paper
“We also detected an additional, albeit much weaker, cooperative interaction between Pip's DBD and PU.1's DBD.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
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In the paper
“glutaraldehyde cross-linking demonstrated that the protein-protein interaction is template directed, because PU.1-Pip cross-linked adducts are detectable only in the presence of cognate DNA.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
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In the paper
“Subsequent assays suggested that this interaction was specific, because a Pip homolog, IRF-1, bound competitively with PU.1 on the λB site.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
hedgeddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“elimination of the regulatory domain results in an 800-fold drop in the affinity of Pip for the PU.1-DNA complex.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Mutations in a predominantly hydrophobic patch at the C-terminus of the helix (amino acids 401-408) resulted in alleviation of autoinhibition.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
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In the paper
“proteins containing this linker were found to be stable in both transient and stable expression systems”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
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In the paper
“kinetic analysis demonstrated that fusion of the two DBDs greatly enhanced DNA-binding stability as compared with wildtype PU.1 or PU.1-Pip”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
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In the paper
“the prototypical members of the IRF family, IRF-1 and IRF-2, bind to DNA with high affinity.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Two IRF subgroups that are structurally and biochemically distinguishable
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In the paper
“The asterisk denotes two chymotrypsin cleavage sites mapped in our assays (Tyr169 and Trp178).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
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In the paper
“When stably expressed, PipPU repressed an EICE-containing gene, IgL λ, more efficiently than the mutant chimeras”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Fused dimers as a general tool for analysis of combinatorial control of transcription in vivo
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In the paper
“PU.1 and Pip cross-linking is DNA template dependent.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
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In the paper
“The PUmut dimer formed a protein-DNA complex that was considerably less stable (half-life ϭ 6 min) as compared with those complexes containing PipPU or Pipmut (half-life ϭ 60 min).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“The wild-type PipPU chimera potently inhibits endogenous immunoglobulin λ gene expression when stably expressed.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
boosteddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Structural determinants required for autoinhibition of Pip DNA binding overlap with, but can be uncoupled from, those required for ternary complex formation.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
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In the paper
“in transient assays, the Pipmut and PUmut chimeras repressed transcription similarly to the wild-type chimera.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Transcription of the J chain gene was also inhibited by the wild-type PipPU chimera.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Fused dimers as a general tool for analysis of combinatorial control of transcription in vivo
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In the paper
“PU.1 binds cooperatively with the DBD of Pip but competitively with the related DBD of IRF-1.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
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In the paper
“Both wild-type and mutant PipPU chimeras repress λ enhancer function in transient transfection assays.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Multiple residues in Pip's interaction helix are important for ternary complex formation with PU.1 in vitro and transcriptional synergy in vivo.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Our gel shift studies revealed that both DBDs contribute to the higher combined affinity and selectivity of the PipPU chimera as compared with either of the mutants.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
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In the paper
“Structural determinants required for autoinhibition of Pip DNA binding overlap with, but can be uncoupled from, those required for ternary complex formation.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
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A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the J chain gene was repressed equivalently by the wild-type and Pipmut repressors.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“PU.1 binds cooperatively with the DBD of Pip but competitively with the related DBD of IRF-1.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Multiple residues in Pip's interaction helix are important for ternary complex formation with PU.1 in vitro and transcriptional synergy in vivo.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
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In the paper
“upon testing the effects of these proteins on endogenous IgL λ gene transcription in stably expressing cells, significant differences in their function were found, with maximal repression depending on the presence of both wild-type Pip and PU.1 DBDs.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“The lymphoid-restricted interferon regulatory factor, Pip (IRF-4), and the hematopoietic-specific Ets protein, PU.1, form complexes in B cells on composite elements present in immunoglobulin light chain (IgL) gene enhancers (Pongubala et al., 1992;Eisenbeis et al., 1993).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Introduction
What the sources say
- Not matchedcites Pongubala et al., 1992
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Not checked — no full text of the sourcecites Eisenbeis et al., 1993 source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Not matched
In the paper
“In each instance, the binding of Pip to DNA is dependent on DNA-bound PU.1, which must be phosphorylated on Ser148 (pSer148; Pongubala et al., 1993).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Introduction
What the sources say
- Not checked — no full text of the sourcecites Pongubala et al., 1993 source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Together, these data suggest that multiple side chains within this region may contact PU.1.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“The crystal structure of the PU.1 DBD bound to DNA shows that the N-terminus of PU.1 faces the binding site for Pip (Kodandapani et al., 1996).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
What the sources say
- Not checked — no full text of the sourcecites Kodandapani et al., 1996 source
plain- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These results suggest that protein-protein and protein-DNA interactions function coordinately in establishing a specific and stable ternary complex.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > PU.1 and the DNA-binding domain of IRF-1 compete for binding to λB DNA
hedgeddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Therefore, the structural determinants of Pip that are important for ternary complex assembly are also required for transcriptional activation in vivo.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Taken together, these observations suggest that the predicted α-helix is essential for PU.1-Pip interaction.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“Therefore, these experiments establish that a functional regulatory domain, containing the regions necessary for ternary complex formation and autoinhibition, resides within an independently folded protein module (amino acids 170-450).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip contains two major structural domains, a DNAbinding domain and a regulatory domain, separated by a linker
boosted- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, the Pip DBD has a low intrinsic affinity for the λB sequence which is increased 20-to 40-fold by PU.1.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Interestingly, these experiments showed that the structural determinants in Pip required for autoinhibition of DNA binding overlap with, but can be uncoupled from, those required for ternary complex formation.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This domain is tethered to the DBD by a proteasesensitive linker (Figure 3A, bottom).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip contains two major structural domains, a DNAbinding domain and a regulatory domain, separated by a linker
