AP-1 subunits converge promiscuously at enhancers to potentiate transcription

The AP-1 transcription factor dimer contributes to many biological processes and environmental responses. The many ways that AP-1 subunits can dimerize has posed a challenge to understanding its regulatory function. To determine patterns of AP-1 dimerization genome-wide, we definitively establish the genome-wide binding patterns and the enhancer function of five AP-1 subunits. We find limited evidence for strong dimerization preferences between specific subunits. In particular, our analysis suggests that canonical AP-1 motifs have the potential to recruit all AP-1 subunits to genomic sites that also have hallmarks of strong enhancer activity. We term those sites AP-1 hotspots. AP-1 hotspots function as a 'hub' for AP-1 subunit binding that elicits changes in cell-type specific AP-1-mediated gene expression. AP-1 hotspots are more predictive of genomic responses to glucocorticoid signaling than super enhancers, and are particularly enriched in disease-associated genetic variants. Together, these results support a model that promiscuous convergence of many subunits to common genomic locations potentiates AP-1-mediated transcription in a cell-type specific fashion. Overall design: ap1_flagtag: A549-derived cell lines with a FLAG epitope inserted at the C-terminus of each of seven AP-1 family members: c-FOS, FOSL1, FOSL2, FOSB, c-JUN, JUNB, and JUND. Directed precise insertion of each FLAG sequence via homologous recombination, using CRISPR/Cas9 to introduce a double strand break in the A549 genome and co-delivering a donor plasmid containing the FLAG tag and a puromycin resistance gene. After selecting for edited cells with puromycin, Cre recombinase was delivered to remove the resistance gene