Evidence map›Paper›PMID 25083876›Full record

SynthesisCell2014

H3K4me3 breadth is linked to cell identity and transcriptional consistency.

Bérénice A Benayoun, Elizabeth A Pollina, Duygu Ucar, Salah Mahmoudi, Kalpana Karra, Edith D Wong, Keerthana Devarajan, Aaron C Daugherty, Anshul B Kundaje, Elena Mancini and 7 more

Erratum issuedAbstract readMeta-Analysis
PubMed Full text at PMC Publisher
In one paragraph

Synthesis in Cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 333 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
333citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

333 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
  3. Article
  4. Review
  5. Article
  6. Article
  7. Article
  8. Computational modelling of cell identity.The Biochemical journal · 2026
    Review
  9. Article
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  11. Article
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  13. Article
  14. Article
  15. Article
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  19. Article
  20. Review

273 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

  • Erratum issued
5 · Who and what money

Authors and funding

17 authors.

Bérénice A BenayounDepartment of Genetics, Stanford University, Stanford CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA.
Elizabeth A PollinaDepartment of Genetics, Stanford University, Stanford CA 94305, USA; Cancer Biology Program, Stanford University, Stanford CA 94305, USA.
Duygu UcarDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Salah MahmoudiDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Kalpana KarraDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Edith D WongDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Keerthana DevarajanDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Aaron C DaughertyDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Anshul B KundajeDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Elena ManciniDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Benjamin C HitzDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Rakhi GuptaDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Thomas A RandoPaul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford CA 94305, USA; RR&D REAP, VA Palo Alto Health Care Systems, Palo Alto, CA 94304,USA.
Julie C BakerDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Michael P SnyderDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
J Michael CherryDepartment of Genetics, Stanford University, Stanford CA 94305, USA.
Anne BrunetDepartment of Genetics, Stanford University, Stanford CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University, Stanford CA 94305, USA; Cancer Biology Program, Stanford University, Stanford CA 94305, USA. Electronic address: anne.brunet@stanford.edu.

Funding

Wnt signaling in muscle stem cell agingP01AG036695 · NIA · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI THOMAS A. RANDO · 2011 to 2026
$29.3M
Leveraging innovative technologies in basic and clinical cancer researchT32CA009302 · NCI · STANFORD UNIVERSITY · PI LAURA D ATTARDI, Aaron M Newman · 1985 to 2026
$19.1M
GENETICS TRAINING PROGRAM FOR PHD CANDIDATEST32GM007790 · NIGMS · STANFORD UNIVERSITY · PI BRUNET, ANNE, KINGSLEY, DAVID M · 1985 to 2020
$12.8M
Project 3: Effect of Age and Longevity Genes on Epigenomic MechanismsP01GM099130 · NIGMS · STANFORD UNIVERSITY · PI WEISSMAN, SHERMAN MORTON · 2011 to 2015
$11.4M
Transgenerational epigenetic inheritance of longevityDP1AG044848 · NIA · STANFORD UNIVERSITY · PI BRUNET, ANNE · 2012 to 2016
$3.9M
Using Embryos to Understand the Chromatin State of Mesoderm InductionR01GM103787 · NIGMS · STANFORD UNIVERSITY · PI BAKER, JULIE C · 2012 to 2015
$1.2M
Broad H3K4me3 Domains: A Discovery Tool for Regulators of Neural Stem Cell AgingF31AG043232 · NIA · STANFORD UNIVERSITY · PI POLLINA, ELIZABETH A · 2012 to 2014
$116k
NCI NIH HHS T32 CA009302NIA NIH HHS DP1 AG044848NIA NIH HHS F31 AG043232NIA NIH HHS P01 AG036695NIGMS NIH HHS P01 GM099130NIGMS NIH HHS R01 GM103787NIGMS NIH HHS T32 GM007790
6 · The paper itself

Abstract

Trimethylation of histone H3 at lysine 4 (H3K4me3) is a chromatin modification known to mark the transcription start sites of active genes. Here, we show that H3K4me3 domains that spread more broadly over genes in a given cell type preferentially mark genes that are essential for the identity and function of that cell type. Using the broadest H3K4me3 domains as a discovery tool in neural progenitor cells, we identify novel regulators of these cells. Machine learning models reveal that the broadest H3K4me3 domains represent a distinct entity, characterized by increased marks of elongation. The broadest H3K4me3 domains also have more paused polymerase at their promoters, suggesting a unique transcriptional output. Indeed, genes marked by the broadest H3K4me3 domains exhibit enhanced transcriptional consistency and [corrected] increased transcriptional levels, and perturbation of H3K4me3 breadth leads to changes in transcriptional consistency. Thus, H3K4me3 breadth contains information that could ensure transcriptional precision at key cell identity/function genes.

Indexed as

Histone CodeTranscription, GeneticAnimalsArtificial IntelligenceCellsGenomicsHistonesHumansLysineMethylationMice, Inbred C57BLNeural Stem CellsRNA Polymerase IIHistonesLysineRNA Polymerase II

Identifiers

PMID25083876
PMCPMC4137894

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.