Widespread contribution of transposable elements to the innovation of gene regulatory networks

Transposable elements (TEs) have been shown to contain functional binding sites for certain transcription factors (TFs). However, the extent to which TEs contribute to the evolution of TF binding sites is not well known. We comprehensively mapped binding sites for 26 pairs of orthologous TFs in two pairs of human and mouse cell lines (representing two cell lineages), along with epigenomic profiles, including DNA methylation and six histone modifications. Overall, we found that 20% of binding sites were embedded within TEs. This number varied across different TFs, ranging from 2% to 40%. We further identified 710 TF-TE relationships in which genomic copies of a TE subfamily contributed a significant number of…

• AC
  American Cancer Society

  Award: RSG-14-049-01-DMC
• MO
  March of Dimes Foundation

  Award: 5-FY10-491
• EM
  Edward Mallinckrodt, Jr. Foundation
• NI
  National Institutes of Health

  Awards: R01HG007354, R01HG007354, R01HG007175, and R01ES024992, R01HG007175, R01ES024992