Tracing the Evolution of Lineage-Specific Transcription Factor Binding Sites in a Birth-Death Framework
Figure 1
Model framework for lineage-specific GATA1 binding sites.
Multiple alignments are shown for two GATA1-bound regions in humans. Red and blue boxes in the alignment correspond to GATA1 binding sites. Phylogenies illustrate the birth-death model framework, where the most likely number of binding sites is assigned to each ancestral node (denoted here as either ‘present’ or ‘absent’, at values 1 or 0 in this example). Highlighted branches denote the branch of origin. Evolutionary comparisons were conducted across ten primate species, as well as 36 non-primate vertebrates (not all are shown). (A) A binding site originating within an LTR insertion. (B) A genomic region containing a human GATA1 binding site originating along the ancestral primate lineage and a GATA1 binding site specific to mouse and rat. Despite nearly identical locations of the ChIP-seq peaks across human and mouse (in analogous Erythroblast cell lines), the ability of the method to identify specific branches of origin allows us to identify cases of TFBS turnover in close proximity.