The DOI matches its Crossref record; 86 of the 86 references it cites were found in a registry or an index; none of the 35 sources its claims cite is checked for support yet.
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
Open accessAbstract
The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. Analysis of translation in mouse embryonic stem cells reveals thousands of strong pause sites and unannotated translation products. These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after differentiation. We also define a class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes.
Overview
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
53 Own result · 29 Not checked yet · 26 Own interpretation · 5 Own method · 1 No basis given
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
“there was a broad distribution encompassing over a 10-fold range in the amount of protein produced per transcript”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
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.
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
“Footprints derived from emetine-treated cells are slightly longer than those from untreated or cycloheximide-treated cells”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
plaincorrelational- 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.
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
“Nonetheless, elongation inhibitors do alter the pattern of ribosome footprints along transcripts.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
plaindirect- 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.
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
“Drug pre-treatment also eliminates the excess of ribosomes seen at the stop codon in untreated cells”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
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.
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
“in mammalian translation we find more pronounced pauses where ribosome density is 25-fold or greater than the median density observed across the body of the gene”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Presence of Strong Ribosomal Pauses
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.
In the paper
“The accumulation is still seen when cells are lysed in the presence of a non-hydrolyzable GTP analogue, suggesting that it does not result from continued elongation in the lysate”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
What the sources say
- Not checked yetcites Stern-Ginossar and Weissman, unpublished data
hedged- 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.
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
“Beyond the initial five to ten-codon window we saw no global variation in ribosome density along coding sequences in any sample.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
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.
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
“Translation speed is also independent of codon usage”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Monitoring Kinetics of Translation
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.
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
“and at termination codons (420 pauses, Table S2C)”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Presence of Strong Ribosomal Pauses
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.
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
“Importantly, we see no enrichment for residues or codons downstream of the A-site, which are not yet being decoded.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Presence of Strong Ribosomal Pauses
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. 32
- Probably not a substantial claim. 15
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
“Interestingly, we saw longer footprints at stop codons (Figure 1B and S1B), suggesting that the accumulating ribosomes are in a different conformation”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
hedgedcorrelational- 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.
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
“The excess of ribosomes at the initiation site and extending over the first five to ten codons is essentially absent from untreated cells”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
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
“we found no evidence for this phenomenon in the majority of other TA proteins (3 / 32 have pauses), nor was it restricted to TA proteins”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Presence of Strong Ribosomal Pauses
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
“There is strong enrichment of glutamate or asparate in the A site at strong pauses, preceded by a proline or glycine and then another proline, with an additional bias towards the GAA glutamate codon and CC(A/T) proline codons.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Presence of Strong Ribosomal Pauses
boostedcorrelational- 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.
In the paper
“we see no evidence that pausing causes secondary ribosome accumulation ~10 codons upstream, where a following ribosome would collide with the stalled one (Wolin and Walter, 1988), nor a depletion of ribosomes within the 10 codon “shadow” resulting from paused ribosomes”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Presence of Strong Ribosomal Pauses
What the sources say
- Not checked yetcites Wolin and Walter, 1988
hedged- 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.
In the paper
“We confirmed the presence of this pause and identified its precise position as residue Asn 256, which is the last codon required for translational arrest”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Presence of Strong Ribosomal Pauses
What the sources say
- Not checked yetcites Yanagitani et al., 2011 source
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
“The majority (65%) of these transcripts contain more than one detectable site of translation initiation, with 16 percent containing four or more sites”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Defining Translation Start Sites
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
“The kinetics of elongation are independent of length and protein abundance and are the same in secreted proteins, whose translation occurs on the ER surface.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Monitoring Kinetics of Translation
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
“We identified 570 genes with potential N-terminal extensions and 870 with N-terminal truncations in the 4994 genes we analyzed.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Characterization of Alternate Open Reading Frames
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
“Nearly half (44%) of the AUG initiation sites that we found are unannotated, and the majority of these were downstream of the annotated start and were predicted to produce N-terminally truncated proteins or ORFs encoded in alternate reading frames”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Characterization of Alternate Open Reading Frames
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
“the growth factor Igf2 has two 5′ UTR variants with the same reading frame annotated in both transcripts, but we observed an isoform-specific N-terminal extension”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Characterization of Alternate Open Reading Frames
plainSingle case- 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.
