Transcriptional enhancers and their communication with gene promoters

In the paper

“The SWI/SNF complex is involved in regulating occupancy and spacing of nucleosomes at promoters and enhancers [58], while the most established role of FACT is in facilitating transcriptional elongation [57].”

What the sources say

• Supported

  The “FACT Function and Architecture” section says human FACT was first identified as essential for transcriptional elongation through chromatin and describes its role in actively transcribed genes. It also discusses roles in replication and repair, consistent with elongation being its most established role. (LLM, conf=0.88)

  cites [57] Winkler DD, Luger K (2011) The histone chaperone FACT: structural insights and mechanisms for nucleosome reorganization. J Biol Chem 286:18369–18374 source

In the paper

“However, open chromatin regions are not limited to active enhancers, and also harbour other regions including active gene promoters, regulatory elements in a ‘poised’ chromatin configuration (discussed below), as well as some structural regions such as tissue-invariant binding sites for the architectural protein CCCTC-binding factor (CTCF) [129–132].”

What the sources say

• Partly supported

  The Results section on DNA regulatory elements reports that accessible chromatin sites are strongly enriched in promoter and enhancer regions. The Discussion suggests that some sites of differential accessibility may reflect poised promoters or enhancers, but does not establish this directly. The Results mention accessibility at CTCF motif sites, but do not identify tissue-invariant CTCF binding sites as open structural regions. (LLM, conf=0.85)

  cites [129] Corces MR, Granja JM, Shams S et al (2018) The chromatin accessibility landscape of primary human cancers. Science 362:eaav1898 sourceExperimental — accuracy not yet measured
• Partly supported

  The Introduction (page unavailable) identifies promoters and chromatin insulators among the active regulatory elements marked by accessible DNA, and says DHSs can appear before functional activation. This supports the claim that open chromatin is not limited to active enhancers, but our copy does not specifically identify poised chromatin configurations or tissue-invariant CTCF-binding sites as examples. (LLM, conf=0.84)

  cites [130] Meuleman W, Muratov A, Rynes E et al (2020) Index and biological spectrum of human DNase I hypersensitive sites. Nature 584:244–251 sourceExperimental — accuracy not yet measured
• Partly supported

  The ‘A registry of DNA elements’ and ‘Groups based on function-associated signatures’ sections link accessible chromatin to active or poised regulatory elements and describe DNase-accessible, CTCF-bound sites with potential insulator or looping functions. The paper also distinguishes active promoter-like elements from enhancer-like elements. The passages found do not establish that the CTCF binding sites are tissue-invariant; no page number is available for these passages. (LLM, conf=0.84)

  cites [131] ENCODE Project Consortium, Moore JE, Purcaro MJ et al (2020) Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583:699–710 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [132] Parelho V, Hadjur S, Spivakov M et al (2008) Cohesins functionally associate with CTCF on mammalian chromosome arms. Cell 132:422–433 source

In the paper

“SMF showed high TF cooperativity at active enhancers and identified cases where TFs bind independently, sequentially or simultaneously [118].”

What the sources say

• Partly supported

  The Discussion (page unavailable in our copy) reports substantial TF cooperativity at 64% of active fly enhancers and independent binding at some others. The Results section, “Cooperative binding is common at active enhancers” (page unavailable), identifies TFs co-bound on single molecules and potential initiating sites. These observations support co-occupancy and a possible binding hierarchy, but do not establish that TFs bind sequentially or simultaneously in time. (LLM, conf=0.86)

  cites [118] Rao S, Ahmad K, Ramachandran S (2021) Cooperative binding between distant transcription factors is a hallmark of active enhancers. Mol Cell 81:1651-1665.e4 sourceExperimental — accuracy not yet measured

In the paper

“An intermediate model for enhancer grammar known as the “TF collective” proposes that a set of the same TFs binds to multiple enhancers but an individual enhancer does not necessarily have the full set of TF binding sites [30, 91].”

What the sources say

• ?Not checked — no full text of the sourcecites [30] Spitz F, Furlong EEM (2012) Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 13:613–626 source
• Supported

  The Results report that multiple enhancers recruit all five cardiogenic TFs despite variation in their binding-site content. The Discussion describes the “TF collective” as cooperative binding with little or no motif grammar, in which motifs for some recruited factors need not be present. (LLM, conf=0.94)

  cites [91] Junion G, Spivakov M, Girardot C et al (2012) A transcription factor collective defines cardiac cell fate and reflects lineage history. Cell 148:473–486 source

In the paper

“However, studies that knock down selected eRNA have found reduced expression of the corresponding gene targets, suggesting functionality [79–81].”

What the sources say

• Supported

  In “shRNA Knockdown of MYC ESE eRNA Reduced MYC Expression,” the paper reports that knocking down the −428 and −525 enhancer RNAs significantly reduced expression of their target gene, MYC, by more than 70%. It also reports no effect on the control gene GAPDH or other enhancer targets, supporting the claim that these selected eRNAs have a functional role. Page numbers are not provided in our copy. (LLM, conf=0.94)

  cites [79] Liang J, Zhou H, Gerdt C et al (2016) Epstein-Barr virus super-enhancer eRNAs are essential for MYC oncogene expression and lymphoblast proliferation. Proc Natl Acad Sci USA 113:14121–14126 source
• Supported

  In the Results section, “L2-produced eRNAs are necessary for proper IFNB1 expression” (page not provided), the authors report that knockdown of either L2 eRNA reduced induction of its target gene, IFNB1. They conclude that the eRNAs are necessary for appropriate virus-induced IFNB1 expression. (LLM, conf=0.94)

  cites [80] Banerjee AR, Kim YJ, Kim TH (2014) A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities. Nucleic Acids Res 42:12537–12554 source
• ?Not checked — no full text of the sourcecites [81] Hsieh C-L, Fei T, Chen Y et al (2014) Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation. Proc Natl Acad Sci USA 111:7319–7324 source

In the paper

“For example, dissection of an enhancer controlling the specification of Drosophila leg precursor cells showed that it was robust against motif disruption, but relied on DNA–protein and protein–protein interactions between a particular set of TFs [94].”

What the sources say

• Supported

  Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [94] Uhl JD, Zandvakili A, Gebelein B (2016) A Hox transcription factor collective binds a highly conserved distal-less cis-regulatory module to generate robust transcriptional outcomes. PLoS Genet 12:e1005981 source

In the paper

“In contrast, the trimethylation of histone H3 lysine 4 (H3K4me3) is typically considered a promoter-associated mark and, in regions proximal to a known TSS, has been used to distinguish the enhancer from a promoter [131].”

What the sources say

• Supported

  In “A registry of DNA elements” (page not provided), the paper calls H3K4me3 characteristic of transcribing promoters and contrasts it with the relative paucity of H3K4me3 associated with active enhancers. “Classifying cCREs” and “Groups based on function-associated signatures” (pages not provided) describe using histone signals and TSS proximity to distinguish promoter-proximal enhancer-like elements from promoter-like elements. (LLM, conf=0.93)

  cites [131] ENCODE Project Consortium, Moore JE, Purcaro MJ et al (2020) Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583:699–710 source

In the paper

“Virtually every nucleotide of the interferon beta enhancer is evolutionarily conserved; this is likely because the eight TFs cooperate to form a composite surface that recognises the entire sequence of the enhancer as one effective binding site [88, 89].”

What the sources say

• ?Not checked — no full text of the sourcecites [88] Thanos D, Maniatis T (1995) Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 83:1091–1100 source
• Supported

  The Discussion says the IFN-β enhancer sequence is nearly invariant and explains this conservation through a composite transcription-factor surface that recognizes the entire sequence. The Figure 4 caption identifies eight polypeptides in that surface. The paper qualifies that cooperativity does not mainly arise from direct contacts between neighboring DNA-binding domains, but the claim does not require that mechanism. (LLM, conf=0.93)

  cites [89] Panne D, Maniatis T, Harrison SC (2007) An atomic model of the interferon-beta enhanceosome. Cell 129:1111–1123 source

In the paper

“Currently mono-methylation of histone H3 lysine 4 (H3K4me1), associated with the binding of Trithorax/MLL complexes, is taken to be the hallmark of both ‘primed’ and active enhancers, whilst active enhancers additionally tend to associate with the acetylation of histone H3 lysine 27 (H3K27ac) [133–137].”