plaincorrelational- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Partial activation of transcription by this mutant protein may be due to its ability to associate weakly with PU.1 and DNA through an interaction between the IRF and ets DBDs (see below).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These data suggest that PU.1 and Pip additionally interact through their DBDs.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These data suggest that any PU.1-induced conformational change within Pip occurs by pivoting of Pip's regulatory domain about the flexible linker.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip contains two major structural domains, a DNAbinding domain and a regulatory domain, separated by a linker
hedgeddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Therefore, the PU.1-Pip interaction detected by glutaraldehyde cross-linking displayed the same requirements as those determined for ternary complex assembly using the gel shift assay (Figure 5A and B).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > PU.1 and the DNA-binding domain of IRF-1 compete for binding to λB DNA
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“This K d value is likely to be an underestimate, because the binding curve shows that at saturation, ~75% of the recombinant PU.1 interacts with Pip and is therefore phosphorylated appropriately.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
hedgeddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, a coordinated set of protein-protein and protein-DNA contacts are essential for PU.1-Pip ternary complex assembly.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Abstract
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Thus, the interaction of Pip's regulatory domain with the PEST region of PU.1 greatly enhances DNAbinding cooperativity.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Pip's regulatory domain greatly stimulates DNA binding cooperativity with PU.1
plaindirect- Asserted: passes — The authors put it forward as true.
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What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“the PipPU and mutant chimeras formed complexes with λB DNA to similar levels”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“it expresses a functionally rearranged Vλ1-Jλ1 IgL allele”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
What the sources say
- Not matchedcites Oi et al., 1983
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
plain- Asserted: passes — The authors put it forward as true.
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- Not matched
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This helix is also required for transcriptional co-activation.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“thus demonstrating that on certain composite elements, 984 fusion of the two DBDs can recapitulate the affinity of the PU.1-Pip complex.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
boosteddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Individual J558L clones that expressed similar levels of the chimeric proteins were identified by Western blotting”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
plain- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“When stably expressed, the wild-type fused dimer strongly repressed the expression of a rearranged immunoglobulin λ gene, thereby establishing the functional importance of PU.1-Pip complexes in B cell gene expression.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Abstract
boosteddirectSingle case- Asserted: passes — The authors put it forward as true.
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In the paper
“suggests that PipPU's binding stability depended on Arg232 and Arg235 of the PU.1 DBD.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
hedgeddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the overall analysis establishes the utility of using the PipPU fused dimer and its variants to distinguish genes regulated by PU.1 and Pip from those regulated by PU.1 alone.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
boosteddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“these data demonstrate that PU.1 alone is required for J chain gene activity.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
boosteddirect- Asserted: passes — The authors put it forward as true.
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None of the sources cited for this claim have been checked yet.
In the paper
“Therefore, such residues may play a more general role in IRF-containing complexes, including those involving IRF-3”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
What the sources say
- Not matchedcites Au et al., 1995
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Not checked — no full text of the sourcecites Wathelet et al., 1998 source
hedgedconditional- Asserted: passes — The authors put it forward as true.
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- Not matched
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Comparable levels of all four chimeric proteins were expressed in transfected cells as determined by Western blotting”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Wild-type, Pipmut and PUmut chimeras repress λ enhancer function in transient assays
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“suggesting that the elevated DNA-binding affinity of the ternary complex, as compared with PU.1, is due to an increased rate of association.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
hedgeddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The ternary complex may also be stabilized by hydrophobic and/or polar contacts between Pip's Leu400, Ile401, Thr402 and His403, and PU.1.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These results demonstrate that fusion of the Pip and PU.1 DBDs created a protein which bound DNA with much greater stability than wildtype PU.1 or its DBD.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
boosteddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“the chimeric proteins were expressed at considerably higher levels than endogenous PU.1”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“our data suggest a possible mechanism for PU.1-Pip association involving an interaction between PU.1's pSer148 and Pip's Arg398 and Lys399.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This repression was dependent on both the PU.1 and Pip DBDs”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“These results establish that PU.1-Pip complexes are essential for the expression of a productively rearranged immunoglobulin λ gene in a plasma cell.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
boosteddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“illustrating that on this site the covalent linkage did not fully recapitulate wild-type affinity”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“determine that expression of the fusion proteins had not altered endogenous PU.1 levels”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The cooperative binding of Pip and PU.1 is largely dependent on the interaction between the phosphorylated PEST region of PU.1 and the regulatory domain of Pip”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, a mutation in Pip's regulatory domain should not perturb the structure of its DBD.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
plain- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“most likely due to the increased protein-DNA contacts elevating the free energy of interaction.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Upon interaction of Pip with PU.1 and DNA, Pip undergoes a conformational change involving the swiveling of its regulatory domain (amino acids 170-450) away from its own DBD, and into direct contact with PU.1's PEST region.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“(i) Pip's regulatory domain autoinhibits DNA binding by masking the DBD via direct hydrophobic contacts.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“The dependence of this subgroup on a DNAbinding partner creates additional specificity in gene regulation, thereby expanding the utility of the IRF DBD.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Two IRF subgroups that are structurally and biochemically distinguishable
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“It is unlikely that the binding properties of PipAS397 are the result of misfolding of this polypeptide, because our proteolytic analysis shows that Pip is composed of two independent structural domains, a DBD domain and a regulatory domain, separated by a flexible linker.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
hedged- Asserted: passes — The authors put it forward as true.
