Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate

Abstract

Various histone modifications decorate nucleosomes within transcribed genes. Among these, monoubiquitylation of histone H2B (H2Bub1) and methylation of histone H3 on lysines 36 (H3K36me2/3) and 79 (H3K79me2/3) correlate positively with gene expression. By measuring the progression of the transcriptional machinery along genes within live cells, we now report that H2B monoubiquitylation occurs cotranscriptionally and accurately reflects the advance of RNA polymerase II (Pol II). In contrast, H3K36me3 and H3K79me2 are less dynamic and represent Pol II movement less faithfully. High-resolution ChIP-seq reveals that H2Bub1 levels are selectively reduced at exons and decrease in an exon-dependent stepwise manner toward the 39 end of genes. Exonic depletion of H2Bub1 in gene bodies is highly correlated with Pol II pausing at exons, suggesting elongation rate changes associated with intron-exon structure. In support of this notion, H2Bub1 levels were found to be significantly correlated with transcription elongation rates measured in various cell lines. Overall, our data shed light on the organization of H2Bub1 within transcribed genes and single out H2Bub1 as a reliable marker for ongoing transcription elongation.

Coactivators and general transcription factors have two distinct dynamic populations dependent on transcription

“…As expected, we observed a quick decrease in H2Bub levels, since the deposition of the H2Bub1 mark is Pol II transcription elongation‐dependent, coupled through RAD6/RNF20/RNF40 and PAF complexes (Kim et al , 2009). On the other hand, we did not detect changes in the levels of H3K36me3 or H3K9ac (a mark read and deposited by the GCN5), in agreement with previous observations (Tjeertes et al , 2009; Fuchs et al , 2014). In agreement with the cross‐talk between H2Bub1 deposition and H3K4 trimethylation machineries (Thornton et al , 2014 and refs therein), we observed a reduction in the level of H3K4me3, a mark read by the tandem tudor domains of SGF29, present in both ATAC and SAGA.…”

H2B monoubiquitination: t'ub or not t'ub for inducible enhancers

“…In mammals, monoubiquitination of histone H2B on lysine 120 (H2Bub1) is catalyzed by the E3-ubiquitin ligase heterodimer RNF20/RNF40. 4 H2Bub1 had been mainly characterized as a histone mark related to transcriptional elongation, [5][6][7] but several other functions have also been attributed to H2Bub1 such as the regulation of RNA processing 8 or DNA replication. 9 However, the role of H2B monoubiquitination in gene expression had remained enigmatic 10 because its inhibition only had an effect on a subset of genes 11 despite its proposed general involvement in transcription elongation.…”

(Ubi)quitin’ the h2bit: recent insights into the roles of H2B ubiquitylation in DNA replication and transcription

“…8,27 Finally, both Bonnet et al and Fuchs et al observed that global H2Bub is lost rapidly following inhibition of transcriptional elongation, and this loss is abolished in the absence of SAGA. 8,28 As such, it appears that SAGA does not require RNAP II to deubiquitylate H2Bub.…”

“…8,9,28 Signals that terminate these processes may thus result in the loss of dynamic H2Bub, and the return of chromatin to a steady, static state. Through being coupled to transcription in this manner, H2Bub may be a self-perpetuating signal of active transcription; this signal may facilitate the engagement of RNAP II at active genes, obviating the need for stochastic recruitment processes that would delay transcription.…”

“…Furthermore, replication stress results in the gradual loss of global H2Bub, and it is thus possible that DNA replication also maintains dynamic H2Bub. 8,9,28 Cessation of these processes may thus result in the underlying chromatin returning to a static and silent state (top panel).…”