Chromatin organization marks exon-intron structure

Nat Struct Mol Biol. 2009 Sep;16(9):990-5. doi: 10.1038/nsmb.1659.


An increasing body of evidence indicates that transcription and splicing are coupled, and it is accepted that chromatin organization regulates transcription. Little is known about the cross-talk between chromatin structure and exon-intron architecture. By analysis of genome-wide nucleosome-positioning data sets from humans, flies and worms, we found that exons show increased nucleosome-occupancy levels with respect to introns, a finding that we link to differential GC content and nucleosome-disfavoring elements between exons and introns. Analysis of genome-wide chromatin immunoprecipitation data in humans and mice revealed four specific post-translational histone modifications enriched in exons. Our findings indicate that previously described enrichment of H3K36me3 modifications in exons reflects a more fundamental phenomenon, namely increased nucleosome occupancy along exons. Our results suggest an RNA polymerase II-mediated cross-talk between chromatin structure and exon-intron architecture, implying that exon selection may be modulated by chromatin structure.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Composition
  • Chromatin* / metabolism
  • Exons*
  • Genome
  • Histones / metabolism
  • Humans
  • Introns*
  • Methylation
  • Protein Processing, Post-Translational
  • RNA Polymerase II / metabolism
  • RNA Splicing


  • Chromatin
  • Histones
  • RNA Polymerase II