What the sources say

• Partly supported

  The introduction (p. 2) says H3K4me1 can mark both active and poised enhancers, and the Results (p. 3) identify H3K27ac as a mark that distinguishes active from poised enhancers. Our copy does not support the additional claim that H3K4me1 is associated with binding of Trithorax/MLL complexes. (LLM, conf=0.86)

  cites [133] Creyghton MP, Cheng AW, Welstead GG et al (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 107:21931–21936 sourceExperimental — accuracy not yet measured
• Partly supported

  The Results section, “Systematic mapping of chromatin marks in multiple cell types” (page unavailable), says H3K4me1 is preferentially associated with enhancers and H3K27ac with active regulatory regions. The copy does not establish the claimed association of H3K4me1 with Trithorax/MLL binding, or explicitly identify it as a hallmark of both primed and active enhancers. (LLM, conf=0.84)

  cites [134] Ernst J, Kheradpour P, Mikkelsen TS et al (2011) Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473:43–49 sourceExperimental — accuracy not yet measured
• Partly supported

  The paper’s opening summary (page not provided) describes H3K4me1 at both active and poised enhancers, with H3K27ac distinguishing the active class. It does not establish the claimed association of H3K4me1 with Trithorax/MLL-complex binding. (LLM, conf=0.88)

  cites [135] Rada-Iglesias A, Bajpai R, Swigut T et al (2011) A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470:279–283 sourceExperimental — accuracy not yet measured
• Partly supported

  The section ‘Identification of three major enhancer classes in mESCs’ (page not available) classifies H3K4me1-positive, H3K27ac-positive enhancers as active and H3K4me1-positive, H3K27me3-positive enhancers as poised, supporting the histone-mark distinction. Our copy does not establish the claimed association with Trithorax/MLL complexes, and it uses ‘poised’ rather than ‘primed.’ (LLM, conf=0.86)

  cites [136] Zentner GE, Tesar PJ, Scacheri PC (2011) Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions. Genome Res 21:1273–1283 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [137] Bonn S, Zinzen RP, Girardot C et al (2012) Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet 44:148–156 source

In the paper

“Another means by which flexible enhancer grammar ensures robust gene expression control is through “suboptimal” TF binding motifs, which reinforce the requirement for TF cooperativity and create opportunities for fine-tuning enhancer activity levels [125–128].”

What the sources say

• Partly supported

  Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [125] Farley EK, Olson KM, Zhang W et al (2015) Suboptimization of developmental enhancers. Science 350:325–328 sourceExperimental — accuracy not yet measured
• Partly supported

  Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [126] Crocker J, Abe N, Rinaldi L et al (2015) Low affinity binding site clusters confer hox specificity and regulatory robustness. Cell 160:191–203 sourceExperimental — accuracy not yet measured
• Partly supported

  Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [127] Datta RR, Ling J, Kurland J et al (2018) A feed-forward relay integrates the regulatory activities of Bicoid and Orthodenticle via sequential binding to suboptimal sites. Genes Dev 32:723–736 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [128] Keller SH, Jena SG, Yamazaki Y, Lim B (2020) Regulation of spatiotemporal limits of developmental gene expression via enhancer grammar. Proc Natl Acad Sci USA 117:15096–15103 source

In the paper

“While much of the evidence for enhancer function was obtained through perturbing these regions artificially, natural genetic variation at enhancers is commonly observed in human populations, consistent with the relatively low sequence constraint of these regions [191, 192].”

What the sources say

• Partly supported

  The Background says variation at DNA regulatory elements is relatively common, and the Results analyze variation at human transcription-factor binding sites. But the paper does not establish that enhancers generally have low sequence constraint: the Background distinguishes limited base-by-base conservation from lack of functional constraint, and the Conclusions say binding sites are functionally constrained despite tolerating some mutations. Our copy provides no page numbers for these passages. (LLM, conf=0.84)

  cites [191] Spivakov M, Akhtar J, Kheradpour P et al (2012) Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol 13:R49 sourceExperimental — accuracy not yet measured
• Partly supported

  The section on LDTF motif mutations reports naturally occurring sequence differences in mouse enhancers and their effects on enhancer activity. The paper studies variation between mouse strains; it does not establish that enhancer variation is common in human populations or that enhancers have relatively low sequence constraint. The supplied passages and searches for human variation and sequence constraint did not substantiate those parts. (LLM, conf=0.83)

  cites [192] Heinz S, Romanoski CE, Benner C et al (2013) Effect of natural genetic variation on enhancer selection and function. Nature 503:487–492 sourceExperimental — accuracy not yet measured

In the paper

“The importance of enhancer variation in human pathology has been further highlighted by genome-wide association studies (GWAS), since GWAS-detected genetic variants associated with complex traits and diseases are typically non-coding, non-promoter associated and highly enriched in enhancers [184, 208, 209].”

What the sources say

• Partly supported

  The Abstract says most causal variants do not alter protein-coding sequences, and ‘Enrichment of GWAS variants in enhancers’ reports strong enhancer enrichment among fine-mapped variants for 72 traits. The copy does not establish that GWAS-detected variants are typically non-promoter-associated; the enrichment analysis also focuses on credible sets without coding or splice-site variants. (LLM, conf=0.85)

  cites [184] Nasser J, Bergman DT, Fulco CP et al (2021) Genome-wide enhancer maps link risk variants to disease genes. Nature. https://doi.org/10.1038/s41586-021-03446-x sourceExperimental — accuracy not yet measured
• Supported

  The Introduction says that genetic risk variants affecting enhancers are estimated to far outnumber those affecting protein-coding genes or promoter function. The section on cell-type-specific enhancer elements says genetic risk variants are highly enriched at enhancers relative to promoters, and Figure 2 describes their distribution across coding, promoter, and noncoding regions. (LLM, conf=0.91)

  cites [208] Corradin O, Scacheri PC (2014) Enhancer variants: evaluating functions in common disease. Genome Med 6:85 source
• Partly supported

  The introductory passage reports that about 93% of disease- and trait-associated variants are noncoding. The section ‘Disease- and trait-associated variants are concentrated in regulatory DNA’ reports enrichment in DNase I hypersensitive sites (DHSs), and ‘DHSs harboring GWAS variants control distant phenotype-relevant genes’ identifies some of those sites as enhancers. The paper does not establish that GWAS variants are typically non-promoter-associated or specifically highly enriched in enhancers, rather than in regulatory DNA more broadly; page numbers were not supplied in our copy. (LLM, conf=0.87)

  cites [209] Maurano MT, Humbert R, Rynes E et al (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science 337:1190–1195 sourceExperimental — accuracy not yet measured

In the paper

“The classic example of this is the Shh ZRS enhancer, which is located within the intron of the Lmbr1 gene approximately 1 megabase distant from Shh [27].”

What the sources say

• Partly supported

  The “Regulation at a distance” section places the ZRS in intron 5 of Lmbr1 and says it is a considerable distance from Shh. Our copy does not give an approximately 1-megabase physical distance for the ZRS–Shh separation; its reference to about 1 Mb concerns other genes. (LLM, conf=0.86)

  cites [27] Lettice LA, Heaney SJH, Purdie LA et al (2003) A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet 12:1725–1735 sourceExperimental — accuracy not yet measured

In the paper

“In addition, whilst genetic variants at epromoters may affect the expression of both the proximal and distal gene, a large proportion are associated with only the distal one [207].”

What the sources say

• Supported

  The Results section, “Many CRMs associated with distal gene expression show features of epromoters,” reports associations with both proximal and distal gene expression, but says that nearly two-thirds of epromoters with an expressed proximal gene showed a detectable association with the distal gene alone. This supports the citing sentence’s qualified claim. (LLM, conf=0.94)

  cites [207] Mitchelmore J, Grinberg NF, Wallace C, Spivakov M (2020) Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters. Nucleic Acids Res 48:2866–2879 source

In the paper

“Finally, some enhancers are marked with H3K27me3 alone and are considered to be “Polycomb-repressed” [139–141].”

What the sources say

• Partly supported

  The Results section ('PRC2-associated silencers transition into active enhancers during differentiation'; page unavailable) describes PRC2-bound silencers that can become active enhancers, supporting the Polycomb-repression aspect. It reports H3K27me3 co-enriched with H3K4me1, however, not enhancers marked by H3K27me3 alone. (LLM, conf=0.85)

  cites [139] Ngan CY, Wong CH, Tjong H et al (2020) Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development. Nat Genet 52:264–272 sourceExperimental — accuracy not yet measured
• Partly supported

  The Results section on element selection describes H3K27me3 as a repressive mark at candidate regulatory elements, including elements that may act as enhancers in another cell type. It does not establish that those enhancers carry H3K27me3 alone or classify them as Polycomb-repressed. In the Results section on validated silencers, only 4 of 29 overlapped Polycomb response elements. (LLM, conf=0.84)

  cites [140] Gisselbrecht SS, Palagi A, Kurland JV et al (2020) Transcriptional silencers in drosophila serve a dual role as transcriptional enhancers in alternate cellular contexts. Mol Cell 77:324-337.e8 sourceExperimental — accuracy not yet measured
• Supported

  In Results, under “Identification of putative regulatory elements and their associated gene promoters” (page not supplied), the paper identifies promoter-interacting regions with H3K27me3 as Polycomb-associated and links that mark to Polycomb-mediated transcriptional repression. Materials and methods specifies that this state has H3K27me3 without H3K4 methylation; the paper also describes promoter-interacting regions as potential enhancers. (LLM, conf=0.88)

  cites [141] Freire-Pritchett P, Schoenfelder S, Várnai C et al (2017) Global reorganisation of regulatory units upon lineage commitment of human embryonic stem cells. Elife 6:e21926 source

In the paper

“While enhancer detection based on chromatin profiling has become standard, this approach may falsely detect regions without appreciable regulatory activity, as well as miss some functional elements [146, 162].”