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In the paper
“In both of these instances, transcription-activating complexes form only upon interaction of the appropriate partners and cognate DNA, thus ensuring the specific regulation of a distinct set of genes.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The independent binding of PUmut may arise from phosphate backbone contacts provided by PU.1's DBD, which stabilize the weak DNAbinding activity of the Pip DBD.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we propose that the biological function of autoinhibition is to prevent Pip and ICSBP from binding inappropriately to IFN-regulated promoters and enhancers.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
hedgeddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We propose that this region inhibits binding by masking the DBD”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
hedgeddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“suggesting that the binding interference between PU.1 and IRF-1 results from the two proteins competing for binding to overlapping sites.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Two IRF subgroups that are structurally and biochemically distinguishable
hedgeddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“It follows then that in the wild-type ternary complex, both the N-terminus of PU.1's DBD (amino acids 160-272) and its PEST region (amino acids 119-159) would be in position to contact Pip.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“we believe this model provides general insight into the concerted action of these transcription factors in both lymphoid and myeloid lineages.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
hedged- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The inability of our cross-linking assays to detect such an interaction is consistent with template DNA stabilizing weak protein-protein contacts between PU.1 and Pip.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“cross-linking experiments have shown that NFAT-AP-1 adducts are detectable only in the presence of specific DNA, arguing that protein-protein interactions alone are of insufficient strength for productive complexation”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
What the sources say
- Not checked — no full text of the sourcecites Chen et al., 1995 source
boosteddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This autoinhibition is alleviated upon interaction with a specific partner, i.e.PU.1 or Spi-B, in the context of a composite regulatory element.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“it is likely that the interaction between the DBDs will be found to be an important component of ternary complex formation.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“in the PU.1 DBD-DNA co-crystal structure, the N-terminus of PU.1 is adjacent to the predicted binding site of Pip.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
What the sources say
- Not checked — no full text of the sourcecites Kodandapani et al., 1996 source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“The recent IRF-1-DNA co-crystal structure (Escalante et al., 1998) reveals that in addition to the specific base contacts made by the recognition helix, IRF-1 makes extensive contacts with DNA backbone phosphates, even as far as six nucleotides upstream of the GAAA recognition core.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Two IRF subgroups that are structurally and biochemically distinguishable
What the sources say
- Not checked — no full text of the sourcecites Escalante et al., 1998 source
plain- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These results suggest that additional conformational changes necessary for cooperativity may occur in the context of the native complex that are not recapitulated within PipPU.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“then partial loss of these interactions may account for the attenuated binding of Pip, ICSBP and p48.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Two IRF subgroups that are structurally and biochemically distinguishable
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“suggesting that this linker may be generally resistant to proteolysis in vivo.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“This last suggestion is supported by the numerous protein-DNA backbone contacts observed in the PU.1-DNA co-crystal structure”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
What the sources say
- Not checked — no full text of the sourcecites Kodandapani et al., 1996 source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“This is consistent with the overall selectivity of a chimeric transcription factor depending on the intermediate affinity and high specificity of the isolated sub-domains”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
What the sources say
- Not checked — no full text of the sourcecites Pomerantz et al., 1995 source
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“demonstrating that PU.1-Pip complexes are essential for IgL λ expression in vivo.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Fused dimers as a general tool for analysis of combinatorial control of transcription in vivo
boosteddirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Additional contacts between Pip's DBD and PU.1's DBD stabilize the ternary complex.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, it is likely that the differential DNA-binding properties of the chimeric proteins account for their varying abilities to repress endogenous IgL λ gene transcription.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
hedgedconditional- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“Transcription of a rearranged IgL λ gene appears to be regulated by two enhancers, E λ2-4 and E λ3-1 , which share high sequence identity.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
hedgedconditional- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“unlike the case with the IgL λ gene, PU.1 alone is required for J chain gene activity.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Fused dimers as a general tool for analysis of combinatorial control of transcription in vivo
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our study establishes the functional requirement for PU.1-Pip complexes for expression of the IgL λ locus in a plasma cell.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Pip's regulatory domain (RD, amino acids 170-450) autoinhibits DNA binding by masking the Pip DBD.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Interaction of Pip with a PU.1-DNA template complex causes the regulatory domain to swivel about the flexible linker region (L) and contact PU.1's PEST region.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the combined analysis of the wildtype dimer with a series of mutants allowed us to distinguish genes regulated by PU.1 and Pip from those regulated by PU.1 alone.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Fused dimers as a general tool for analysis of combinatorial control of transcription in vivo
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“E λ2-4 and E λ3-1 also contain juxtaposed binding sites occupied by multiple factors”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
What the sources say
- Not matchedcites Rudin and Storb, 1992
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
plaincorrelational- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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- Not matched
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the stable binding of both its DBDs may be necessary to compete with endogenous Ets and IRF proteins for site occupancy.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
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What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Gel shift analyses of these purified proteins confirmed that they possesed similar specific activities to their mammalian counterparts.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Protein purification
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“PipPU's enhanced DNA-binding properties may allow it to locate more effectively a small number of endogenous EICEs”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus the kinetic stability of the fused dimer-DNA complexes correlates with their ability to repress transcription in vivo”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The PipPU fused dimer probably represses IgL λ gene transcription by disrupting the function of both λ enhancers via the displacement of PU.1-Pip complexes.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
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- It may state two separate claims as one. 42
- Probably not a substantial claim. 24
Every source the paper cites for this claim was checked and supports it.
