Evidence map›Paper›PMID 18371437›Full record

ArticleCell stem cell2008

Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation.

Shaun D Fouse, Yin Shen, Matteo Pellegrini, Steve Cole, Alexander Meissner, Leander Van Neste, Rudolf Jaenisch, Guoping Fan

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell stem cell, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 220 papers.

0numbers the graph read from it
0cells of the map it votes in
220citing papers in PubMed
23.9field-weighted citation impact, top 1% of its field
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

220 citing papers in PubMed, 466 citations in OpenAlex.

  1. Article
  2. Article
  3. Review
  4. Polycomb function in early mouse development.Cell death and differentiation · 2025
    Review
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Review
  13. Review
  14. Regulation of Embryonic Stem Cell Self-Renewal.Life (Basel, Switzerland) · 2022
    Review
  15. Review
  16. Article
  17. Review
  18. Article
  19. Article
  20. Article

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

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 4 institutions in 2 countries.

Shaun D FouseDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Yin Shen
Matteo Pellegrini
Steve Cole
Alexander Meissner
Leander Van Neste
Rudolf Jaenisch
Guoping Fan
University of California, Los Angeles · USGhent University · BEMassachusetts Institute of Technology · USWhitehead Institute for Biomedical Research · US

Funding

DNA methylation in Neuronal and Glial DifferentiationR01NS044405 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI FAN, GUOPING · 2003 to 2007
$1.8M
DNA Hypomethylation and Cortical Neuronal DegenerationR01NS051411 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI FAN, GUOPING · 2005 to 2009
$1.7M
DNA HYPOMETHYLATION AND CORTICAL NEURONAL DEGENERATIONR56NS051411 · NINDS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI FAN, GUOPING · 2010 to 2010
$385k
Regulation of MHCI genes in the CNS by DNA methylationF31MH070204 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI FOUSE, SHAUN · 2005 to 2007
$89k
NIMH NIH HHS 1F31MH070204NIMH NIH HHS F31 MH070204NINDS NIH HHS NS044405NINDS NIH HHS NS051411NINDS NIH HHS R01 NS044405NINDS NIH HHS R01 NS051411NINDS NIH HHS R56 NS051411
6 · The paper itself

Abstract

We report here genome-wide mapping of DNA methylation patterns at proximal promoter regions in mouse embryonic stem (mES) cells. Most methylated genes are differentiation associated and repressed in mES cells. By contrast, the unmethylated gene set includes many housekeeping and pluripotency genes. By crossreferencing methylation patterns to genome-wide mapping of histone H3 lysine (K) 4/27 trimethylation and binding of Oct4, Nanog, and Polycomb proteins on gene promoters, we found that promoter DNA methylation is the only marker of this group present on approximately 30% of genes, many of which are silenced in mES cells. In demethylated mutant mES cells, we saw upregulation of a subset of X-linked genes and developmental genes that are methylated in wild-type mES cells, but lack either H3K4 and H3K27 trimethylation or association with Polycomb, Oct4, or Nanog. Our data suggest that in mES cells promoter methylation represents a unique epigenetic program that complements other regulatory mechanisms to ensure appropriate gene expression.

Indexed as

CpG IslandsDNA MethylationGene Expression Regulation, DevelopmentalPromoter Regions, GeneticAnimalsAntigens, DifferentiationCell ProliferationEmbryonic Stem CellsEpigenesis, GeneticGene Expression ProfilingGene SilencingHistonesHomeodomain ProteinsMethylationMiceNanog Homeobox ProteinAntigens, DifferentiationHistonesHomeodomain ProteinsNanog Homeobox ProteinNanog protein, mouseOctamer Transcription Factor-3Polycomb-Group ProteinsPou5f1 protein, mouseRepressor Proteins

Identifiers

PMID18371437
PMCPMC3070208
OpenAlexW2158668089

What OpenQuestion holds

Textmetadata
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.