What the sources say

• Supported

  In “p300 predicts enhancer activity patterns” (page unavailable), 13% of tested p300 ChIP-seq candidates lacked reproducible enhancer activity. The Discussion (page unavailable) reports that absence of p300 enrichment corresponded to absence of enhancer activity in 93% of tested tissue-specific cases, leaving some active cases without a detected peak. These findings support the qualified claim that chromatin-based detection may produce both false positives and missed activity. (LLM, conf=0.88)

  cites [146] Visel A, Blow MJ, Li Z et al (2009) ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457:854–858 source
• Partly supported

  The Online methods (Model assessment; page unavailable) describe non-STARR-seq regions with H3K27ac signal, supporting the possibility that a chromatin signal can occur without measured enhancer activity. The Introduction (page unavailable) says active enhancers are *usually* in open chromatin, but the copy does not directly establish that chromatin-based detection misses functional elements. (LLM, conf=0.79)

  cites [162] Sethi A, Gu M, Gumusgoz E et al (2020) Supervised enhancer prediction with epigenetic pattern recognition and targeted validation. Nat Methods 17:807–814 sourceExperimental — accuracy not yet measured

In the paper

“In a Drosophila assay, unidirectionally transcribing elements were more likely to drive strong promoter and limited enhancer activity, whilst bi-directionally transcribing elements had strong potential for enhancer activity and could also function as weak promoters [248].”

What the sources say

• Supported

  Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [248] Mikhaylichenko O, Bondarenko V, Harnett D et al (2018) The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription. Genes Dev 32:42–57 source

In the paper

“Therefore, enhancers predisposed to convert into promoters may have a particular GC sequence composition and presence of 5′ splicing regulatory motif patterns [100].”

What the sources say

• Supported

  The Introduction states that distinct GC sequence compositions and stabilizing 5′ splicing (U1) regulatory motif patterns may have predisposed promoter/enhancer elements to repurposing. It also says that most detected events were conversions of putative ancestral enhancers into promoters, matching the citing sentence’s hedged paraphrase. (LLM, conf=0.94)

  cites [100] Carelli FN, Liechti A, Halbert J et al (2018) Repurposing of promoters and enhancers during mammalian evolution. Nat Commun 9:4066 source

In the paper

“In terms of their sequence properties, enhancers and promoters tend to differ in GC content, with many promoters and only a subset of enhancers containing CpG islands [74, 249].”

What the sources say

• Supported

  The Conclusions (page not provided) attribute apparent enhancer–promoter sequence differences to local GC content, noting that transcribed enhancers tend to have GC-poor motifs like non-CpG-island promoters. The Results report that enhancer candidates are depleted of CpG islands, while the Methods identify a substantial set of CpG-island-associated promoter clusters. Together these support the qualified comparison in the claim. (LLM, conf=0.88)

  cites [74] Andersson R, Gebhard C, Miguel-Escalada I et al (2014) An atlas of active enhancers across human cell types and tissues. Nature 507:455–461 source
• Partly supported

  The Introduction (page unavailable) says CpG islands are prevalent at vertebrate promoters. The Results, under “Genetic properties of PE-associated oCGIs” (page unavailable), report that roughly 60–80% of the poised enhancers studied lie near a CpG island and that their associated islands can have lower GC content than classically defined islands. The paper does not establish the claimed GC-content difference or CpG-island frequency for enhancers generally. (LLM, conf=0.84)

  cites [249] Pachano T, Sánchez-Gaya V, Ealo T et al (2021) Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness. Nat Genet. https://doi.org/10.1038/s41588-021-00888-x sourceExperimental — accuracy not yet measured

In the paper

“Both active enhancers and promoters occupy nucleosome-free chromatin, bind RNAP and can be divergently transcribed [73, 236, 237].”

What the sources say

• Supported

  The Results section, “Architecture of Initiation at Promoters and Enhancers” (page not provided), describes divergent initiation and transcription complexes at both promoters and enhancers, with positioned nucleosomes flanking their initiation regions. The Discussion (page not provided) describes these as open DNA regions where Pol II is recruited, supporting the claim’s description of nucleosome-free chromatin, polymerase binding, and divergent transcription. (LLM, conf=0.90)

  cites [73] Core LJ, Martins AL, Danko CG et al (2014) Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet 46:1311–1320 source
• Partly supported

  The paper states that human protein-coding gene promoters and enhancers can be divergently transcribed (Abstract) and analyzes transcribed DNase-hypersensitive sites associated with promoters and enhancers (Directional bias and exosome sensitivity discern RNA biotypes; page unavailable). Our copy does not establish the more specific claims that both occupy nucleosome-free chromatin and bind RNAP. (LLM, conf=0.82)

  cites [236] Andersson R, Refsing Andersen P, Valen E et al (2014) Nuclear stability and transcriptional directionality separate functionally distinct RNA species. Nat Commun 5:5336 sourceExperimental — accuracy not yet measured
• Partly supported

  The Introduction describes divergent transcription at mammalian promoters and many enhancers. Results, under “Divergent TSSs have a common organization” (page unavailable), reports largely nucleosome-depleted regions between enhancer-RNA and promoter-transcript start sites. Our copy does not explicitly establish RNAP binding at both types of site, so that part of the claim is not supported. (LLM, conf=0.82)

  cites [237] Chen Y, Pai AA, Herudek J et al (2016) Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Nat Genet 48:984–994 sourceExperimental — accuracy not yet measured

In the paper

“Functional analysis of the ZRS enhancer revealed that these mutations either create gain-of-function binding sites for activating TFs (ETS1 and GABPα) [199], or abolish a repressive TF site [200], leading to ectopic SHH expression.”

What the sources say

• Supported

  Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [199] Lettice LA, Williamson I, Wiltshire JH et al (2012) Opposing functions of the ETS factor family define Shh spatial expression in limb buds and underlie polydactyly. Dev Cell 22:459–467 source
• Supported

  Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [200] Lettice LA, Devenney P, De Angelis C, Hill RE (2017) The conserved sonic hedgehog limb enhancer consists of discrete functional elements that regulate precise spatial expression. Cell Rep 20:1396–1408 source

In the paper

“Notably, while many such elements control house-keeping genes in cis (as promoters), they may regulate lineage-specific or inducible genes distally (as enhancers) [240, 247].”

What the sources say

• ?Not checked — no full text of the sourcecites [240] Dao LTM, Galindo-Albarrán AO, Castro-Mondragon JA et al (2017) Genome-wide characterization of mammalian promoters with distal enhancer functions. Nat Genet 49:1073–1081 source
• Partly supported

  The Results passage on genomic distributions (labelled Abstract in our copy; no page supplied) reports that many housekeeping-core-promoter enhancers overlap or lie near transcription start sites and can act as enhancers from a distal position in reporter assays. Extended Data Figure 5 also discusses their promoter-like appearance. The paper does not show that those same elements distally regulate lineage-specific or inducible genes; it instead describes developmental and housekeeping enhancers as largely distinct classes. (LLM, conf=0.87)

  cites [247] Zabidi MA, Arnold CD, Schernhuber K et al (2015) Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation. Nature 518:556–559 sourceExperimental — accuracy not yet measured

In the paper

“Meanwhile, ZNF143 binds to promoters globally [367] and was found at the anchors of many lineage-specific enhancer–promoter loops in human and mouse cells [362–364, 368].”

What the sources say

• Supported

  The citation to this paper [367] supports the promoter-binding clause, not the separate claim about enhancer–promoter loop anchors, which cites other papers. The Discussion reports 1,175 conserved ZNF143-binding sites across 938 mammalian promoters and ChIP validation of binding at 90% of 295 tested promoters. (LLM, conf=0.93)

  cites [367] Myslinski E, Gérard M-A, Krol A, Carbon P (2006) A genome scale location analysis of human Staf/ZNF143-binding sites suggests a widespread role for human Staf/ZNF143 in mammalian promoters. J Biol Chem 281:39953–39962 source
• Partly supported

  The Results section reports that ZNF143 is enriched at interacting loci and that enhancer–promoter interactions differ between two human cell lines. It does not establish that ZNF143 anchors the cell-type-specific enhancer–promoter loops specifically, and its own interaction map is of human, not mouse, cells. The separate promoter-binding clause is cited to [367], not this paper. (LLM, conf=0.85)

  cites [362] Heidari N, Phanstiel DH, He C et al (2014) Genome-wide map of regulatory interactions in the human genome. Genome Res 24:1905–1917 sourceExperimental — accuracy not yet measured
• Partly supported

  The Results sections on promoter binding and chromatin-interaction anchors report genome-wide promoter-associated ZNF143 binding and enrichment at anchors of promoter–distal regulatory-element interactions in human cell lines. They also link ZNF143 binding to cell-type-specific interactions. The study does not show this finding in mouse cells, so the human-and-mouse scope of the claim is not fully supported by this source. (LLM, conf=0.87)

  cites [363] Bailey SD, Zhang X, Desai K et al (2015) ZNF143 provides sequence specificity to secure chromatin interactions at gene promoters. Nat Commun 2:6186 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [364] Ye B-Y, Shen W-L, Wang D et al (2016) ZNF143 is involved in CTCF-mediated chromatin interactions by cooperation with cohesin and other partners. Mol Biol 50:496–503 source
• Partly supported

  The Results (Fig. 2; page unavailable) show ZNF143 at promoter–enhancer loop anchors in murine hematopoietic stem and progenitor cells. This source does not establish the same finding in human cells or show that the loops are lineage-specific. The separate promoter-binding clause is cited to [367], not this source. (LLM, conf=0.85)

  cites [368] Zhou Q, Yu M, Tirado-Magallanes R et al (2021) ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function. Nat Commun 12:43 sourceExperimental — accuracy not yet measured

In the paper

“Artificial tethering of CTCF to the Vcan promoter using a dCas9-CTCF construct effectively rescues the loop and, partially, the expression of Vcan [301].”