In the paper
“Therefore, this domain contains structural determinants important for both PU.1 interaction and autoinhibition (Brass et al., 1996).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Introduction
What the sources say
- Supportedcites Brass et al., 1996 source
The paper’s “Structural basis for PU.1-dependent DNA-binding of Pip” section states that Pip amino acids 138–450 contain structural determinants for both autoinhibition of DNA binding and specific association with PU.1, and identifies this region as a regulatory domain. This directly supports the attributed claim. (LLM, conf=0.95)
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Pip deletion mutants which retained the ability to form a ternary complex with PU.1 (1-439 and 1-419; Brass et al., 1996; data not shown) stimulated transcription comparable with full-length Pip.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
What the sources say
- Partly supportedcites Brass et al., 1996 sourceExperimental — accuracy not yet measured
In the section on Pip amino acids 410–439 (page not supplied), Brass et al. report that deleting Pip to residue 439 did not affect ternary complex formation with PU.1. Our copy does not report the 1–419 mutant or show that these two mutants stimulated transcription comparably to full-length Pip; the citing sentence labels the transcription result “data not shown.” (LLM, conf=0.86)
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
- Partly supported
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“This linker was chosen because it flexibly connects the POU homeo-and POUspecific domains (Herr and Cleary, 1995), and appears unstructured in the Oct-1-DNA co-crystal structure (Klemm et al., 1994).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
What the sources say
- Supportedcites Herr and Cleary, 1995 source
Herr and Cleary is cited for the linker’s flexible connection between the POU-specific and POU homeo domains. The POU domain and POU-domain linker sections explicitly describe that connection and its flexibility. The co-crystal observation is separately attributed to Klemm et al. in the citing sentence, so it is not required of this citation. (LLM, conf=0.94)
- Not checked — no full text of the sourcecites Klemm et al., 1994 source
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
- Supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“As shown previously, full-length Pip cannot bind to DNA in the absence of PU.1; however, a C-terminal deletion mutant, Pip 1-410, can bind DNA independently (Figure 2A, compare lanes 2 and 3; Brass et al.,1996).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
What the sources say
- Partly supportedcites Brass et al., 1996 sourceExperimental — accuracy not yet measured
The deletion-analysis section reports that full-length Pip did not bind DNA independently in its gel-shift assay, while Pip 1–410 did. But the ‘Pip functions as a dichotomous regulator’ section says full-length Pip could bind DNA without PU.1 in cell extracts under different conditions, so the unqualified ‘cannot’ overstates the result. (LLM, conf=0.86)
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“J558L B cells also express the J chain gene, the transcription of which has been suggested to be regulated by PU.1 binding to the J chain promoter”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
What the sources say
- Partly supportedcites Shin and Koshland, 1993 sourceExperimental — accuracy not yet measured
The Discussion (page unavailable) reports that PU.1 binds a regulatory element in the J-chain promoter and activates J-chain transcription. The paper identifies S194 as a J-chain-expressing cell line, but the passages found do not establish that J558L cells express the gene; the cell-line-specific part of the claim is unsupported. (LLM, conf=0.84)
hedgedconditional- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
- Partly supported
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“we identified a predicted α-helix within Pip's C-terminus (amino acids 395-413) that is critical for both formation of a ternary complex and autoinhibition of DNA binding”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
What the sources say
- Partly supportedcites Brass et al., 1996 sourceExperimental — accuracy not yet measured
The Structural basis section postulates that a putative α-helical region may play a key role in ternary complex formation and autoinhibition; the Model section identifies that region as amino acids 399–413, not 395–413. The paper’s deletion results establish the importance of a broader segment, amino acids 410–439, but do not establish that the predicted helix itself is critical. (LLM, conf=0.88)
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
- Partly supported
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“Probes B1 and C1 differ in their flanking sequences”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
What the sources say
- Could not verifycites Brass et al., 1996 sourceExperimental — accuracy not yet measured
The Gel mobility shift assays section describes a murine κB-site probe, and the Pip is NF-EM5 section describes complexes formed on that probe, but neither identifies probes B1 and C1 or compares their flanking sequences. Searches for “B1 and C1,” “C1 probe,” and “flanking sequences” found no passage addressing the claimed difference. (LLM, conf=0.75)
- Not matchedcites Himmelman et al., 1997
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Could not verify
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“IRF-3 possesses a C-terminal autoinhibitory region.Regulated phosphorylation of this region upon viral infection stimulates DNA binding”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
What the sources say
- Partly supportedcites Lin et al., 1998 sourceExperimental — accuracy not yet measured
The Discussion proposes a C-terminal autoinhibitory domain and a model in which virus-induced phosphorylation relieves autoinhibition and leads to DNA binding; the Abstract also reports stimulated DNA binding. The claim states the proposed domain as established and implies that the autoinhibitory domain itself is phosphorylated. The Discussion places that domain at amino acids 407–427, but the phosphorylation sites at 396–405. (LLM, conf=0.84)
- Partly supportedcites Yoneyama et al., 1998 sourceExperimental — accuracy not yet measured
