Histone H2B monoubiquitylation regulates elongation-to-termination transition in RNA polymerase II transcription

RNA Polymerase II (Pol II) transcription is tightly regulated across initiation, elongation, and termination, with key transitions at initiation-to-elongation and elongation-to-termination. While elongation and termination are well-studied, their transition remains unclear. Using chromatin immunoprecipitation (ChIP) and sequencing, we show in Schizosaccharomyces pombe that Cdk9, with its cyclin partner Pch1, disengages from the elongation complex as Pol II nears the cleavage and polyadenylation signal (CPS), while Dis2 (PP1 ortholog) binding increases beyond the CPS, showing an inverse relationship with Cdk9. ChIP-seq analysis reveals histone H2B monoubiquitylation (H2Bub1) regulates Cdk9 occupancy, promoting its recruitment during elongation and dissociation at the CPS, mirroring pSpt5 distribution. Dis2, a pSpt5 phosphatase, exhibits an inverse pattern, decreasing with H2Bub1 loss (htb1-K119R) and increasing with persistent H2Bub1 (ubp8Δ). H2Bub1 perturbations inversely affect Pol II CTD Tyr1/Ser2 phosphorylation, Ser2 kinase Lsk1, mRNA 3'-end processing factors (Pfs2, Pla1), and termination factors (Rhn1, Pcf11)-H2Bub1 loss reduces recruitment, while its persistence enhances occupancy. These findings align with a model in which H2Bub1 loss disrupts termination, whereas its sustained presence reinforces it. Collectively, our findings suggest that H2Bub1-mediated Cdk9 eviction at the CPS facilitates Dis2 binding, pSpt5 dephosphorylation, Pol II slowing, and efficient termination, revealing a yet unknown regulatory paradigm in transcription.