Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

Yoichiro Shibata is with Duke University, Nathan C. Sheffield is with Duke University, Olivier Fedrigo is with Duke University, Courtney C. Babbitt is with Duke University, Matthew Wortham is with Duke University, Alok K. Tewari is with Duke University, Darin London is with Duke University, Lingyun Song is with Duke University, Bum-Kyu Lee is with UT Austin, Vishwanath R. Iyer is with UT Austin, Stephen C. J. Parker is with the National Institutes of Health, Elliott H. Margulies is with the National Institutes of Health, Gregory A. Wray is with Duke University, Terrence S. Furey is with The University of North Carolina at Chapel Hill, Gregory E. Crawford is with Duke University. ; Understanding the molecular basis for phenotypic differences between humans and other primates remains an outstanding challenge. Mutations in non-coding regulatory DNA that alter gene expression have been hypothesized as a key driver of these phenotypic differences. This has been supported by differential gene expression analyses in general, but not by the identification of specific regulatory elements responsible for changes in transcription and phenotype. To identify the genetic source of regulatory differences, we mapped DNaseI hypersensitive (DHS) sites, which mark all types of active gene regulatory elements, genome-wide in the same cell type isolated from human, chimpanzee, and macaque. Most DHS sites were conserved among all three species, as expected based on their central role in regulating transcription. However, we found evidence that several hundred DHS sites were gained or lost on the lineages leading to modern human and chimpanzee. Species-specific DHS site gains are enriched near differentially expressed genes, are positively correlated with increased transcription, show evidence of branch-specific positive selection, and overlap with active chromatin marks. Species-specific sequence differences in transcription factor motifs found within these DHS sites are linked with species-specific changes in chromatin ...