The Discussion reports that viral stimulation induces IRF-3 phosphorylation and sequence-specific DNA-binding activity; the Functional domains of IRF-3 section implicates C-terminal serines 385 and 386 in the virus-induced response. Our copy does not identify a C-terminal autoinhibitory region, and the Discussion says the order of phosphorylation and DNA-binding activation could not be determined. (LLM, conf=0.85)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
- Partly supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“A recent study using protein-protein interaction assays suggests that PU.1 and Pip can interact in the absence of template DNA”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
What the sources say
- Supportedcites Perkel et al., 1998 source
The section “Interaction of GST-Pip and PU.1 in solution requires the PU.1 ETS domain” reports a protein-interaction assay in which PU.1 bound GST-Pip without DNA. It explicitly concludes that PU.1 and Pip can physically interact in solution. (LLM, conf=0.95)
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“recent work has shown that PU.1 nucleates a multi-transcription factor complex on the E κ3Ј”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
What the sources say
- Supportedcites Pongubala and Atchison, 1997 source
The paper states that PU.1 participates with other transcription factors in forming a higher-order complex on the immunoglobulin κ 3′ enhancer. The Discussion describes PU.1 as important to the complex’s formation and calls the mechanism nucleation of enhancer-binding proteins. The supplied passages have section labels but no page numbers. (LLM, conf=0.92)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
- Supported
Every source the paper cites for this claim was checked and supports it.
In the paper
“The PU.1-and Pip-binding sites have been underlined based on methylation interference analysis of the λB site(Eisenbeis et al., 1995).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
What the sources say
- Supportedcites Eisenbeis et al., 1995 source
The methylation-interference results (Fig. 2C; page unavailable in our copy) delimit the Pip-binding site adjacent to the previously determined PU.1-binding site. The Figure 2 caption says the paper compares its Pip results with methylation-interference results for PU.1, supporting the cited basis for marking both sites. (LLM, conf=0.90)
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Supported
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Alanine substitution of amino acids 401-404 and 405-408 resulted in 9-and 15-fold increases in binding above background, respectively.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
plaindirect- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Further deletion into the region encompassing the putative α-helix (1-410) severely reduced ternary complex formation and abolished synergistic activation of transcription.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
plaindirect- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This mutant protein, PipAS397, is defective in its interaction with PU.1, but is autoinhibited.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the Pip mutant (Pipmut) exhibited reduced affinity for the composite sites, and therefore its binding properties resembled those of PU.1”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The estimated half-life for the PipPU-DNA complex (60 min) was considerably longer than that for PU.1 (6 min) or the PU.1 DBD (8 min).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the significantly longer half-life of the Pipmut-DNA complex (60 min) as compared with that of the PUmut-DNA complex (6 min)”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering a PU.1-Pip chimeric repressor
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“transcriptional repression by PipPU was specific, since it did not inhibit the activity of a reporter construct containing a Vκ promoter and the intron κ enhancer”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Wild-type, Pipmut and PUmut chimeras repress λ enhancer function in transient assays
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Enhancer activity was strongly inhibited by expression of the PipPU, Pipmut and PUmut, but not by the DM fused dimer”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Wild-type, Pipmut and PUmut chimeras repress λ enhancer function in transient assays
boosteddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The mutant protein, PipAS397, is defective in its interaction with PU.1, but is autoinhibited.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“resulted in the Pipmut protein, which bound DNA with similar specificity to PU.1, but with a longer half-life.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the PUmut protein, which contains mutations within the PU.1 DBD, independently bound DNA with high affinity and thus acted quite differently from Pip.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Pip, ICSBP and p48 possess considerably lower DNA affinity, relying on partners to form high affinity complexes.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Two IRF subgroups that are structurally and biochemically distinguishable
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The PipPU chimera bound the λB site less well than the wild-type proteins; however, on a composite element containing a lower affinity PU.1 site, the chimera and PU.1-Pip bound equivalently.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Our strategy produced a chimera, PipPU, which preferred a composite site to a PU.1 site by a factor of 3 (λB) or 8 (CD20), correlating with the affinity of wild-type PU.1 for these sites.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Pip contains two major structural domains, a DNA-binding domain and a regulatory domain, separated by a linker.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“all three PipPU chimeras (PipPU, Pipmut and PUmut) repressed transcription of a λ enhancercontaining reporter in transient assays, with PipPU being somewhat more effective than the mutant chimeras.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Fusing the DBDs of Pip and PU.1 generates a chimeric protein which preferentially binds composite elements with increased stability.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“However, the role of PU.1-Pip complexes in regulating the expression of endogenous IgL genes remains to be elucidated.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Introduction
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: passes — The paper’s conclusions depend on it.
