SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
Fig 7
Context determinants of DNase binding signals.
(A) DNase peaks across cell types show significant differences in the underlying sequence preferences depending on the context. DNase peaks that are common to both GM12878 and H1-hESC cell lines show strong preferences for either insulator proteins (CTCF) or promoter associated regulators (NFY) whereas again cell-type specific peaks show preferences for cell-type specific regulators (BATF, IRF, RUNX in GM12878 and OCT, SMAD, NANOG in H1-hESC). (B) The chromatin context of a DNase peak also defines a context for specific binding preferences. DNase peaks in active promoter regions are associated with NRF, SP1 and NFY motifs whereas peaks in the enhancer regions are associated with CTCF, SOX and TEAD motifs.