Context transcription factors establish cooperative environments and mediate enhancer communication

Abstract

Many enhancers play a crucial role in regulating gene expression by assembling regulatory factor (RF) clusters, also referred to as condensates. This process is essential for facilitating enhancer communication and establishing cellular identity. However, how DNA sequence and transcription factor (TF) binding instruct the formation of such high RF environments is still poorly understood. To address this, we developed a novel approach leveraging enhancer-centric chromatin accessibility quantitative trait loci (caQTLs) to nominate RF clusters genome-wide. By analyzing TF binding signatures within the context of caQTLs, we discovered a new class of TFs that specifically contributes to establishing cooperative environments. These “context-only” TFs bind promiscuously with cell type-specific pioneers, recruit coactivators, and, like super enhancers, render downstream gene expression sensitive to condensate-disrupting molecules. We further demonstrate that joint context-only and pioneer TF binding explains enhancer compatibility and provides a mechanistic rationale for how a loose TF syntax can still confer regulatory specificity.