What the sources say

• Supported

  The Results section reports that tethering dCas9-CTCF to the mutated Vcan promoter partially restored Vcan expression. It also reports restored promoter-anchored contacts and re-established long-range contact with the distal Xrcc4/Tmem167 promoter, matching the claimed loop rescue. (LLM, conf=0.94)

  cites [301] Kubo N, Ishii H, Xiong X et al (2021) Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nat Struct Mol Biol 28:152–161 source

In the paper

“(although short-term YY1 depletion has only a modest effect on both [350]).”

What the sources say

• Supported

  The section “Acute YY1 depletion has little effect on global gene expression and E-P and P-P interactions” reports that, after three hours of YY1 depletion, most enhancer–promoter loops showed only a very minor change in intensity and relatively few genes showed altered expression. It also notes exceptions at specific loci, consistent with the claim’s qualified wording. (LLM, conf=0.94)

  cites [350] Hsieh TS, Cattoglio C, Slobodyanyuk E, Hansen AS, Darzacq X, Tjian R (2021) Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1. BioRxiv. https://doi.org/10.1101/2021.07.14.452365 source

In the paper

“LIM domain-binding protein 1 (LDB1) is a dimeric cofactor that does not have direct DNA-binding capacity, but interacts with the LIM domain of other TFs to form multi-protein complexes [370].”

What the sources say

• Partly supported

  The Abstract identifies NLI as Ldb1 and describes its homodimerization and LIM-interaction domains. The Results report that NLI dimers link LIM-domain transcription factors in tetrameric complexes. Our copy does not establish the separate claim that Ldb1 has no direct DNA-binding capacity. (LLM, conf=0.84)

  cites [370] Jurata LW, Pfaff SL, Gill GN (1998) The nuclear LIM domain interactor NLI mediates homo- and heterodimerization of LIM domain transcription factors. J Biol Chem 273:3152–3157 sourceExperimental — accuracy not yet measured

In the paper

“Therefore, 3C-derived methods and FISH cannot be considered merely as “mutually validating” techniques, and they may produce genuinely divergent results, which need to be interpreted carefully [307].”

What the sources say

• Supported

  The Discussion says 3C experiments cannot be simply validated or invalidated by FISH without careful attention to technical details. The Results explain that spatial distance and contact frequency can behave divergently, supporting the need to interpret apparent discrepancies carefully. (LLM, conf=0.94)

  cites [307] Fudenberg G, Imakaev M (2017) FISH-ing for captured contacts: towards reconciling FISH and 3C. Nat Methods 14:673–678 source

In the paper

“Polycomb-mediated looping is likely to work largely independently of CTCF and cohesin and is potentially even counteracted by the looping activities of these factors in ESCs [357].”

What the sources say

• Partly supported

  The Introduction and Results report that Polycomb-domain interactions persist without cohesin and are strengthened when cohesin is removed, supporting independence from—and counteraction by—cohesin in ESCs. The Results section ‘Cohesin Counteracts Polycomb Chromatin Domain Interactions Independently of CTCF and Insulation’ says CTCF removal did not strengthen those interactions, so the paper does not support attributing a counteracting effect to CTCF. Page numbers were not provided in our copy. (LLM, conf=0.85)

  cites [357] Rhodes JDP, Feldmann A, Hernández-Rodríguez B et al (2020) Cohesin disrupts polycomb-dependent chromosome interactions in embryonic stem cells. Cell Rep 30:820-835.e10 sourceExperimental — accuracy not yet measured

In the paper

“Forced looping between these loci could also be achieved in HEK293 cells, in which they are heterochromatic, but in this case β-globin derepression was not achieved [313].”

What the sources say

• Partly supported

  The Representative Results report induced β-globin–LCR contacts in heterochromatic HEK 293T cells, without an increase in β-globin expression. The cited experiments used HEK 293T cells specifically, whereas the claim identifies them as HEK293 cells. (LLM, conf=0.83)

  cites [313] Morgan SL, Chang EY, Mariano NC et al (2018) CRISPR-mediated reorganization of chromatin loop structure. J Vis Exp. https://doi.org/10.3791/57457 sourceExperimental — accuracy not yet measured

In the paper

“recent studies suggest that loops that require CTCF might be preferentially long-range (> 100 kb) and situated in loci where enhancers are generally sparse [301, 349].”

What the sources say

• Supported

  The Results section ('Promoter-proximal CTCF-regulated genes tend to reside in enhancer sparse regions'; page not provided) reports that CTCF-dependent genes generally have long-range enhancer–promoter and promoter–promoter contacts (≥100 kb), especially in NPCs. It also reports that genes down-regulated after CTCF depletion tend to lie in enhancer-sparse regions. This supports the citing sentence’s hedged characterization. (LLM, conf=0.89)

  cites [301] Kubo N, Ishii H, Xiong X et al (2021) Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nat Struct Mol Biol 28:152–161 source
• Partly supported

  The Results section (“Cohesin-Dependent and -Independent Promoter Interactions Have Distinct Properties”; page unavailable) associates longer interaction distances with cohesin-dependent contacts and reports CTCF binding at contacts lost upon cohesin depletion. The Discussion (page unavailable) reports relatively fewer active enhancer-containing interacting regions among those contacts. These findings do not establish a >100 kb threshold, show that the loops require CTCF specifically, or demonstrate that their surrounding loci are generally enhancer-sparse. (LLM, conf=0.84)

  cites [349] Thiecke MJ, Wutz G, Muhar M et al (2020) Cohesin-dependent and -independent mechanisms mediate chromosomal contacts between promoters and enhancers. Cell Rep 32:107929 sourceExperimental — accuracy not yet measured

In the paper

“Unlike CTCF and cohesin, long-term depletion of YY1 or ZNF143 in mammalian cells causes a significant reduction of enhancer–promoter loops, coupled with substantial changes in gene expression [295, 368, 369]”

What the sources say

• Partly supported

  The Results section reports that YY1 depletion in mouse embryonic stem cells significantly reduced interactions between YY1-occupied enhancers and promoters, while 60% of genes connected by those loops showed significant expression changes. The Methods specify 24 hours of YY1 depletion. Our copy does not establish the claimed effect for ZNF143 or characterize this experiment as long-term depletion. (LLM, conf=0.88)

  cites [295] Weintraub AS, Li CH, Zamudio AV et al (2017) YY1 Is a structural regulator of enhancer-promoter loops. Cell 171:1573-1588.e28 sourceExperimental — accuracy not yet measured
• Partly supported

  The Results section on ZNF143 depletion reports significantly fewer promoter–enhancer loops in Znf143-deleted murine hematopoietic stem and progenitor cells; the Results section on regulated pathways reports significant gene-expression changes. This supports the ZNF143 portion of the multiply cited sentence, but this paper does not establish the stated long-term timescale or extend the finding beyond the murine cells studied. The YY1 portion is not attributed specifically to this source. (LLM, conf=0.83)

  cites [368] Zhou Q, Yu M, Tirado-Magallanes R et al (2021) ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function. Nat Commun 12:43 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [369] Wen Z, Huang Z-T, Zhang R, Peng C (2018) ZNF143 is a regulator of chromatin loop. Cell Biol Toxicol 34:471–478 source

In the paper

“Consistent with this, significant numbers of enhancer–promoter contacts remain unaffected upon rapid degradation of these proteins, and some contacts even appear de novo [349, 350].”

What the sources say

• Supported

  The Results report thousands of promoter interactions maintained or gained after rapid cohesin or CTCF depletion. The Discussion states that many promoter–active-enhancer interactions are retained and a smaller number of promoter–enhancer contacts are gained; it also describes some promoter interactions as emerging de novo. (LLM, conf=0.93)

  cites [349] Thiecke MJ, Wutz G, Muhar M et al (2020) Cohesin-dependent and -independent mechanisms mediate chromosomal contacts between promoters and enhancers. Cell Rep 32:107929 source
• Partly supported

  The section on loop-extrusion factors reports that approximately 80% of enhancer–promoter contacts remained unaltered after acute CTCF or cohesin depletion. It does not establish that enhancer–promoter contacts appeared de novo after either depletion; the emerging long-range loops it describes followed WAPL depletion and are not identified there as enhancer–promoter contacts. (LLM, conf=0.87)

  cites [350] Hsieh TS, Cattoglio C, Slobodyanyuk E, Hansen AS, Darzacq X, Tjian R (2021) Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1. BioRxiv. https://doi.org/10.1101/2021.07.14.452365 sourceExperimental — accuracy not yet measured

In the paper

“In addition, using high-resolution live imaging, it was observed that genes regulated by a single enhancer can localise surprisingly large distances away from each other in 3D (at least 100–200 nm), and yet show coordinated bursts in transcription, which is inconsistent with their direct looping to the shared enhancer [409].”

What the sources say

• Partly supported

  Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [409] Heist T, Fukaya T, Levine M (2019) Large distances separate coregulated genes in living embryos. Proc Natl Acad Sci USA 116:15062–15067 sourceExperimental — accuracy not yet measured

In the paper

“Moreover, there was no correlation between Sox2 transcriptional level and enhancer–promoter distance, or any obvious reduction in distance prior to transcription initiation, suggesting that this enhancer may activate Sox2 transcription via a looping-independent mechanism [402].”

What the sources say

• Supported

  Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [402] Alexander JM, Guan J, Li B et al (2019) Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity. eLife 8:e41769 source

In the paper

“For instance, whilst TFs were shown to form high-concentration stochastic hubs with chromatin in living human cells, overexpression of their low complexity domains beyond endogenous levels was required for LLPS to occur [412].”