In the paper
“We found an N-terminal extension on the DNA repair protein Swi5 (Figure 4G); its protein sequence is conserved, and there is experimental evidence that endogenous mouse Swi5 is larger than the annotated 89 amino acid protein”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Characterization of Alternate Open Reading Frames
What the sources say
- Not checked yetcites Akamatsu and Jasin, 2010
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
“both have multiple uORFs and alternate translation products initiating at both AUG and near-cognate sites”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Translation of uORFs
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.
In the paper
“Withdrawal of leukemia inhibitory factor (LIF) induced differentiation (Figure S4A), which we assessed visually and by the down-regulation of the direct LIF target Klf4 (Niwa et al., 2009), followed by loss of Oct4 expression and the induction of developmental and lineage-specific genes (Figures S4B and S4C and Tables S5A-S5F).”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Changes in Translation During Embryoid Body Formation
What the sources say
- Not checked yetcites Niwa et al., 2009 source
plaindirect- 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
“The gene Pih1d1 has two 5′ UTR variants with distinct uORFs.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Translation of uORFs
plainSingle case- 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.
In the paper
“We also observe widespread translation upstream of mammalian protein-coding genes, similar to but more extensive than upstream translation that we observed in yeast (Ingolia et al., 2009).”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > DISCUSSION
What the sources say
- Not checked yetcites Ingolia et al., 2009 source
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.
In the paper
“Our data are consistent with recent work that indirectly infers translation levels from absolute mRNA and protein abundance measurements”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
What the sources say
- Not checked yetcites Schwanhausser et al., 2011 source
plaincorrelational- 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.
In the paper
“they found that translation was the single largest contributor to protein abundance”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
What the sources say
- Not checked yetcites Schwanhausser et al., 2011 source
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.
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 distribution is asymmetric, suggesting a maximal rate of protein production from an mRNA and substantial dynamic range for decreased translational efficiency.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
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.
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
“We concluded that brief treatment of cells with elongation inhibitors did not significantly change which transcripts were associated with ribosomes and did not distort translation measurements made by ribosome profiling.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > A Simplified Mammalian Ribosome Profiling Assay
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 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 findings suggest that tRNA identity and nascent peptide sequence can influence the kinetics of elongation, whereas even for rare codons, tRNA recruitment is not rate-limiting.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Presence of Strong Ribosomal Pauses
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.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“This effect likely occurs because harringtonine binds to free 60s subunits, but not those that are joined into an 80s ribosome. Thus, elongating ribosomes are immune to harringtonine, whereas a 60s subunit bound by harringtonine will form an 80s at a start site that does not move forward”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Defining Translation Start Sites
What the sources say
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.
It may state two separate claims as one.
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
“Actual false negative and false positive rates may be considerably lower, as not all annotated start sites are correct and there is a substantial rate of translation initiation from non-canonical start sites.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Defining Translation Start Sites
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.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
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
“Extensions most often resulted from near-cognate initiation (Figure S2B), probably because computational gene annotation selects the first in-frame AUG”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Characterization of Alternate Open Reading Frames
hedgedconditional- 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 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 classify these RNAs as short, polycistronic, ribosome-associated coding RNAs (sprcRNAs) based on our observation that they contain small coding sequences that are bound by elongating ribosomes, and frequently contain multiple ORFs.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Exploring Translation of sprcRNAs
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.
None of the sources cited for this claim have been checked yet.
In the paper
“The first uORF in the Atf4 transcript is constitutively translated and ribosomes then reinitiate at either the second uORF or the CDS”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Translation of uORFs
What the sources say
- Not checked yetcites Calvo et al., 2009 source
- Not checked yetcites Lu et al., 2004
- Not checked yetcites Morris and Geballe, 2000
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.
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 establish that the majority of lincRNAs are exported to the cytoplasm and effectively engaged by the protein translation machinery.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Exploring Translation of sprcRNAs
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 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 exemplifies two roles of uORFs—some permit downstream reinitiation, whereas others capture some fraction of scanning pre-initiation complexes and decrease CDS translation.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Translation of uORFs
plaindirectSingle case- 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.
None of the sources cited for this claim have been checked yet.
In the paper
“Internal initiation in the Ets family transcription factor Etv5 produces a product that lacks the predicted activation domain (Monte et al., 1996) but contains the domain that mediates DNA binding (Monte et al., 1994)”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Characterization of Alternate Open Reading Frames
What the sources say
- Not checked yetcites Monte et al., 1996 source
- Not checked yetcites Monte et al., 1994
plaindirect- 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 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, alternative splicing generates transcripts with different upstream initiation sites and results in different uORF translation.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Widespread Translation of uORFs
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.
