Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain.
Nucleic Acids Res. 2020 Jul 27;48(13):7154-7168. doi: 10.1093/nar/gkaa474.
Mono-ubiquitylation of histone H2B (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. It remained unclear whether Cdk9 and H2Bub1 cooperate to regulate the expression of individual genes. Here, we show that Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of ∼10% of fission yeast genes, with each perturbation affecting largely distinct subsets; ablation of both pathways de-represses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both modifications are enriched, and directly proportional to each other, in coding regions, and decrease abruptly around the cleavage and polyadenylation signal (CPS). Cdk9-dependence of antisense suppression at specific genes correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Genetic interactions link Cdk9, H2Bub1 and the histone deacetylase Clr6-CII, while combined Cdk9 inhibition and H2Bub1 loss impair Clr6-CII recruitment to chromatin and lead to decreased occupancy and increased acetylation of histones within gene coding regions. These results uncover novel interactions between co-transcriptional histone modification pathways, which link regulation of RNAPII transcription elongation to suppression of aberrant initiation.
组蛋白 H2B 的单泛素化（H2Bub1）和延伸因子 Spt5 的磷酸化由 RNA 聚合酶 II（RNAPII）在转录过程中发生，并且在裂殖酵母中相互依赖。尚不清楚 Cdk9 和 H2Bub1 是否合作来调节单个基因的表达。在这里，我们表明 Cdk9 抑制或 H2Bub1 缺失诱导裂殖酵母约 10%基因的基因内反义转录，每个扰动影响的基因大部分不同；两种途径的缺失都会使基因组的一半以上反义转录去抑制。H2Bub1 和磷酸化 Spt5 在全基因组范围内具有相似的分布；这两种修饰在编码区富集，并彼此直接相关，并且在切割和多聚腺苷酸化信号（CPS）周围急剧减少。特定基因的反义抑制对 Cdk9 的依赖性与高 H2Bub1 占有率以及启动子近端 RNAPII 暂停相关。遗传相互作用将 Cdk9、H2Bub1 和组蛋白去乙酰化酶 Clr6-CII 联系起来，而 Cdk9 抑制和 H2Bub1 缺失的联合作用会损害 Clr6-CII 向染色质的募集，并导致基因编码区中组蛋白占有率降低和乙酰化增加。这些结果揭示了转录共发生的组蛋白修饰途径之间的新相互作用，这些作用将 RNAPII 转录延伸的调节与异常起始的抑制联系起来。