What the sources say

• Partly supported

  The Results and Discussion report dynamic, high-concentration TF LCD hubs at endogenous genomic loci in live cells. The Discussion says apparent liquid–liquid phase separation was detected with gross LCD overexpression, but not detected in hubs at endogenous expression levels. That observation does not establish that overexpression is required for phase separation to occur. (LLM, conf=0.87)

  cites [412] Chong S, Dugast-Darzacq C, Liu Z et al (2018) Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science 361:eaar2555 sourceExperimental — accuracy not yet measured

In the paper

“Recruiting activators such as VP64, Mediator and SIX3 to this enhancer also increased the enhancer–promoter distance whilst upregulating Shh expression [407].”

What the sources say

• Supported

  The Results sections report that targeting VP64 to Shh enhancers induced Shh expression and increased enhancer–promoter separation. They also report increased separation after recruitment of Mediator or SIX3, although the associated Shh expression was low-level for Mediator and very low and variable for SIX3. (LLM, conf=0.90)

  cites [407] Benabdallah NS, Williamson I, Illingworth RS et al (2019) Decreased enhancer-promoter proximity accompanying enhancer activation. Mol Cell 76:473-484.e7 source

In the paper

“Ectopic tethering of LDB1 to chromatin is sufficient for loop formation, increased deposition of the enhancer mark H3K4me1 and transcriptional activation [372, 374].”

What the sources say

• Supported

  The Results section (‘Forced Ldb1 targeting to Pax3 sites induces myogenesis’) reports that a PAX3–LDB1 fusion induced looping and upregulated Pax3 target genes. The Discussion reports increased H3K4me1 at a subset of PAX3-bound sites following expression of the fusion. Thus, the claim is supported in the paper’s tested context of tethering LDB1 to PAX3-bound sites. (LLM, conf=0.90)

  cites [372] Magli A, Baik J, Pota P et al (2019) Pax3 cooperates with Ldb1 to direct local chromosome architecture during myogenic lineage specification. Nat Commun 10:2316 source
• Partly supported

  The Discussion reports that tethering the Ldb1 self-association domain increased γ-globin promoter–LCR contacts and activated transcription. Neither the cited passages nor searches for H3K4me1 and histone H3 lysine 4 monomethylation support the claimed increase in deposition of that enhancer mark. (LLM, conf=0.88)

  cites [374] Deng W, Rupon JW, Krivega I et al (2014) Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell 158:849–860 sourceExperimental — accuracy not yet measured

In the paper

“Loop extrusion was initially proposed theoretically based on molecular dynamics simulations [342, 435] and then validated in single-molecule assays [436, 437].”

What the sources say

• ?Not checked — no full text of the sourcecites [342] Sanborn AL, Rao SSP, Huang S-C et al (2015) Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc Natl Acad Sci USA 112:E6456–E6465 source
• Partly supported

  The Introduction and Results describe a theoretical model of TAD formation by loop extrusion tested with polymer simulations. But the Introduction says loop extrusion had been proposed earlier, so this paper does not support the implication that it was initially proposed through these simulations. The single-molecule-assay clause is attached to different citations and is not assessed here. (LLM, conf=0.82)

  cites [435] Fudenberg G, Imakaev M, Lu C et al (2016) Formation of chromosomal domains by loop extrusion. Cell Rep 15:2038–2049 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [436] Davidson IF, Bauer B, Goetz D et al (2019) DNA loop extrusion by human cohesin. Science 366:1338–1345 source
• Supported

  This source supports the single-molecule-assay portion of the sentence, not the earlier theoretical-proposal portion, which is assigned to different citations. Its Abstract reports direct visualization of cohesin extruding DNA loops using single-molecule imaging. (LLM, conf=0.92)

  cites [437] Kim Y, Shi Z, Zhang H et al (2019) Human cohesin compacts DNA by loop extrusion. Science 366:1345–1349 source

In the paper

“The Sox2 gene has an essential enhancer, the Sox2 Control Region (SCR), which was found by 3C-derived techniques to loop to the Sox2 promoter (for example, [379, 401]).”

What the sources say

• Partly supported

  In Results, “Constitutive and cell type-specific features of 3-D chromatin organization” (page unavailable), the paper reports that 5C data show looping interactions between Sox2 and a putative downstream enhancer in ES cells. It does not identify that enhancer as the Sox2 Control Region (SCR) or establish that it is essential. (LLM, conf=0.87)

  cites [379] Phillips-Cremins JE, Sauria MEG, Sanyal A et al (2013) Architectural protein subclasses shape 3D organization of genomes during lineage commitment. Cell 153:1281–1295 sourceExperimental — accuracy not yet measured
• Partly supported

  The Results section (Figure 7G; page not provided) reports Hi-C contacts between the Sox2 promoter and an embryonic-stem-cell-specific enhancer. It does not identify that enhancer as the Sox2 Control Region (SCR) or establish in this paper that it is essential. (LLM, conf=0.84)

  cites [401] Bonev B, Mendelson Cohen N, Szabo Q et al (2017) Multiscale 3D genome rewiring during mouse neural development. Cell 171:557-572.e24 sourceExperimental — accuracy not yet measured

In the paper

“Stripe domains tend to anchor at a single CTCF binding site (as opposed to two divergent CTCF sites in the classic case for TADs), which points towards a nearby site for the cohesin-loading factor NIPBL [456, 457].”

What the sources say

• ?Not checked — no full text of the sourcecites [456] Vian L, Pękowska A, Rao SSP et al (2018) The energetics and physiological impact of cohesin extrusion. Cell 173:1165-1178.e20 source
• Partly supported

  The Results sections on CTCF occupancy and enhancer accessibility (page unavailable) report a prominent CTCF site and maximal NIPBL signal at the anchored border of stripe domains. They do not say that the CTCF site points toward a nearby NIPBL site; they also report multiple CTCF-binding sites within stripe domains, so the 'single site' description is too strong. (LLM, conf=0.86)

  cites [457] Barrington C, Georgopoulou D, Pezic D et al (2019) Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology. Nat Commun 10:2908 sourceExperimental — accuracy not yet measured

In the paper

“in the developing Drosophila embryo, enhancer–promoter loops are formed before TADs, and likely also precede the onset of zygotic transcription [453, 454].”

What the sources say

• Partly supported

  In “Cis-regulatory networks emerge before TADs and gene expression” (page unavailable), the paper reports promoter–CRM loops at nc11, before TAD formation and expression of the studied doc genes. It places TAD emergence at nc14 during the major wave of zygotic gene activation, but does not establish that the loops precede the onset of zygotic transcription generally. (LLM, conf=0.85)

  cites [453] Espinola SM, Götz M, Bellec M et al (2021) Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development. Nat Genet 53:477–486 sourceExperimental — accuracy not yet measured
• Partly supported

  The Results report detecting enhancer–promoter loops in 3–4 and 6–8 hpf Drosophila embryos. The Introduction and Results place widespread TAD formation around zygotic genome activation, but do not establish that enhancer–promoter loops formed before TADs or before zygotic transcription began. No page numbers are available in our copy. (LLM, conf=0.84)

  cites [454] Hug CB, Grimaldi AG, Kruse K, Vaquerizas JM (2017) Chromatin architecture emerges during zygotic genome activation independent of transcription. Cell 169:216-228.e19 sourceExperimental — accuracy not yet measured

In the paper

“LADs represent ~ 500 kb-long chromatin regions localised at the nuclear periphery.”

What the sources say

• Supported

  The “Definition and characteristics of LADs” section defines LADs as genomic regions that contact the nuclear lamina and gives their median size in mouse and human cells as approximately 0.5 Mb. The “Multivalent interactions” section also describes a typical LAD as 500 kb long. The length is typical, not a fixed size for every LAD. (LLM, conf=0.94)

  cites [462] van Steensel B, Belmont AS (2017) Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression. Cell 169:780–791 source

In the paper

“The A/B compartment structure does not disappear (and is in fact even strengthened) upon cohesin/CTCF depletion [344, 346–348], but, like TADs, dissolves in mitosis [459].”

