Regulatory element copy number differences shape primate expression profiles

Proc Natl Acad Sci U S A. 2012 Jul 31;109(31):12656-61. doi: 10.1073/pnas.1205199109. Epub 2012 Jul 13.


Gene expression differences are shaped by selective pressures and contribute to phenotypic differences between species. We identified 964 copy number differences (CNDs) of conserved sequences across three primate species and examined their potential effects on gene expression profiles. Samples with copy number different genes had significantly different expression than samples with neutral copy number. Genes encoding regulatory molecules differed in copy number and were associated with significant expression differences. Additionally, we identified 127 CNDs that were processed pseudogenes and some of which were expressed. Furthermore, there were copy number-different regulatory regions such as ultraconserved elements and long intergenic noncoding RNAs with the potential to affect expression. We postulate that CNDs of these conserved sequences fine-tune developmental pathways by altering the levels of RNA.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Cell Line
  • DNA, Intergenic / physiology*
  • Gene Dosage / physiology*
  • Gene Expression Regulation / physiology*
  • Humans
  • Macaca mulatta
  • Pan troglodytes
  • Pseudogenes / physiology*
  • RNA, Untranslated / physiology*
  • Regulatory Elements, Transcriptional / physiology*
  • Species Specificity


  • DNA, Intergenic
  • RNA, Untranslated

Associated data

  • GEO/GSE33960
  • GEO/GSE38572