In the paper
“Polysome profiling experiments have suggested a global increase in cellular translation during early ES cell differentiation, and we see a modest upregulation of RPs in our early timepoint (Sampath et al., 2008).”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Changes in Translation During Embryoid Body Formation
What the sources say
- Not checked yetcites Sampath et al., 2008 source
hedgeddirect- 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.
None of the sources cited for this claim have been checked yet.
In the paper
“Such a shift has been associated with proliferation in tumorigenesis, and has been linked to the translational control of RPs (Mamane et al., 2006; Ruggero and Sonenberg, 2005).”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > RESULTS > Changes in Translation During Embryoid Body Formation
What the sources say
- Not checked yetcites Mamane et al., 2006 source
- Not checked yetcites Ruggero and Sonenberg, 2005
plaincorrelational- 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.
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
“A set of well-expressed genes was selected based on median footprint density across the coding sequence, excluding the first 15 and last 5 codons due to the accumulation of ribosomes (Figures 1C and 1D).”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > EXPERIMENTAL PROCEDURES > Footprint Profile Analysis
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.
In the paper
“More broadly, it has been implicated in the production of peptides for immune surveillance (Malarkannan et al., 1999), and additional roles will likely emerge as we understand more about which non-AUG codons are used and how this selection is regulated.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > DISCUSSION
What the sources say
- Not checked yetcites Malarkannan et al., 1999 source
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.
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 approaches provide experimentally based maps of the protein coding potential of complex genomes, and reveal in depth information about the kinetics and mechanism of translation elongation and coupled co-translational events.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > DISCUSSION
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.
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
“Metagene profiles from harringtonine run-off were further normalized by the median value over codons 800-1000, which appeared undepleted at harringtonine treatment times used in this study, and smoothed by averaging disjoint 5-codon windows.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > EXPERIMENTAL PROCEDURES > Harringtonine Depletion Profile Analysis
hedged- 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.
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 preferential assignment of initiation sites to AUG codons may lead to a modest bias against detecting near-cognate initiation.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > EXPERIMENTAL PROCEDURES > Initiation Site Prediction
hedgedconditional- 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.
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
“More generally mass spectrometry and ribosome profiling represent highly complementary approaches; for example, comparison between changes in rate of synthesis measured by ribosome profiling and abundance measured by mass spectrometry should reveal examples of regulated degradation of proteins.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > DISCUSSION
plaincorrelational- 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.
In the paper
“The SVMlight pattern recognition tool (Joachims, 1999) was trained on an arbitrary set of 3200 transcripts, using the annotated start codon as a positive example and ten other positions as negative examples.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > EXPERIMENTAL PROCEDURES > Initiation Site Prediction
What the sources say
- Not checked yetcites Joachims, 1999
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.
Probably not a substantial claim. It may state two separate claims as one.
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
“Initiation sites were defined as one or more consecutive nucleotide positions that passed an SVM score threshold as well as a minimum of 50 harringtonine footprints total amongst all samples.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > EXPERIMENTAL PROCEDURES > Initiation Site Prediction
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.
Probably not a substantial claim.
In the paper
“For most analyses, footprint alignments were assigned to specific A site nucleotides by using the position and total length of each alignment, calibrated from footprints at the beginning and the end of CDSes (Figures S1A and S1B) as previously described (Ingolia et al., 2009).”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > EXPERIMENTAL PROCEDURES > Footprint Sequence Alignment
What the sources say
- Not checked yetcites Ingolia et al., 2009 source
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.
Probably not a substantial claim.
None of the sources cited for this claim have been checked yet.
In the paper
“Translation of a uORFs can modulate the expression of the downstream protein-coding gene in response to global (Sonenberg and Hinnebusch, 2009) or gene-specific regulatory signals (Medenbach et al., 2011).”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > DISCUSSION
What the sources say
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.
None of the sources cited for this claim have been checked yet.
In the paper
“LincRNAs were collected from reconstructed transcripts (Guttman et al., 2010) that lay entirely within the lincRNA chromatin signatures identified by Guttman et al. (Guttman et al., 2009), which excluded known protein-coding genes.”
§ Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity of Mammalian Proteomes > EXPERIMENTAL PROCEDURES > LincRNA Analysis
What the sources say
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.
Probably not a substantial claim. It may state two separate claims as one.
The paper relies on this without support.
The number of ribosome footprints at a codon is proportional to the average time a ribosome dwells there.
“The footprint count on a codon should be proportional to the average ribosome dwell time there”
The paper relies on this without support.
Most productive protein synthesis begins at a classical AUG codon.
“While most productive protein synthesis starts at a classical AUG codon, initiation at CUG and GUG codons is widespread and is likely to have broad biological significance.”
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 source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Ribosome profiling has also shown that translation rates change only several fold upon cellular differentiation and, with the exception of the translation machinery, the change affects all expressed genes to a similar degree (Ingolia et al., 2011)”
From System wide analyses have underestimated protein abundances and the importance of transcription in mammals (2014) · cites this paper as Ingolia et al., 2011
Experimental — accuracy not yet measuredIn the citing paper
“Ribosome profiling has also shown that long non-coding RNAs in the cytosol, many of which are known to be spliced, capped, and polyadenylated in a similar manner to mRNAs62, can be engaged by the polyribosome56, but do not code for protein63.”
From Decoding neuroproteomics: integrating the genome, translatome and functional anatomy (2014) · cites this paper as [56]
In the citing paper
“Importantly, those studies that have attempted deliberate co-analysis of RNA and protein have consistently observed a limited correlation (between 0.5–0.7) in abundance.”
From Decoding neuroproteomics: integrating the genome, translatome and functional anatomy (2014) · cites this paper as [56]
In the citing paper
“As such, measurements of mRNA abundance alone are insufficient to be considered predictive of protein abundance54–56, reinforcing the requirement for cellular analysis at the proteome level.”
From Decoding neuroproteomics: integrating the genome, translatome and functional anatomy (2014) · cites this paper as [56]
Citations
Cites
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Global quantification of mammalian gene expression control
Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · cited 1×
“with recent work that indirectly infers translation levels from absolute mRNA and protein abundance measurements (Schwanhäusser et al., 2011).”
BackgroundAdvances in kernel methods: support vector learning
Schölkopf, B., Burges, C. J. C., & Smola, A. J. (1999) · doi:10.5555/299094 · Cited by 5,809
Control of inositol 1,4,5-trisphosphate-induced Ca2+ release by cytosolic Ca2+
Bootman, M. D., Missiaen, L., Parys, J. B., SMEDT, H. D., & Casteels, R. (1995) · Biochemical Journal · doi:10.1042/bj3060445 · Cited by 5,131
Making Large-Scale SVM Learning PracticalPreprint
Joachims, T. (1998) · RePEc: Research Papers in Economics · doi:10.17877/de290r-14262 · Cited by 4,517
What is a support vector machine?
Noble, W. S. (2006) · Nature Biotechnology · doi:10.1038/nbt1206-1565 · Cited by 4,450
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature · doi:10.1038/nature07672 · Cited by 4,098
Niwa, H., Miyazaki, J., & Smith, A. G. (2000) · Nature Genetics · doi:10.1038/74199 · Cited by 3,904
Mammalian microRNAs predominantly act to decrease target mRNA levels
Guo, H., Ingolia, N. T., Weissman, J. S., & Bartel, D. P. (2010) · Nature · doi:10.1038/nature09267 · Cited by 3,886
Self-citationGenome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853
