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.
Competing Interests: DECLARATION OF INTERESTS The authors declare no competing interests.