A cis-regulatory lexicon of DNA motif combinations mediating cell-type-specific gene regulation

Gene expression is controlled by transcription factors (TFs) that bind cognate DNA motif sequences in cis-regulatory elements (CREs). The combinations of DNA motifs acting within homeostasis and disease, however, are unclear. Gene expression, chromatin accessibility, TF footprinting, and H3K27ac-dependent DNA looping data were generated and a random-forest-based model was applied to identify 7,531 cell-type-specific cis-regulatory modules (CRMs) across 15 diploid human cell types. A co-enrichment framework within CRMs nominated 838 cell-type-specific, recurrent heterotypic DNA motif combinations (DMCs), which were functionally validated using massively parallel reporter assays. Cancer cells engaged DMCs linked to neoplasia-enabling processes operative in normal cells while also activating new DMCs only seen in the neoplastic state. This integrative approach identifies cell-type-specific cis-regulatory combinatorial DNA motifs in diverse normal and diseased human cells and represents a general framework for deciphering cis-regulatory sequence logic in gene regulation. [Display omitted] •Profiling of 15 diploid human cell types via RNA-seq, ATAC-seq, and H3K27ac HiChIP•Identification of 838 cell-type-specific, recurrent heterotypic DNA motif combinations•Functional validation of regulatory DMCs via massively parallel reporter assays•Cancer-type-specific DMCs are linked to neoplasia-enabling processes The cis-regulatory logic encoded within DNA sequences that mediate cell-type-specific gene expression is undefined. Here Donohue et al. generate multi-omics data across 15 diploid human cell types and present a new integrative framework for identifying regulatory DNA motif combinations (DMCs). Specifically, they identify cell-type- and -state-specific DMCs and anticipate broad applicability of the approach.