Self-citationMutation of the mouse klotho gene leads to a syndrome resembling ageing
Kuro-o, M., Matsumura, Y., Aizawa, H., Kawaguchi, H., Suga, T., Utsugi, T., Ohyama, Y., Kurabayashi, M., Kaname, T., Kume, E., et al. (1997) · Nature · doi:10.1038/36285 · Cited by 3,837
Accurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans
Lau, N. C., Lim, L. P., Weinstein, E. G., & Bartel, D. P. (2001) · Science · doi:10.1126/science.1065062 · Cited by 3,345
Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets
Sonenberg, N., & Hinnebusch, A. G. (2009) · Cell · doi:10.1016/j.cell.2009.01.042 · Cited by 3,304
IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA
Calfon, M. A., Zeng, H., Urano, F., Till, J. H., Hubbard, S. R., Harding, H. P., Clark, S. G., & Ron, D. (2002) · Nature · doi:10.1038/415092a · Cited by 2,907
Khalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B. E., van Oudenaarden, A., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904715106 · Cited by 2,872
A "Silent" Polymorphism in the MDR 1 Gene Changes Substrate Specificity
Kimchi-Sarfaty, C., Oh, J. M., Kim, I.-W., Sauna, Z. E., Calcagno, A. M., Ambudkar, S. V., & Gottesman, M. M. (2007) · Science · doi:10.1126/science.1135308 · Cited by 2,416
FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism
Darnell, J. C., Van Driesche, S. J., Zhang, C., Hung, K. Y. S., Mele, A., Fraser, C. E., Stone, E. F., Chen, C., Fak, J. J., Chi, S. W., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.013 · Cited by 2,072
lincRNAs act in the circuitry controlling pluripotency and differentiation
Guttman, M., Donaghey, J., Carey, B. W., Garber, M. G., Grenier, J. K., Munson, G., Young, G., Lucas, A. B., Ach, R. A., Bruhn, L., et al. (2011) · Nature · doi:10.1038/nature10398 · Cited by 1,883
Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps
Chi, S. W., Zang, J. B., Mele, A., & Darnell, R. B. (2009) · Nature · doi:10.1038/nature08170 · Cited by 1,791
The Sequence of the Human Genome
Venter, J. C., Smith, H. O., & Adams, M. D. (2015) · Clinical Chemistry · doi:10.1373/clinchem.2014.237016 · Cited by 1,665
Pten is essential for embryonic development and tumour suppression
Cristofano, A. D., Pesce, B., Cordon‐Cardo, C., & Pandolfi, P. P. (1998) · Nature Genetics · doi:10.1038/1235 · Cited by 1,518
Clemson, C. M., Hutchinson, J. N., Sara, S. A., Ensminger, A. W., Fox, A. H., Chess, A., & Lawrence, J. B. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.01.026 · Cited by 1,445
RNA-binding proteins: modular design for efficient function
Lunde, B. M., Moore, C. L., & Varani, G. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2178 · Cited by 1,322
Guttman, M., Garber, M., Levin, J. Z., Donaghey, J., Robinson, J., Adiconis, X., Fan, L., Koziol, M. J., Gnirke, A., Nusbaum, C., et al. (2010) · Nature Biotechnology · doi:10.1038/nbt.1633 · Cited by 1,253
Identification of microRNAs of the herpesvirus family
Pfeffer, S., Sewer, A., Lagos‐Quintana, M., Sheridan, R., Sander, C., Grässer, F. A., van Dyk, L. F., Ho, C. K., Shuman, S., Chien, M., et al. (2005) · Nature Methods · doi:10.1038/nmeth746 · Cited by 1,178
CLIP Identifies Nova-Regulated RNA Networks in the Brain
Ule, J., Jensen, K. B., Ruggiu, M., Mele, A., Ule, A., & Darnell, R. B. (2003) · Science · doi:10.1126/science.1090095 · Cited by 1,120
Brockdorff, N., Ashworth, A., Kay, G. F., McCabe, V. M., Norris, D. P., Cooper, P. J., Swift, S., & Rastan, S. (1992) · Cell · doi:10.1016/0092-8674(92)90519-i · Cited by 1,060
Inhibition of eukaryotic translation elongation by cycloheximide and lactimidomycin
Schneider‐Poetsch, T., Ju, J., Eyler, D. E., Dang, Y., Bhat, S., Merrick, W. C., Green, R., Shen, B., & Liu, J. O. (2010) · Nature Chemical Biology · doi:10.1038/nchembio.304 · Cited by 1,050
mRNA localization: Gene expression in the spatial dimension
Martin, K. C., & Ephrussi, A. (2009) · Cell · doi:10.1016/j.cell.2009.01.044 · Cited by 1,048
