Whole-Genome Analysis of Histone H3 Lysine 4 and Lysine 27 Methylation in Human Embryonic Stem Cells

Guangjin Pan, Shulan Tian, Jeff Nie, Chuhu Yang, Victor Ruotti, Hairong Wei, Gudrun A. Jonsdottir, Ron Stewart, James A. Thomson

Research output: Contribution to journalArticlepeer-review


We mapped Polycomb-associated H3K27 trimethylation (H3K27me3) and Trithorax-associated H3K4 trimethylation (H3K4me3) across the whole genome in human embryonic stem (ES) cells. The vast majority of H3K27me3 colocalized on genes modified with H3K4me3. These comodified genes displayed low expression levels and were enriched in developmental function. Another significant set of genes lacked both modifications and was also expressed at low levels in ES cells but was enriched for gene function in physiological responses rather than development. Comodified genes could change expression levels rapidly during differentiation, but so could a substantial number of genes in other modification categories. SOX2, POU5F1, and NANOG, pluripotency-associated genes, shifted from modification by H3K4me3 alone to colocalization of both modifications as they were repressed during differentiation. Our results demonstrate that H3K27me3 modifications change during early differentiation, both relieving existing repressive domains and imparting new ones, and that colocalization with H3K4me3 is not restricted to pluripotent cells.

Original languageEnglish (US)
Pages (from-to)299-312
Number of pages14
JournalCell Stem Cell
Issue number3
StatePublished - Sep 13 2007



ASJC Scopus subject areas

  • Molecular Medicine
  • Genetics
  • Cell Biology


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