Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures

Genome Res. 2014 Sep;24(9):1455-68. doi: 10.1101/gr.167742.113. Epub 2014 Jun 10.


Human and chimpanzee genomes are 98.8% identical within comparable sequences. However, they differ structurally in nine pericentric inversions, one fusion that originated human chromosome 2, and content and localization of heterochromatin and lineage-specific segmental duplications. The possible functional consequences of these cytogenetic and structural differences are not fully understood and their possible involvement in speciation remains unclear. We show that subtelomeric regions--regions that have a species-specific organization, are more divergent in sequence, and are enriched in genes and recombination hotspots--are significantly enriched for species-specific histone modifications that decorate transcription start sites in different tissues in both human and chimpanzee. The human lineage-specific chromosome 2 fusion point and ancestral centromere locus as well as chromosome 1 and 18 pericentric inversion breakpoints showed enrichment of human-specific H3K4me3 peaks in the prefrontal cortex. Our results reveal an association between plastic regions and potential novel regulatory elements.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Centromere / genetics*
  • Chromosome Aberrations
  • Chromosome Breakpoints
  • Genome, Human*
  • Histones / genetics*
  • Histones / metabolism
  • Humans
  • Organ Specificity
  • Pan troglodytes / genetics
  • Prefrontal Cortex / metabolism
  • Species Specificity
  • Telomere / genetics*
  • Transcription Initiation Site


  • Histones