SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
Fig 4
Candidate binding partners for a transcription factor are dependent on genomic context, cell type, and expression levels of partners.
(A) Multitask learning identifies different candidate binding partners of POU2F2 at proximal and distal locations to genes. The proximal partners are associated with factors that preferentially bind to CG-rich motifs whereas the distal partners are associated with cell-type specific regulators. As expected, the POU/octamer motif is present in both contexts. (B) Similarly, TCF12 binding profiles in GM12878 and H1-hESC shows preference for cell-type specific regulators at the cell-type specific sites, and the TCF motif is associated with peaks of both cell types. (C-D) The enhancer bound factor p300 shows highly cell-type specific binding and predicted TF signals. The cell-type specific expression of the p300 candidate binding partners partially explains the differing binding profiles of p300 across cell types.