Computational analysis of associations between alternative splicing and histone modifications

FEBS Lett. 2013 Mar 1;587(5):516-21. doi: 10.1016/j.febslet.2013.01.032. Epub 2013 Jan 24.


Pre-mRNA splicing is a complex process involving combinatorial effects of cis- and trans-elements. Here, we focused on histone modifications as typical trans-regulatory elements and performed systematic analyses of associations between splicing patterns and histone modifications by using publicly available ChIP-Seq, mRNA-Seq, and exon-array data obtained in two human cell lines. We found that several types of histone modifications including H3K36me3 were associated with the inclusion or exclusion of alternative exons. Furthermore, we observed that the levels of H3K36me3 and H3K79me1 in the cell lines were well correlated with the differences in alternative splicing patterns between the cell lines.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing*
  • Cell Line
  • Computational Biology
  • Exons
  • Histones / metabolism*
  • Histones / physiology
  • Humans
  • Methylation
  • Protein Isoforms / genetics
  • Protein Isoforms / metabolism
  • Protein Processing, Post-Translational*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Sequence Analysis, DNA
  • Sequence Analysis, RNA


  • Histones
  • Protein Isoforms
  • RNA, Messenger