H3K4me2/3 modulate the stability of RNA polymerase II pausing (PRO-Seq)

Modifications of histones are intricately linked with the regulation of gene expression, with demonstrated roles in various physiological processes and disease pathogenesis. Methylation of histone H3 lysine 4 (H3K4), implemented by the COMPASS family, is enriched at promoters and associated cis-regulatory elements, with H3K4 trimethylation (H3K4me3) considered a hallmark of active gene promoters. However, the relative roles of deposition and removal of H3K4 methylation, as well as the extent to which these events contribute to transcriptional regulation have so far remained unclear. Here, through rapid depletion of either of two shared subunits of COMPASS family members, we reveal a dynamic turnover of H3K4me2 and H3K4me3 mediated by the KDM5 family of histone demethylases. Loss of H3K4me2 and H3K4me3 following COMPASS disruption does not impair the recruitment of TFIID and initiating RNA polymerase II (Pol II). Instead, their loss leads to reductions in the paused form of Pol II on chromatin while inducing the relative enrichment of the Integrator-PP2A (INTAC) termination complex, leading to reduced levels of elongating polymerases, thus revealing how H3K4me2 and H3K4me3 dynamics can regulate Pol II pausing to sustain or attenuate transcription. We performed ChIP-seq, PRO-seq, or RNA-seq to investigate the role of methylation of histone H3 lysine 4 (H3K4) in regulating transcription. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 6, 12,or 24 hours, the corresponding control cells were treated for the same duration with vehicle only (DMSO) at the same vol/vol dilution.