Lu, P. D., Harding, H. P., & Ron, D. (2004) · The Journal of Cell Biology · doi:10.1083/jcb.200408003 · Cited by 1,006
Calvo, S. E., Pagliarini, D. J., & Mootha, V. K. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810916106 · Cited by 914
An evolutionarily conserved mechanism for controlling the efficiency of protein translation
Tuller, T., Carmi, A., Vestsigian, K., Navon, S., Dorfan, Y., Zaborske, J., Pan, T., Dahan, O., Furman, I., & Pilpel, Y. (2010) · Cell · doi:10.1016/j.cell.2010.03.031 · Cited by 874
A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells
Niwa, H., Ogawa, K., Shimosato, D., & Adachi, K. (2009) · Nature · doi:10.1038/nature08113 · Cited by 872
Solving the riddle of codon usage preferences: a test for translational selection
dos Reis, M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh834 · Cited by 745
Upstream Open Reading Frames as Regulators of mRNA Translation
Morris, D. R., & Geballe, A. P. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.23.8635-8642.2000 · Cited by 736
Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
Arava, Y., Wang, Y., Storey, J. D., Liu, C. L., Brown, P. O., & Herschlag, D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0635171100 · Cited by 663
mTOR, translation initiation and cancer
Mamane, Y., Petroulakis, E., LeBacquer, O., & Sonenberg, N. (2006) · Oncogene · doi:10.1038/sj.onc.1209888 · Cited by 607
Transient ribosomal attenuation coordinates protein synthesis and co-translational folding
Zhang, G., Hubalewska, M., & Ignatova, Z. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1554 · Cited by 553
The Ribosomal Exit Tunnel Functions as a Discriminating Gate
Nakatogawa, H., & Ito, K. (2002) · Cell · doi:10.1016/s0092-8674(02)00649-9 · Cited by 533
Hsu, F., Kent, W. J., Clawson, H., Kuhn, R. M., Diekhans, M., & Haussler, D. H. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl048 · Cited by 503
Hann, S. R., King, M. W., Bentley, D. L., Anderson, C. W., & Eisenman, R. N. (1988) · Cell · doi:10.1016/0092-8674(88)90507-7 · Cited by 474
Mass spectrometry in high-throughput proteomics: ready for the big time
Nilsson, T., Mann, M., Aebersold, R., Yates, J. R., Bairoch, A., & Bergeron, J. J. M. (2010) · Nature Methods · doi:10.1038/nmeth0910-681 · Cited by 470
Ribosome pausing and stacking during translation of a eukaryotic mRNA.
Wolin, S. L., & Walter, P. (1988) · The EMBO Journal · doi:10.1002/j.1460-2075.1988.tb03233.x · Cited by 454
Translational Pausing Ensures Membrane Targeting and Cytoplasmic Splicing of XBP1u mRNA
Yanagitani, K., Kimata, Y., Kadokura, H., & Kohno, K. (2011) · Science · doi:10.1126/science.1197142 · Cited by 362
Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis
Kondo, T., Plaza, S., Zanet, J., Benrabah, E., Valenti, P., Hashimoto, Y., Kobayashi, S., Payre, F., & Kageyama, Y. (2010) · Science · doi:10.1126/science.1188158 · Cited by 348
Regulation of gene expression by alternative untranslated regions
Hughes, T. A. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.01.001 · Cited by 337
ECSIT is an evolutionarily conserved intermediate in the Toll/IL-1 signal transduction pathway
Kopp, E., Medzhitov, R., Carothers, J., Xiao, C., Douglas, I., Janeway, C. A., & Ghosh, S. (1999) · Genes & Development · doi:10.1101/gad.13.16.2059 · Cited by 334
Alkalaeva, E. Z., Pisarev, A. V., Frolova, L. Y., Kisselev, L. L., & Pestova, T. V. (2006) · Cell · doi:10.1016/j.cell.2006.04.035 · Cited by 331
A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting
Namy, O., Moran, S. J., Stuart, D. I., Gilbert, R. J. C., & Brierley, I. (2006) · Nature · doi:10.1038/nature04735 · Cited by 330
Lin, F., MacDougald, O. A., Diehl, A. M., & Lane, M. D. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.20.9606 · Cited by 311
Inhibition of translation in eukaryotic systems by harringtonine