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Probably not a substantial claim.
In the paper
“In eukaryotes, gene expression appears to be regulated by the assembly of distinct combinations of transcription factors at promoters and enhancers.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Introduction
What the sources say
- Not checked — no full text of the sourcecites Carey, 1998 source
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Mutation of E406 to proline also generated a protein which bound DNA independently (32-fold above background), suggesting that overall helix integrity is necessary for both autoinhibition and ternary complex formation (Figure 2A, compare lanes 2 and 12).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
hedgeddirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Therefore, the DBDs of IRF-1 and Pip have structurally diverged, such that Pip binds cooperatively with PU.1, while IRF-1 displaces PU.1 from the composite element.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > PU.1 and the DNA-binding domain of IRF-1 compete for binding to λB DNA
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In the paper
“Thus, the α-helical region in Pip's C-terminus is important for both interaction with PU.1 in vitro and transcriptional synergy in vivo.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
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In the paper
“Previous work has shown that the E λ2-4 construct (OPC 20) is preferentially active in B cells, and mutations in either the PU.1-or Pip-binding site within this construct abolish enhancer function”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Wild-type, Pipmut and PUmut chimeras repress λ enhancer function in transient assays
What the sources say
- Not checked — no full text of the sourcecites Eisenbeis et al., 1993 source
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In the paper
“Therefore, in transient assays, both the wild-type (PipPU) and mutant chimeras (Pipmut and PUmut) effectively blocked enhancer function, presumably by displacement of endogenous PU.1-Pip complexes.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Wild-type, Pipmut and PUmut chimeras repress λ enhancer function in transient assays
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In the paper
“Each of the chimeric proteins was expressed comparably with endogenous Pip and their expression did not alter wild-type Pip levels”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
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In the paper
“β-actin transcripts were used both as a specificity control and for normalization.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > The PipPU chimeric repressor blocks endogenous IgL λ gene expression when stably expressed in B cells
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In the paper
“An interaction analogous to the one between PU.1 and Pip, involving the pKID domain of the CREB transcription factor and the KIX domain of the co-activator CBP, is mediated by a phosphoserine residue located within pKID”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
What the sources say
- Not checked — no full text of the sourcecites Parker et al., 1996 source
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In the paper
“A Pip deletion mutant, Pip 1-410, which does not form a ternary complex with PU.1 fails to activate transcription synergistically with PU.1.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
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In the paper
“a single hydrogen bond between this phosphoserine and a tyrosine residue within CBP is critical for complexation”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
What the sources say
- Not checked — no full text of the sourcecites Radhakrishnan et al., 1997 source
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In the paper
“Protein-protein contacts also occur between Pip's DBD and PU.1's DBD and may contribute additional specificity and stability to the ternary complex.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
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In the paper
“a binding partner, such as PU.1 or STATs, may provide these lost contacts to Pip or p48 in trans, via protein-protein interactions.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Two IRF subgroups that are structurally and biochemically distinguishable
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In the paper
“we propose that PU.1-Pip ternary complex assembly is regulated by two template-directed proteinprotein contacts, one between PU.1's PEST region and Pip's regulatory domain, and the second depending on association of PU.1's DBD with that of Pip.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
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In the paper
“The ICSBP DBD strongly repressed both interferon (IFN)-stimulated gene expression and the anti-proliferative effects of IFN, while the full-length protein had little effect on these activities.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
What the sources say
- Not checked — no full text of the sourcecites Thornton et al., 1996 source
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In the paper
“In the NFAT-AP-1-DNA complex, the Rel homology region of NFAT and the bZip domain of AP-1 make extensive contacts with one another that are both necessary and sufficient for complex formation on DNA”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
What the sources say
- Not checked — no full text of the sourcecites Chen et al., 1998 source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“This association is dependent on multiple residues within Pip's interaction helix, including an electrostatic interaction between Pip's Lys399 and PU.1's pSer148.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Cooperative binding by PU.1 and Pip is regulated by multiple interdependent DNA-protein and protein-protein interactions
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In the paper
“Previous studies have either created chimeric transcription factors which recognize synthetic regulatory elements by fusing domains from biologically unrelated proteins, or used phage display technology to create a zinc finger protein which recognizes a DNA site generated by a chromosomal translocation”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
What the sources say