What the sources say

• Partly supported

  The Results report that A/B compartment assignments remained highly correlated after cohesin depletion in noncycling thymocytes. The paper does not show that compartment structure was strengthened or test CTCF depletion. The mitosis clause has a separate citation and is not attributed to this paper. (LLM, conf=0.88)

  cites [344] Seitan VC, Faure AJ, Zhan Y et al (2013) Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments. Genome Res 23:2066–2077 sourceExperimental — accuracy not yet measured
• Partly supported

  The Results section, “Disruption of Local Insulation Does Not Affect Higher-Order Chromosome Folding,” reports that A/B compartmentalization is maintained after CTCF depletion. It also reports a minor (~10%) reduction in compartmentalization strength, not strengthening. This paper does not directly test cohesin depletion; the mitosis clause has a separate citation. (LLM, conf=0.88)

  cites [346] Nora EP, Goloborodko A, Valton A-L et al (2017) Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169:930–944.e22 sourceExperimental — accuracy not yet measured
• Supported

  The Results section, “Loss of cohesin is associated with stronger genome compartmentalization,” reports that compartmentalization is preserved after cohesin loss and that its plaid pattern becomes stronger. It also reports that prior CTCF-depletion findings are consistent with preserved compartmentalization. The separate mitosis claim is attached to citation [459], not to this source. (LLM, conf=0.90)

  cites [347] Rao SSP, Huang S-C, Glenn St Hilaire B et al (2017) Cohesin loss eliminates all loop domains. Cell 171:305-320.e24 source
• Partly supported

  In “Enhanced and finer compartmentalization” (page unavailable), the paper reports that A/B compartmentalization persists and is enhanced about 1.8-fold after Nipbl deletion, supporting the cohesin-depletion part of the cited clause. It does not report strengthened A/B compartments after CTCF depletion. The mitosis clause carries a separate citation and is not assessed here. (LLM, conf=0.86)

  cites [348] Schwarzer W, Abdennur N, Goloborodko A et al (2017) Two independent modes of chromatin organization revealed by cohesin removal. Nature 551:51–56 sourceExperimental — accuracy not yet measured
• Supported

  The Results section (‘Loss of chromosome compartments and TADs in metaphase’) reports that compartmentalization disappears in mitotic cells and that the TAD signal is strongly reduced. This supports the mitosis clause attributed to this source; the cohesin/CTCF-depletion clause is attributed to other citations. (LLM, conf=0.94)

  cites [459] Naumova N, Imakaev M, Fudenberg G et al (2013) Organization of the mitotic chromosome. Science 342:948–953 source

In the paper

“These 10–50 kb pair stripes are enriched in promoter–promoter and enhancer–promoter interactions and are largely unassociated with CTCF/cohesin binding [276].”

What the sources say

• Supported

  The Results section, “Identification of E-P stripes, dots, and domains” (page not provided), describes ~10–50 kb stripes that predominantly link promoter–promoter or promoter–enhancer sites and do not predominantly correspond to CTCF or cohesin binding. (LLM, conf=0.95)

  cites [276] Hsieh T-HS, Cattoglio C, Slobodyanyuk E et al (2020) Resolving the 3D landscape of transcription-linked mammalian chromatin folding. Mol Cell 78:539-553.e8 source

In the paper

“A subset of B compartments corresponds to lamina-associated domains (LADs) [462].”

What the sources say

• Supported

  The section “LADs, TADs and Compartment B” says that LADs correspond to B-type domains. It also notes that compartment B may include other heterochromatin compartments, consistent with the claim referring to a subset rather than all B domains. (LLM, conf=0.93)

  cites [462] van Steensel B, Belmont AS (2017) Lamina-associated domains: links with chromosome architecture, heterochromatin, and gene repression. Cell 169:780–791 source

In the paper

“single-cell studies show both a substantial cell-to-cell heterogeneity of TADs and large numbers of inter-TAD chromosomal contacts [448, 452].”

What the sources say

• Partly supported

  The section ‘Super-resolution chromatin tracing reveals TAD-like structures in single cells’ reports substantial cell-to-cell variation in TAD-like domain boundaries. It also describes extensive overlap between regions from different ensemble sub-TADs in one example cell, but does not establish large numbers of inter-TAD chromosomal contacts. (LLM, conf=0.85)

  cites [448] Bintu B, Mateo LJ, Su J-H et al (2018) Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362:eaau1783 sourceExperimental — accuracy not yet measured
• Supported

  The Discussion reports that individual cells exhibit widely distinct TAD structures and that interactions between neighboring TADs are common. The Results section on intra- and inter-TAD interactions finds only modest enrichment of within-TAD contacts over distance-matched between-TAD contacts, supporting both parts of the claim. (LLM, conf=0.92)

  cites [452] Finn EH, Pegoraro G, Brandão HB et al (2019) Extensive heterogeneity and intrinsic variation in spatial genome organization. Cell 176:1502-1515.e10 source

In the paper

“the probabilities of enhancer–promoter contacts showed a strong dependence on linear distance within the TAD and fell sharply near and across the TAD boundaries [405].”

What the sources say

• Supported

  The Main text states that contact probabilities steeply decayed with increasing genomic distance from the promoter, fell drastically approaching the TAD boundaries, and dropped further across them. This directly supports the attributed pattern. (LLM, conf=0.94)

  cites [405] Zuin J, Roth G, Zhan Y et al (2021) Nonlinear control of transcription through enhancer–promoter interactions. BioRxiv. https://doi.org/10.1101/2021.04.22.440891 source

In the paper

“rapid depletion of cohesin or CTCF quickly abolishes TADs but, as mentioned above, has only relatively mild effects on gene expression [301, 345–347, 448].”

What the sources say

• Partly supported

  The Results report that acute CTCF depletion significantly weakened TAD boundaries and left expression of most genes unaffected, supporting much of the claim. But the same Results section says some TAD boundaries remained relatively well preserved—not that TADs were abolished—and reports significant expression decreases in hundreds of genes. The paper discusses cohesin's limited expression effects but does not report a comparable rapid cohesin-depletion experiment. (LLM, conf=0.88)

  cites [301] Kubo N, Ishii H, Xiong X et al (2021) Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation. Nat Struct Mol Biol 28:152–161 sourceExperimental — accuracy not yet measured
• ?Not checked — no full text of the sourcecites [345] Zuin J, Dixon JR, van der Reijden MIJA et al (2014) Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells. Proc Natl Acad Sci USA 111:996–1001 source
• Partly supported

  The Results section reports that CTCF depletion caused loss of insulation at more than 80% of TAD boundaries, and the Discussion describes rather limited immediate transcriptional effects. But 18% of boundaries persisted, so saying TADs were abolished overstates the finding. This paper directly tests CTCF depletion; it mentions cohesin depletion in a parallel study rather than testing it here. (LLM, conf=0.84)

  cites [346] Nora EP, Goloborodko A, Valton A-L et al (2017) Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization. Cell 169:930–944.e22 sourceExperimental — accuracy not yet measured
• Partly supported

  The Discussion section, “The interplay between cohesin and gene regulation” (page unavailable), reports that most genes are not strongly affected after rapid cohesin loss. The STAR METHODS section, “Quantification and Statistical Analysis” (page unavailable), says cohesin loss eliminates loop domains but leaves compartment-derived contact domains. The paper does not show that rapid CTCF depletion abolishes all TADs or has similarly mild effects on gene expression; its Discussion reports disappearance of only a subset of contact domains after CTCF depletion. (LLM, conf=0.90)

  cites [347] Rao SSP, Huang S-C, Glenn St Hilaire B et al (2017) Cohesin loss eliminates all loop domains. Cell 171:305-320.e24 sourceExperimental — accuracy not yet measured
• Partly supported

  The section “TAD-like structures remain in single cells after cohesin depletion” reports that six hours of induced cohesin degradation largely eliminated population-averaged TADs in the imaged regions. It does not report CTCF depletion or show that either depletion has only mild effects on gene expression. The paper also distinguishes the loss of population-averaged TADs from the persistence of TAD-like domains in single cells. (LLM, conf=0.88)

  cites [448] Bintu B, Mateo LJ, Su J-H et al (2018) Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362:eaau1783 sourceExperimental — accuracy not yet measured

In the paper

“Chromosomal contacts follow the law of constrained Brownian motion (reviewed in [465]), with the contact probabilities showing a strong power–law dependence on the “linear” genomic distance [272, 466].”

What the sources say

• Supported

  The citation to this source is attached to the constrained-Brownian-motion clause, not the later power-law claim, which cites [272, 466]. The Abstract states that chromatin loci generally show constrained Brownian motion. (LLM, conf=0.88)

  cites [465] Woodcock CL, Ghosh RP (2010) Chromatin higher-order structure and dynamics. Cold Spring Harb Perspect Biol 2:a000596 source
• Supported

  The citation to this paper is attached to the power-law claim, not the preceding constrained-Brownian-motion claim. In the supplied passage labelled Abstract, the authors report that contact probability scales approximately as s⁻¹ with linear genomic distance between about 500 kb and 7 Mb. (LLM, conf=0.92)

  cites [272] Lieberman-Aiden E, van Berkum NL, Williams L et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293 source
• ?Not checked — no full text of the sourcecites [466] Barbieri M, Chotalia M, Fraser J et al (2012) Complexity of chromatin folding is captured by the strings and binders switch model. Proc Natl Acad Sci USA 109:16173–16178 source

In the paper

“Whilst many LADs remain generally invariant across cell types and conditions, others can move away from the nuclear periphery, for example, upon T cell differentiation [463].”

What the sources say

• Partly supported

  The introductory passage describes constitutive LADs as unchanging and facultative LADs as moving to or from the periphery during differentiation. The Results section, “Important T-cell genes are released from the periphery,” reports that 2.5% of the genome shifted from peripheral to interior association in Jurkat T cells, but this was during T-cell activation, not T-cell differentiation. The paper explicitly distinguishes activation from differentiation. (LLM, conf=0.88)

  cites [463] Robson MI, de Las Heras JI, Czapiewski R et al (2017) Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments. Genome Res 27:1126–1138 sourceExperimental — accuracy not yet measured

In the paper

“recent dissection of an enhancer chain in the INK4a/ARF locus revealed that perturbing any promoter-interacting enhancer within the chain abolished the functionality of the entire network, but deleting the enhancers further down the chain had more moderate effects [491].”