FRESNO, M., JIMÉNEZ, A., & VÁZQUEZ, D. (1977) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1977.tb11256.x · Cited by 295
Sampath, P., Pritchard, D. K., Pabon, L., Reinecke, H., Schwartz, S. M., Morris, D. R., & Murry, C. E. (2008) · Cell Stem Cell · doi:10.1016/j.stem.2008.03.013 · Cited by 277
A ribosome-associating factor chaperones tail-anchored membrane proteins
Mariappan, M., Li, X., Stefanovic, S., Sharma, A., Mateja, A., Keenan, R. J., & Hegde, R. S. (2010) · Nature · doi:10.1038/nature09296 · Cited by 272
Leahy, A., Xiong, J., Kuhnert, F., & Stuhlmann, H. (1999) · Journal of Experimental Zoology · doi:10.1002/(sici)1097-010x(19990615)284:1 · Cited by 243
Regulatory Nascent Peptides in the Ribosomal Tunnel
Tenson, T., & Ehrenberg, M. (2002) · Cell · doi:10.1016/s0092-8674(02)00669-4 · Cited by 240
Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes
Pisarev, A. V., KOLUPAEVA, V. G., Yusupov, M., Hellen, C. U. T., & Pestova, T. V. (2008) · The EMBO Journal · doi:10.1038/emboj.2008.90 · Cited by 227
Ivanov, I. P., Firth, A. E., Michel, A. M., Atkins, J. F., & Baranov, P. V. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr007 · Cited by 220
The Akt of translational control
Ruggero, D., & Sonenberg, N. (2005) · Oncogene · doi:10.1038/sj.onc.1209098 · Cited by 197
Boström, K. B., WETTESTEN, M., Borén, J., Bondjers, G., Wiklund, O., & Olofsson, S. ‐. (1986) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)67090-5 · Cited by 191
Genome-Wide Translational Profiling by Ribosome Footprinting
Ingolia, N. T. (2010) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(10)70006-9 · Cited by 177
Self-citationYanagitani, K., Imagawa, Y., Iwawaki, T., Hosoda, A., Saito, M., Kimata, Y., & Kohno, K. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.02.033 · Cited by 166
Codon Pair Utilization Biases Influence Translational Elongation Step Times
Irwin, B., Heck, J. D., & Hatfield, G. W. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.39.22801 · Cited by 166
Recoding: Expansion of Decoding Rules Enriches Gene Expression
Atkins, J. F., & Gesteland, R. F. (2010) · Nucleic acids and molecular biology · doi:10.1007/978-0-387-89382-2 · Cited by 150
Harringtonine, an Inhibitor of Initiation of Protein Biosynthesis
Huang, M. (1975) · Molecular Pharmacology · doi:10.1016/s0026-895x(25)10662-7 · Cited by 144
Translational control via protein-regulated upstream open reading frames
Medenbach, J., Seiler, M., & Hentze, M. W. (2011) · Cell · doi:10.1016/j.cell.2011.05.005 · Cited by 140
Genome annotation past, present, and future: How to define an ORF at each locusPreprint
Brent, M. R. (2005) · Genome Research · doi:10.1101/gr.3866105 · Cited by 136
Genetic Identification of Nascent Peptides That Induce Ribosome Stalling
Tanner, D. R., Cariello, D. A., Woolstenhulme, C. J., Broadbent, M. A., & Buskirk, A. R. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.039040 · Cited by 132
Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster
Tupy, J. L., Bailey, A. M., Dailey, G. M., Evans-Holm, M. E., Siebel, C. W., Misra, S., Celniker, S., & Rubin, G. M. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0501422102 · Cited by 123
Malarkannan, S., Horng, T., Shih, P. P., Schwab, S., & Shastri, N. (1999) · Immunity · doi:10.1016/s1074-7613(00)80067-9 · Cited by 106
Monté, D., Baert, J., Defossez, P., de Launoit, Y., & Stéhelin, D. (1994) · PubMed · Cited by 106
Ivanov, I. P., Loughran, G., & Atkins, J. F. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801590105 · Cited by 103
Hamilton, T. L., Stoneley, M., Spriggs, K. A., & Bushell, M. (2006) · Biochemical Society Transactions · doi:10.1042/bst0340012 · Cited by 91
Altering chemosensitivity by modulating translation elongation
Robert, F., Carrier, M., Rawe, S., Chen, S., Lowe, S., & Pelletier, J. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005428 · Cited by 90
Addressing mRNAs to the ER: cis sequences act up!