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“this approach not only serves to test the proposed functions of interacting activators in vivo, but should also enable the identification of novel genes specifically regulated by such activator complexes.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Fused dimers as a general tool for analysis of combinatorial control of transcription in vivo
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In the paper
“Pip-deficient animals develop normal numbers of B cells (including λ-expressors) which cannot undergo activation”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
What the sources say
- Not checked — no full text of the sourcecites Mittrucker et al., 1997 source
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In the paper
“The structures of all constructs were confirmed by dideoxy sequencing.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Plasmids
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What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“PU.1 and the chimeric proteins are present in equimolar amounts.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
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In the paper
“Each determination represents the average of at least three independent experiments.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Gel mobility shift assays
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In the paper
“The proteins were Ͼ80% pure as judged by densitometric analysis of Coomassie Blue-stained 12.5% SDS-PAGE gels.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Protein purification
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In the paper
“Fold-activation (solid bars) indicates CAT activity normalized to the control expression vector and is the average of two independent experiments.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
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In the paper
“This may be attributable to the higher ratio of target DNA to non-specific DNA as well as increased levels of protein expression in a transient assay.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
hedgedconditional- Asserted: passes — The authors put it forward as true.
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In the paper
“These data are representative of three independent experiments each using different RNA preparations.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Solid bars indicate average CAT activity (percentage chloramphenicol acetylation) of two independent transfections.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plain- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This contact is mediated by multiple residues in Pip's interaction helix, including an electrostatic interaction between K399 of Pip and PU.1's pSer148 (P-S148).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plaindirect- Asserted: passes — The authors put it forward as true.
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What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Equimolar amounts of Pip or PipK399A, and PU.1 or PU.1S148A were used in the binding reactions.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, Pip is dispensable for IgL λ transcription during B cell development but may be required for the enhanced expression of this locus during B cell activation and terminal differentiation.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Engineering PU.1-Pip chimeric repressors
hedgedconditional- Asserted: passes — The authors put it forward as true.
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What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Equimolar amounts of the Pip proteins were used based on PhosphorImager analysis of SDS-PAGE gels.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“All Pip proteins are present in equimolar amounts.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Northern blot analysis
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim.
The paper relies on this without support.
PU.1 and Pip act as mutually dependent transcriptional activators in vivo.
“As noted, PU.1 and Pip function as mutually dependent transcriptional activators in vivo.”
The paper relies on this without support.
The λB probe's high-affinity PU.1 site (AAGGAA) could mask some of the DNA-binding gain provided by fusing the Pip DBD.
“The λB probe contains a high affinity PU.1-binding site (AAGGAA), which might mask some of the gain in DNA binding provided by the fusion of the Pip DBD.”
The paper relies on this without support.
The CD20 composite element contains a lower-affinity PU.1-binding site (AAAGAA).
“the composite element from the CD20 promoter, which contains a lower affinity PU.1-binding site (AAAGAA”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“Similar protein-protein interaction between PU.1 and PIP has been detected in the Ig λ light chain enhancer and the CD20 promoter (27-29”
From AKT Induces Transcriptional Activity of PU.1 through Phosphorylation-mediated Modifications within Its Transactivation Domain (2001) · cites this paper as [28]
In the citing paper
“A model was proposed for PU.1/Pip ternary complex. In this two-step recruitment mechanism, PU.1/Pip interaction is DNA template-directed and involves two distinct protein–protein interaction surfaces: (i) the ETS (PU.1) and IRF (Pip) DNA binding domains and (ii) the phosphorylated PEST domain of PU.1 and a putative α helix in Pip [118, 119] (Fig. 9).”
From PU.1 and partners: regulation of haematopoietic stem cell fate in normal and malignant haematopoiesis (2009) · cites this paper as [119]
In the citing paper
“More dramatically, however, the phosphorylated PEST sequence of SPI1 interacts with an autoinhibitory region of IRF4 to enhance DNA binding by almost three orders of magnitude (154).”
From Genomic and biochemical insights into the specificity of ETS transcription factors (2011) · cites this paper as [154]
In the citing paper
“The low affinity of the winged helix-turn-helix DNA-binding domain of IRF4 for the λB enhancer is increased 20–40-fold by the presence of SPI1 at this site (154, 155).”
From Genomic and biochemical insights into the specificity of ETS transcription factors (2011) · cites this paper as [154]
In the citing paper
“the PU.1-ICSBP interaction is dependent on the IAD domain in the C-terminal region, although the DBD is also required for this interaction (5, 38).”
