Positional specificity of different transcription factor classes within enhancers. Positional specificity of different transcription factor classes within enhancers

Gene expression is controlled by sequence-specific transcription factors (TFs), which bind to regulatory sequences in DNA. The degree to which the arrangement of motif sites within regulatory elements determines their function remains unclear. Here, we show that the positional distribution of TF motif sites within NDRs fall into six distinct classes. These patterns are highly consistent across cell types, and bring together factors that have similar functional and binding properties. Furthermore, the position of motif sites appears to be related to their known functions. Our results suggest TFs play distinct roles in forming a functional enhancer, facilitated by their position within a regulatory sequence. Overall design: ATAC-seq in two immune cell lines, Jurkat and U937. H3K27ac ChIP-seq in two immune cell lines, Jurkat and U937, representing a re-analysis of SRR1057274 from sample GSM1296384 (Jurkat) and ERR671846 from sample ERS420369 (U937). We generated the following processed data files: Jurkat-H3K27ac.gappedPeak.gz U937-H3K27ac.gappedPeak.gz.