Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs [ChIP-nexus]

Low-affinity transcription factor motifs are an important element of the cis-regulatory code, yet they cannot be mapped by local sequence scanning without knowledge of the sequence context in which they are functional. Here we leverage sequence-to-profile models of chromatin accessibility and binding in mouse embryonic stem cells to reliably map low-affinity motifs across the genome and deduce the mechanisms by which they become functional. We show that low-affinity motifs are used by pioneer transcription factors and that their effect is disproportionately enhanced by intra-nucleosomal cooperativity with stronger pioneer motifs. By exploring the underlying nucleosome-mediated mechanism with a kinetic model, we discover that pioneer cooperativity, and not low-affinity motifs per se, renders enhancers more responsive to changes in TF concentrations by increasing their regulatory potential. These results show that low-affinity motifs can be accurately mapped and suggest that their inherently strong cooperativity is an important property of developmental enhancers. Overall design: Chromatin immunoprecipitation experiments with nucleotide resolution through exonuclease, unique barcode and single ligation (ChIP-nexus) experiments were conducted in mouse embryonic stem cell lines (R1) across wildtype lines and one set of CRISPR/Cas9 clones at an upstream Akr1cl enhancer.