Regulation of enhancer transcription by Spt5 directly couples enhancer activation with enhancer function

Transcription is a ubiquitous feature of active enhancers, yet the regulatory role of enhancer transcription or transcripts remains debated. Here, we depleted the RNA polymerase II pausing and elongation factor Spt5 in activated mouse B cells and found that approximately 50% of enhancer-gene pairs showed correlated changes in transcription, consistent with a potential functional requirement for enhancer transcription. In particular, Spt5 depletion led to loss of super-enhancer-promoter physical interaction and gene expression at the immunoglobulin heavy chain locus (Igh), abrogating antibody class switch recombination. This defect correlated strictly with loss of enhancer transcription and did not affect enhancer activation, as inferred from histone H3K27 acetylation, chromatin accessibility and occupancy of Mediator and cohesin. Strikingly, CRISPRa-mediated rescue of enhancer transcription in Spt5-depleted cells restored Igh gene expression. Thus, Spt5-mediated enhancer transcription serves as a direct and causal link between Igh super-enhancer activation and its physical interaction with target promoters. For all experiments, we ablated the Supt5h gene in vitro by adding 4-hydroxy tamoxifen (4-HT) to primary Supt5hFl/- Rosa26ERT2-cre/+ mouse primary mature B cells for 32 hours. As controls, we used Rosa26ERT2-cre/+ primary B cells treated with 4-HT for 32 hours (referred to as wild-type, WT).