Cdk9 and histone H2B mono-ubiquitylation cooperate to suppress antisense transcription in fission yeast

Cyclin-dependent kinase 9 (Cdk9) and monoubiquitylation of histone H2B (H2Bub1) are both implicated in transcription elongation by RNA polymerase II (RNAPII). In the fission yeast Schizosaccharomyces pombe, Cdk9 and H2Bub1 reciprocally regulate each other through a feedback loop involving phosphorylation of the conserved elongation factor Spt5. Conversely, genetic evidence points to opposing functions of H2Bub1 and Cdk9 that operate through a distinct pathway. To understand the complex interactions between H2Bub1 and Cdk9, we analyzed steady-state RNA levels after H2Bub1 loss, chemical-genetic Cdk9 inhibition, or both, by strand-specific RNA-seq in S. pombe. Cdk9 inhibition or H2Bub1 loss increased levels of antisense transcription initiating within coding regions of distinct, small subsets of genes; ablation of both pathways led to derepression of antisense transcription affecting more than half the genome. Biochemical, genetic and bioinformatic analyses indicated that Cdk9 and H2Bub1 cooperate to suppress antisense transcription by promoting the function of the Clr6-CII histone deacetylase (HDAC) complex in gene bodies. H2Bub1 plays a second, Cdk9-independent role in antagonizing Clr6-CII function to promote sense transcription in subtelomeric regions of the genome. Therefore, functional genomics revealed both collaborative and antagonistic functions of H2Bub1 and Cdk9 in fission yeast.