What the sources say

• Partly supported

  The Results (‘An interdependent enhancer network operates within the enhancer cluster’; page unavailable) report that blocking any of the three tested promoter-interacting enhancers reduced activity of the others. The Results (‘Each promoter-interacting enhancer fully regulates INK4a/ARF genes’; page unavailable) report that deleting E21 had only marginal effects on ARF and INK4b and no effect on INK4a. But E21 is described as a non-promoter-interacting enhancer, not as one of multiple enhancers ‘further down the chain’; the paper describes the interacting network as equal-weighted rather than a directional chain. (LLM, conf=0.87)

  cites [491] Farooq U, Saravanan B, Islam Z et al (2021) An interdependent network of functional enhancers regulates transcription and EZH2 loading at the INK4a/ARF locus. Cell Rep 34:108898 sourceExperimental — accuracy not yet measured

In the paper

“Analysis of enhancer chains suggests that the promoter-connected enhancer is often more distal than downstream enhancers in the same chain, yet binds more tissue-appropriate TFs, suggesting that enhancer chains might involve pioneer enhancers [490].”

What the sources say

• Partly supported

  Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [490] Song W, Sharan R, Ovcharenko I (2019) The first enhancer in an enhancer chain safeguards subsequent enhancer–promoter contacts from a distance. Genome Biol 20:197 sourceExperimental — accuracy not yet measured

In the paper

“Evidence from Hi-C data analysis has suggested that the “first” enhancer in the chain, i.e. the enhancer with direct looping to the gene promoter, is often more distal than the “second” enhancer, attracts more tissue-specific factors and is more enriched for eQTLs than other enhancers within the chain [490].”

What the sources say

• Partly supported

  The Abstract (Results) reports that the first enhancer directly contacts the promoter and is commonly farther from it than the second; the Results section on baseline gene regulation reports higher tissue-specific eQTL density in first enhancers. The factor claim is less well supported: the Results report enrichment of loop factors in first enhancers, but do not establish that they attract more tissue-specific factors than other chain enhancers. A separate Results comparison says overall bound-transcription-factor enrichment is similar across chain enhancers. (LLM, conf=0.87)

  cites [490] Song W, Sharan R, Ovcharenko I (2019) The first enhancer in an enhancer chain safeguards subsequent enhancer–promoter contacts from a distance. Genome Biol 20:197 sourceExperimental — accuracy not yet measured

In the paper

“In developing mouse limb tissue, for instance, genes were regulated by a median of three functional enhancers and some genes, which coded for limb-specific TFs, had more than ten associated enhancers [480].”

What the sources say

• Partly supported

  The Text reports a median of three associated distal enhancers for limb-biased genes and says some limb-biased transcription-factor genes had more than a dozen. But these counts come from a correlation-based estimate of enhancer–gene associations; the paper does not establish that every counted enhancer functionally regulates its assigned gene. (LLM, conf=0.87)

  cites [480] Osterwalder M, Barozzi I, Tissières V et al (2018) Enhancer redundancy provides phenotypic robustness in mammalian development. Nature 554:239–243 sourceExperimental — accuracy not yet measured

In the paper

“While both methods could successfully reveal multi-way contacts across TADs and chromosomes, their resolution currently limits robust detection of individual CRUs.”

What the sources say

• Partly supported

  In ‘Detecting interacting triplets’ (page unavailable), the paper reports that GAM detects simultaneous multi-way contacts between TADs, but that the current dataset resolves triplets only at hundreds-of-kilobases scale; the Discussion says larger datasets could enable higher resolution. The paper does not assess SPRITE or detection of individual CRUs, and its TAD-triplet analysis is restricted to TADs on the same chromosome, so it does not establish the full claim about both methods and contacts across chromosomes. (LLM, conf=0.87)

  cites [497] Beagrie RA, Scialdone A, Schueler M et al (2017) Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543:519–524 sourceExperimental — accuracy not yet measured
• Partly supported

  The Results section reports that SPRITE measures simultaneous contacts among multiple DNA molecules and that larger clusters show interactions between distinct TADs; the Key Resources Table also identifies TAD triplets detected by GAM. But our copy does not say that the resolution of either method limits robust detection of individual CRUs. No page numbers are available in the indexed passages. (LLM, conf=0.85)

  cites [403] Quinodoz SA, Ollikainen N, Tabak B et al (2018) Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell 174:744-757.e24 sourceExperimental — accuracy not yet measured

In the paper

“it was recently shown that deletion of a relatively weak distal enhancer in the mouse Sox9 sex determination locus leads to sex reversal, while the phenotypic effects of deleting stronger and more proximal Sox9 enhancers are much less pronounced [510].”

What the sources say

• Partly supported

  The paper reports that deleting distal Enh13 causes complete XY sex reversal, while deleting the more proximal Enh14 did not alter the measured gonadal gene expression, and deleting TES had relatively little effect at E11.5 (indexed under Abstract; no page available). It describes robust reporter activity for Enh14, but does not establish the broader comparison that Enh13 is relatively weak and the more proximal enhancers are stronger as a group. (LLM, conf=0.84)

  cites [510] Gonen N, Futtner CR, Wood S et al (2018) Sex reversal following deletion of a single distal enhancer of. Science 360:1469–1473 sourceExperimental — accuracy not yet measured

In the paper

“Enhancers vastly outnumber promoters in human and mouse genomes [131], and consistently promoters often contact more than one enhancer in the same cell type [141, 243, 278, 279].”

What the sources say

• Partly supported

  The paper’s cCRE classification reports that enhancer-like elements make up 87.4% of human cCREs, versus 3.7% classified as promoter-like (Interactive use of cCREs via SCREEN; page unavailable). It applies the classification to mouse as well, but the retrieved text does not give a comparable mouse breakdown. Citation [131] is attached only to the first clause; the statement about promoters contacting multiple enhancers has separate citations and is not assessed here. (LLM, conf=0.83)

  cites [131] ENCODE Project Consortium, Moore JE, Purcaro MJ et al (2020) Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583:699–710 sourceExperimental — accuracy not yet measured
• Supported

  The citation is attached to the second clause, not the claim that enhancers outnumber promoters. In Results, “The cis-regulatory unit: an integrated view of promoter interactions” (page unavailable), the paper reports a median of four promoter-interacting regions per interacting promoter in each of two human cell types. It identifies these regions as containing known and putative enhancers, supporting the claim that promoters often contact more than one enhancer within a cell type. (LLM, conf=0.88)

  cites [141] Freire-Pritchett P, Schoenfelder S, Várnai C et al (2017) Global reorganisation of regulatory units upon lineage commitment of human embryonic stem cells. Elife 6:e21926 source
• Supported

  The citation to Javierre et al. is attached to the second clause, not the claim that enhancers outnumber promoters. In Results, “Promoter Capture Hi-C” (page unavailable), the paper reports a median of four interactions per promoter fragment per cell type; Results, “Enhancer Activity Associates with Lineage-Specific Gene Expression” describes the additive effects of promoter contacts with active enhancers. Together these support the paraphrase that promoters often contact more than one enhancer within a cell type. (LLM, conf=0.86)

  cites [243] Javierre BM, Burren OS, Wilder SP et al (2016) Lineage-specific genome architecture links enhancers and non-coding disease variants to target gene promoters. Cell 167:1369-1384.e19 source
• ?Not checked — no full text of the sourcecites [278] Mifsud B, Tavares-Cadete F, Young AN et al (2015) Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C. Nat Genet 47:598–606 source
• Supported

  This source is cited for the second clause, about promoters contacting multiple enhancers; the first clause has a separate citation. In Results > Enhancer–promoter contacts, the paper reports that 39.5% of analyzed promoters interact with 2–10 enhancers and 12.1% with more than 10 in ESCs, supporting frequent multiple contacts within a cell type. (LLM, conf=0.93)

  cites [279] Schoenfelder S, Furlan-Magaril M, Mifsud B et al (2015) The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements. Genome Res 25:582–597 source

In the paper

“Upon early neural differentiation, about a third of single-state CRUs in human ESCs became dual-state, while around half of all dual-state CRUs became single-state [141].”

What the sources say

• Partly supported

  The Results section (‘ESC differentiation is associated with the dynamic reorganisation of CRUs’; page unavailable) confirms that CRUs gained and lost dual-state configurations during ESC-to-NEC differentiation. But its figures use different denominators: 65% of initially single-state CRUs remained single-state, while 13% and 11% of CRUs acquired and lost dual-state configurations, respectively. It does not establish that a third of initially single-state CRUs became dual-state or that half of initially dual-state CRUs became single-state. (LLM, conf=0.86)

  cites [141] Freire-Pritchett P, Schoenfelder S, Várnai C et al (2017) Global reorganisation of regulatory units upon lineage commitment of human embryonic stem cells. Elife 6:e21926 sourceExperimental — accuracy not yet measured

In the paper

“Changes in CRU state were predominantly driven by coordinated alterations in the chromatin state of enhancers and their promoter contacts, and were associated with significant changes in gene expression [141].”

What the sources say

• Supported

  The Discussion section on CRU reconfiguration says that changes involve both chromatin-state changes at promoter-interacting regions and rewiring of promoter contacts, and that these processes tend to occur together. The Results section on ESC differentiation reports that CRU state transitions are significantly associated with changes in target-gene expression (p<0.005). (LLM, conf=0.87)

  cites [141] Freire-Pritchett P, Schoenfelder S, Várnai C et al (2017) Global reorganisation of regulatory units upon lineage commitment of human embryonic stem cells. Elife 6:e21926 source

In the paper

“synergistic effects were observed in mammalian cell fate determination systems, for example, at Fgf5 enhancers during the differentiation of mouse embryonic stem cells to epiblast-like cells (EpiLCs) [523] and at up to 20% enhancers upon transdifferentiation of human leukemia B-cells into macrophages [524].”

