Ras-induced changes in H3K27me3 occur after those in transcriptional activity

PLoS Genet. 2013 Aug;9(8):e1003698. doi: 10.1371/journal.pgen.1003698. Epub 2013 Aug 29.

Abstract

Oncogenic signaling pathways regulate gene expression in part through epigenetic modification of chromatin including DNA methylation and histone modification. Trimethylation of histone H3 at lysine-27 (H3K27), which correlates with transcriptional repression, is regulated by an oncogenic form of the small GTPase Ras. Although accumulation of trimethylated H3K27 (H3K27me3) has been implicated in transcriptional regulation, it remains unclear whether Ras-induced changes in H3K27me3 are a trigger for or a consequence of changes in transcriptional activity. We have now examined the relation between H3K27 trimethylation and transcriptional regulation by Ras. Genome-wide analysis of H3K27me3 distribution and transcription at various times after expression of oncogenic Ras in mouse NIH 3T3 cells identified 115 genes for which H3K27me3 level at the gene body and transcription were both regulated by Ras. Similarly, 196 genes showed Ras-induced changes in transcription and H3K27me3 level in the region around the transcription start site. The Ras-induced changes in transcription occurred before those in H3K27me3 at the genome-wide level, a finding that was validated by analysis of individual genes. Depletion of H3K27me3 either before or after activation of Ras signaling did not affect the transcriptional regulation of these genes. Furthermore, given that H3K27me3 enrichment was dependent on Ras signaling, neither it nor transcriptional repression was maintained after inactivation of such signaling. Unexpectedly, we detected unannotated transcripts derived from intergenic regions at which the H3K27me3 level is regulated by Ras, with the changes in transcript abundance again preceding those in H3K27me3. Our results thus indicate that changes in H3K27me3 level in the gene body or in the region around the transcription start site are not a trigger for, but rather a consequence of, changes in transcriptional activity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / genetics*
  • Chromatin Immunoprecipitation
  • DNA Methylation / genetics*
  • Epigenomics
  • Gene Expression Regulation
  • Genes, ras*
  • Jumonji Domain-Containing Histone Demethylases / genetics*
  • Mice
  • Polycomb-Group Proteins / genetics
  • Promoter Regions, Genetic
  • Transcription Initiation Site
  • Transcription, Genetic*

Substances

  • Chromatin
  • Polycomb-Group Proteins
  • Jumonji Domain-Containing Histone Demethylases
  • Kdm6b protein, mouse

Grants and funding

M Hosogane was supported by a research fellowship for young scientists from Japan Society for the Promotion of Science. This study was supported in part by a Grant-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology of Japan, by the Funding Program for Next Generation World-Leading Researchers (Next Program) and by the Global Center of Excellence Program of Japan.The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.