Sequence and chromatin determinants of cell-type-specific transcription factor binding

Gene regulatory programs in distinct cell types are maintained in large part through the cell-type specific binding of transcription factors (TFs). The determinants of IF binding include direct DNA sequence preferences, DNA sequence preferences of cofactors, and the local cell-dependent chromatin context. To explore the contribution of DNA sequence signal, histone modifications, and DNase accessibility to cell-type-specific binding, we analyzed 286 ChIP-seq experiments performed by the ENCODE Consortium. This analysis included experiments for 67 transcriptional regulators, 15 of which were profiled in both the GMI2878 (lymphoblastoid) and K562 (erythroleukemic) human hematopoietic cell lines. To model TF-bound regions, we trained support vector machines (SVMs) that use flexible k-mer patterns to capture DNA sequence signals more accurately than traditional motif approaches. In addition, we trained SVM spatial chromatin signatures to model local histone modifications and DNase accessibility, obtaining significantly more accurate IF occupancy predictions than simpler approaches. Consistent with previous studies, we find that DNase accessibility can explain cell-line specific binding for many factors. However, we also find that of the 10 factors with prominent cell-type specific binding patterns, four display distinct cell-type-specific DNA sequence preferences according to our models. Moreover, for two factors we identify cell-specific binding sites that are accessible in both cell types but bound only in one. For these sites, cell-type specific sequence models, rather than DNase accessibility, are better able to explain differential binding. Our results suggest that using a single motif for each IF and filtering for chromatin accessible loci is not always sufficient to accurately account for cell-type specific binding profiles.