What the sources say

• Supported

  Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [523] Thomas HF, Kotova E, Jayaram S et al (2021) Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements. Mol Cell 81:969-982.e13 source
• Supported

  Split into 2 atoms — 2 confirmed, 0 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.

  cites [524] Choi J, Lysakovskaia K, Stik G et al (2021) Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. Elife 10:e65381 source

In the paper

“they propose that an enhancer’s contact with a promoter may facilitate the transition of the promoter from a low-activity state to a highly active state [405, 406], which in turn may generate bursts at a higher frequency.”

What the sources say

• Supported

  The Main text describes a model in which enhancer–promoter interactions trigger steps that shift the promoter from a low-activity to a higher-activity regime. It also predicts that, within the studied range of contact probabilities, increased contact mainly affects burst frequency. The claim appropriately presents this as a proposed mechanism. (LLM, conf=0.91)

  cites [405] Zuin J, Roth G, Zhan Y et al (2021) Nonlinear control of transcription through enhancer–promoter interactions. BioRxiv. https://doi.org/10.1101/2021.04.22.440891 source
• Supported

  The citation is attached to the proposed transition from low to high promoter activity. In Results, “Promoter futile cycles and hypersensitive response” (page unavailable), the model predicts that increased enhancer–promoter contact can shift promoters from an unbound state to a mature condensate state with substantially higher transcription. The subsequent suggestion about burst frequency follows the citation and is not needed to support that attributed proposition. (LLM, conf=0.88)

  cites [406] Xiao J, Hafner A, Boettiger AN (2020) How subtle changes in 3D structure can create large changes in transcription. BioRxiv. https://doi.org/10.1101/2020.10.22.351395 source

In the paper

“Some deviations from enhancer additivity could potentially be explained by steric constraints arising from enhancer competition [519] or involvement of “pioneer enhancers” [525], but these considerations may not readily explain other reported cases [523, 526].”

What the sources say

• Supported

  The citation is attached to the 'other reported cases' clause, not the proposed steric or pioneer-enhancer explanations. The Results report super-additive activity of the kni enhancers, and the Discussion says the simple enhancer-competition model requires an additional state to explain it. Our copy provides section labels but no page numbers. (LLM, conf=0.88)

  cites [519] Bothma JP, Garcia HG, Ng S et al (2015) Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo. eLife 4:e07956 source
• Supported

  The Results section, “A seed enhancer in mammary-specific Wap super enhancer” (page unavailable), reports that disrupting the E1 seed enhancer prevented the other two enhancers from being established. The Discussion says E1 is required to launch those accessory enhancers. This supports the possibility attributed to [525] that a pioneer or seed enhancer can affect how constituent enhancers act together; the other explanations in the sentence have separate citations. (LLM, conf=0.87)

  cites [525] Shin HY, Willi M, HyunYoo K et al (2016) Hierarchy within the mammary STAT5-driven Wap super-enhancer. Nat Genet 48:904–911 source
• Partly supported

  The Discussion (pp. 14, 16) reports super-additive enhancer action and proposes that PE amplifies the other elements’ contributions, supporting an enhancer-based explanation for a deviation from additivity. But the paper calls PE a “poised enhancer” (p. 4), not a “pioneer enhancer,” and does not identify pioneer enhancers as the explanation. The steric-competition and other-cases clauses are attached to different citations. (LLM, conf=0.82)

  cites [523] Thomas HF, Kotova E, Jayaram S et al (2021) Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements. Mol Cell 81:969-982.e13 sourceExperimental — accuracy not yet measured
• Supported

  The Discussion (“Explaining Differences in Signal Integration across the Krüppel Expression Pattern”; page unavailable) explicitly says the competition model cannot account for the combined enhancer output across the whole Krüppel expression domain. It reports differences at the anterior and posterior borders and over time, supporting the cited point that competition does not readily explain all reported deviations. The separate reference to pioneer enhancers is attached to another citation, not this paper. (LLM, conf=0.90)

  cites [526] Scholes C, Biette KM, Harden TT, DePace AH (2019) Signal integration by shadow enhancers and enhancer duplications varies across the drosophila embryo. Cell Rep 26:2407-2418.e5 source

In the paper

“As the quest for a mechanistic understanding of enhancers continues, the function of these elements emerges as a complex phenomenon that integrates multiple levels of nuclear organisation, from primary DNA sequence and sequence-specific transcription factors to higher-order chromatin architecture through chromatin remodelling complexes, chromosomal loops and potentially phase-separated condensates”

In the paper

“Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa.”

In the paper

“In mice and humans, the pioneer factors OCT4 and SOX2 form a core part of the regulatory network controlling stem cell pluripotency [36].”

What the sources say

• ?Not checked — no full text of the sourcecites [36] Boyer LA, Lee TI, Cole MF et al (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122:947–956 source

In the paper

“Meanwhile, population genetics studies have revealed the enrichment of these elements for genetic variants associated with common diseases.”

In the paper

“We now know that the ability to function remotely and independently of orientation are classic features of enhancers.”

In the paper

“Active enhancers reside in open chromatin and occupy regions away from gene TSSs.”

In the paper

“At the rigid end, the “enhanceosome” model suggests that the TF binding sites must remain in the same order and orientation for the enhancer to work.”

What the sources say

• ?Not checked — no full text of the sourcecites [88] Thanos D, Maniatis T (1995) Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell 83:1091–1100 source

In the paper

“Finally, gene control is maintained by the multiplicity of enhancer inputs to the same gene and its regulation by the broader chromatin context, as will be reviewed below.”

In the paper

“This enhancer contains clusters of TF binding sites, with the sites for transcriptional repressors overlapping those for the activators.”

In the paper

“Activating TFs Bicoid and Hunchback are expressed only in the anterior section of the embryo, while the repressors Giant and Kruppel are expressed in anterior and posterior regions on either side of stripe 2, such that the stripe 2 enhancer is only activated within a 2–3 cell-wide section of the embryo [108, 121, 124].”

What the sources say

• ?Not checked — no full text of the sourcecites [108] Borok MJ, Tran DA, Ho MCW, Drewell RA (2010) Dissecting the regulatory switches of development: lessons from enhancer evolution in Drosophila. Development 137:5–13 source
• ?Not checked — no full text of the sourcecites [121] Stanojevic D, Small S, Levine M (1991) Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. Science 254:1385–1387 source
• ?Not checked — no full text of the sourcecites [124] Arnosti DN, Barolo S, Levine M, Small S (1996) The eve stripe 2 enhancer employs multiple modes of transcriptional synergy. Development 122:205–214 source

In the paper

“These findings supported a dynamic looping model rather than a linking or scanning model; neither of which predicted physical proximity between the LCR and the distal gene promoters.”

In the paper

“Enhancer–promoter looping occurred in erythroid cells, in which the β-globin genes are expressed, but not in brain cells, in which they are not [266].”

What the sources say

• ?Not checked — no full text of the sourcecites [266] Tolhuis B, Palstra R-J, Splinter E et al (2002) Looping and Interaction between hypersensitive sites in the active β-globin locus. Mol Cell 10:1453–1465 source

In the paper

“3C confirmed that the LCR comes into close contact with active β-globin genes, whilst the intervening inactive genes are looped out [266].”

What the sources say

• ?Not checked — no full text of the sourcecites [266] Tolhuis B, Palstra R-J, Splinter E et al (2002) Looping and Interaction between hypersensitive sites in the active β-globin locus. Mol Cell 10:1453–1465 source

In the paper

“In 4C experiments, the LCR was found to interact with multiple highly transcribed genes in the corresponding active cell type (foetal liver) but with different, transcriptionally silent genes in an inactive cell type (brain tissue) [269].”

What the sources say

• ?Not checked — no full text of the sourcecites [269] Simonis M, Klous P, Splinter E et al (2006) Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C). Nat Genet 38:1348–1354 source

In the paper

“Polycomb group (PcG) complexes have long been known to orchestrate the epigenetic silencing of chromatin throughout development.”

What the sources say

• ?Not checked — no full text of the sourcecites [351] Croce LD, Di Croce L, Helin K (2013) Transcriptional regulation by Polycomb group proteins. Nat Struct Mol Biol 20:1147–1155 source

In the paper

“Polycomb Repressive Complex 1 (PRC1), which has E3 ligase activity causing the monoubiquitination of histone H2A lysine 118 (Drosophila) or 119 (vertebrates)”

What the sources say

• ?Not checked — no full text of the sourcecites [351] Croce LD, Di Croce L, Helin K (2013) Transcriptional regulation by Polycomb group proteins. Nat Struct Mol Biol 20:1147–1155 source

In the paper

“Polycomb Repressive Complex 2 (PRC2), which catalyses the di- or tri- methylation of histone H3 lysine 27 [351].”

What the sources say

• ?Not checked — no full text of the sourcecites [351] Croce LD, Di Croce L, Helin K (2013) Transcriptional regulation by Polycomb group proteins. Nat Struct Mol Biol 20:1147–1155 source

In the paper

“At present, standard DNA FISH cannot reliably detect contacts between loci that are located short genomic distances away (dozens of kilobases) from each other, and have a limited throughput that may miss rare but functionally significant genomic contacts.”

In the paper

“Thus, despite their importance for transcription, Mediator and BRD4 are likely not essential for looping between regulatory elements.”