Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework
Figure 2
Time of origins for binding sites of six TFs in humans.
Binding motifs were determined using human ChIP-seq data for GATA1, SOX2, MYC, CTCF, ETS1, and MAX. The branch of origin was determined for each binding site within the (−100,+100) region relative to a human ChIP-seq peak summit. (Left) Distribution of the branch of origin for each binding site. Branch labels correspond to those in Figure 1B. ‘Ancestral’ binding sites have origins prior to human-mouse divergence. (Right) The rate of binding site creation along branches ancestral to humans. Rates were estimated by dividing the number of sites originating along each branch by evolutionary time, including only binding sites currently existing in humans.