Kraut‐Cohen, J., & Gerst, J. E. (2010) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2010.02.006 · Cited by 69
Hansen, M. B., Mitchelmore, C., Kjærulff, K. M., Rasmussen, T., Pedersen, K. M., & Jensen, N. A. (2002) · Genomics · doi:10.1006/geno.2002.6838 · Cited by 61
Inhibition of Protein Synthesis in Intact HeLa Cells
Tscherne, J. S., & Pestka, S. (1975) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.8.4.479 · Cited by 58
Role for the Mammalian Swi5-Sfr1 Complex in DNA Strand Break Repair through Homologous Recombination
Akamatsu, Y., & Jasin, M. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1001160 · Cited by 58
A distinct translation initiation mechanism generates cryptic peptides for immune surveillance
Starck, S. R., Ow, Y., Jiang, V., Tokuyama, M., Rivera, M., Qi, X., Roberts, R. W., & Shastri, N. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003460 · Cited by 48
Lazarowitz, S. G., & Robertson, H. D. (1977) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)41043-x · Cited by 37
Culture of Mouse Embryonic Stem Cells
Tremml, G., Singer, M. A., & Malavarca, R. (2008) · Current Protocols in Stem Cell Biology · doi:10.1002/9780470151808.sc01c04s5 · Cited by 35
Expression of two novel transcripts in the mouse definitive endoderm
Hassan, A. S., Hou, J., Wei, W., & Hoodless, P. A. (2010) · Gene Expression Patterns · doi:10.1016/j.gep.2010.02.001 · Cited by 31
Genomic organization of the human ERM (ETV5) gene, a PEA3 group member of ETS transcription factors
Monté, D., Coutte, L., Dewitte, F., Defossez, P.-A., Le Coniat, M., Stéhelin, D., Berger, R., & de Launoit, Y. (1996) · Genomics · doi:10.1006/geno.1996.0345 · Cited by 29
Stoneley, M., Hamilton, T. L., Spriggs, K. A., & Bushell, M. (2005) · Biochemical Society Transactions · doi:10.1042/bst20060012 · Cited by 23
Research works printed but not linked: 2
- Niwa, H., Ogawa, K., Shimosato, D., and Adachi, K. (2009). A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells. Nature 460, 118–122. · DOI · Paper page
- Tremml, G., Singer, M., and Malavarca, R. (2008). Culture of mouse embryonic stem cells. In Current Protocols in Stem Cell Biology Chapter 1, Unit 1C 4. · DOI
Cited by
Sorted by citations
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
Vogel, C., & Marcotte, E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3185 · Cited by 4,195
Genome Regulation by Long Noncoding RNAs
Rinn, J. L., & Chang, H. Y. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-051410-092902 · Cited by 4,091
Unique features of long non-coding RNA biogenesis and function
Quinn, J. J., & Chang, H. Y. (2015) · Nature Reviews Genetics · doi:10.1038/nrg.2015.10 · Cited by 3,700
lincRNAs: Genomics, Evolution, and Mechanisms
Ulitsky, I., & Bartel, D. P. (2013) · Cell · doi:10.1016/j.cell.2013.06.020 · Cited by 2,652
Metadata
- Authors
- Ingolia, N. T., Lareau, L. F., & Weissman, J. S.
- Affiliations
- QB3 (US)
- Stanford University (US)
- Corresponding author
- Ingolia, Nicholas T.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2011-11
- Volume
- 147
- Issue
- 4
- Pages
- 789-802
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3225288
- OpenAlex
- W2071849521
- Cited by
- 2,187
- References
- 86
- Citations by year
- 2026: 96 · 2025: 127 · 2024: 136 · 2023: 143 · 2022: 135 · 2021: 153 · 2020: 189 · 2019: 134 · 2018: 167 · 2017: 164 · 2016: 168 · 2015: 154 · 2014: 171 · 2013: 139 · 2012: 102
- FWCI
- 54.59
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 624 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- Damon Runyon Cancer Research Foundation (DRG-2033-09)
- National Institutes of Health (AG10770)
- National Institute on Aging (P01 AG10770, P01AG010770)
- National Institute of General Medical Sciences (F32GM080853, GM080853)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- ribosome profiling, mouse embryonic stem cells, translation elongation, pause sites, harringtonine, translation initiation, upstream open reading frames, amino-terminal extension, protein truncation, small proteins, proteome complexity, cell differentiation
- MeSH terms
- Algorithms, Animals, Artificial Intelligence, Harringtonines, Kinetics, Peptide Chain Initiation, Translational, Ribosomes, RNA, Protein Biosynthesis, Open Reading Frames, Sequence Analysis, RNA, Genomics, Mice, Embryonic Stem Cells, Embryoid Bodies, High-Throughput Nucleotide Sequencing
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 2026-10-05, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-05 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
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 ›
Are you an author, or do you see a problem with this page? Request a review
