Ldb1 establishes multi-enhancer networks to regulate gene expression [ChIP-Seq]
How enhancers specifically connect to gene promoters is still unclear. Besides the CTCF/cohesin machinery, only a small set of nuclear factors have been studied for a direct role in physically connecting regulatory elements. Here, we show via acute degradation experiments that LDB1 directly and broadly promotes enhancer-promoter loops. Utilizing multiple degron systems, we demonstrate that most endogenous LDB1-mediated contacts can form in the absence of CTCF, cohesin and YY1. Furthermore, an engineered/forced, LDB1-driven chromatin loop can form in the absence of cohesin. Yet, in a fraction of cases cohesin driven extrusion may promote LDB1 anchored loops. Leveraging the dynamic reorganization of nuclear architecture during the transition from mitosis to G1 phase, we establish a relationship between LDB1-dependent interactions in the context of TAD organization and gene activation. Tri-C and Region Capture Micro-C reveal that LDB1 organizes multi-enhancer networks to activate transcription. This establishes LDB1 as direct driver of connectivity between regulatory elements. Overall design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Pol2, LDB1, CTCF, RAD21 and YY1 in LDB1-AID cells (untreated and 4 hour auxin-treated conditions). ChIP-seq for LDB1 and RAD21 in SMC3-AID cells (untreated and 4 hour auxin-treated conditions). ChIP-seq for LDB1 in G1E-ER4 md-mCherry subline (nocodazole 8.5 hours). ChIP-seq for CTCF and LDB1 in CTCF-AID cells (untreated and 4 hour auxin-treated conditions).