From Gamma Interferon Triggers Interaction between ICSBP (IRF-8) and TEL, Recruiting the Histone Deacetylase HDAC3 to the Interferon-Responsive Element (2002) · cites this paper as [5]
In the citing paper
“ICSBP has been known to interact with PU.1, a hematopoietic-cellspecific member of the Ets family (4, 5, 38).”
From Gamma Interferon Triggers Interaction between ICSBP (IRF-8) and TEL, Recruiting the Histone Deacetylase HDAC3 to the Interferon-Responsive Element (2002) · cites this paper as [5]
In the citing paper
“PU.1 requires the PEST domain, which is N-terminal to the Ets domain, for interacting with ICSBP (5).”
From Gamma Interferon Triggers Interaction between ICSBP (IRF-8) and TEL, Recruiting the Histone Deacetylase HDAC3 to the Interferon-Responsive Element (2002) · cites this paper as [5]
In the citing paper
“It also associates with PU.1 and stimulates activity of the Ets/IRF composite element (EICE), which also contains IRS and is present in the immunoglobulin (Ig) k and l , gp91 phox , scavenger receptor, toll-like receptor-4 (TLR-4), and interleukin (IL)-1 b genes. (5,23,26-30)”
From Review: ICSBP/IRF-8: Its Regulatory Roles in the Development of Myeloid Cells (2002) · cites this paper as [26]
In the citing paper
“Notably, Irf8 peaks were enriched for EICE motifs, which are co-bound by PU.126.”
From Single-cell analysis of mixed-lineage states leading to a binary cell fate choice (2016) · cites this paper as [26]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
“The λB composite element (AAAGGAAGTGAAACCA) contains a PU.1-binding site at its 5Ј end separated by 2 bp from the Pip-binding site.”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Two IRF subgroups that are structurally and biochemically distinguishable
“Comparison of the IRF recognition site (GAGAAGTGAAAGT, IRF-1 core in bold) with the λB EICE (AAGGAGTGAAACC, PU.1 core emboldened)”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
“Next, we attempted to disrupt the folding of the interaction helix by substituting a proline for glutamine at position 406 (PipE406P).”
§ Assembly requirements of PU.1-Pip (IRF-4) activator complexes: inhibiting function in vivo using fused dimers > Results
“Importantly, mutation of this Glu406 to an alanine had no effect on ternary complex formation, indicating that the nature of the side chain was not critical (data not shown).”
Citations
Cites
Empirical Predictions of Protein Conformation
Chou, P. Y., & Fasman, G. D. (1978) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.47.070178.001343 · Cited by 3,099
Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages
Scott, E. W., Simon, M. C., Anastasi, J., & Singh, H. (1994) · Science · doi:10.1126/science.8079170 · Cited by 1,532
Self-citationVirus induction of human IFNβ gene expression requires the assembly of an enhanceosome
Thanos, D., & Maniatis, T. (1995) · Cell · doi:10.1016/0092-8674(95)90136-1 · Cited by 1,014
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“Regulated phosphorylation of this region upon viral infection stimulates DNA binding (Lin et al., 1998; Yoneyama et al., 1998).”
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Metadata
- Authors
- Brass, A. L., Zhu, A. Q., & Singh, H.
- Affiliations
- Howard Hughes Medical Institute (US)
- Corresponding author
- Singh, Harinder
- ORCID
- Singh, Harinder
- Venue
- The EMBO Journal
- Published
- 1999-02-15
- Volume
- 18
- Issue
- 4
- Pages
- 977-991
- ISSN
- 0261-4189 (ISSN-L)
- 1460-2075
- PMC
- PMC1171190
- OpenAlex
- W2121496836
- Semantic Scholar
- a3891c3b25fac116b2b2c86acc2cf094353cc3d7
- Cited by
- 204
- References
- 64
- Citations by year
- 2026: 2 · 2025: 9 · 2024: 8 · 2023: 8 · 2022: 6 · 2021: 9 · 2020: 9 · 2019: 7 · 2018: 8 · 2017: 8 · 2016: 6 · 2015: 5 · 2014: 6 · 2013: 9 · 2012: 8
- FWCI
- 4.12
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- The EMBO Journal (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- University of Toronto
- National Institutes of Health
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD-07009)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Life Sciences › Immunology and Microbiology › Immunology › Cytokine Signaling Pathways and Interactions
- Keywords
- PU.1, IRF4, Pip, ETS transcription factors, transcription factor interaction, B cell gene expression, transcriptional repression, protein-DNA contacts, protein-protein interaction surfaces
- MeSH terms
- Interferon Regulatory Factor-4, Proto-Oncogene Protein Spi-1, Amino Acid Sequence, Animals, B-Lymphocytes, DNA-Binding Proteins, Enhancer Elements, Genetic, Gene Expression Regulation, Immunoglobulin lambda-Chains, Molecular Sequence Data, Mutation, Proto-Oncogene Proteins, Recombinant Fusion Proteins, Repressor Proteins, Transcription Factors, Transfection, Tumor Cells, Cultured, Protein Engineering, Transcriptional Activation, Trans-Activators, Sequence Alignment, Dimerization, Interferon Regulatory Factors, Mice
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-07, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-07 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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