Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection
(a) Analysis pipeline. DNase-sequences from each species were aligned to the native genome and lifted over to the human genome for analysis. Regions are filtered at various steps of the analysis to remove alignment and orthology artifacts (Materials and Materials). Correlation plots of DNase-seq signals (b) and DGE-seq signals (c) expression data show that both chromatin and expression data from human (Hu), chimpanzee (Ch), and macaque (Ma) are more highly correlated between biological replicates from the same tissue within a single species. Additionally, the same cell type from different species is more similar than different cell types from the same species.