Formation of co-transcriptional histone modification patterns

Transcription by RNA polymerase II (RNAPII) is accompanied by a complex pattern of histone modifications. This pattern is a universal feature of transcription, yet how it is generated is still not known. The C-terminal domains (CTDs) of Spt5 and the large subunit of RNAPII itself (Rpb1) are important parts of these mechanisms. The Rpb1 and Spt5 CTDs are composed of multiple repeats of short amino acid motifs. The Rpb1 CTD contains the conserved heptad Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7 while the Spt5 CTD is composed of a more variable motif that often begins with Thr. The CTDs are critical for assembly of the RNAPII elongation complex and interact with numerous factors, including histone modification enzymes. Remarkably, all of the phosphorylatable residues in these repeats are phosphorylated at different stages of transcription, suggesting that CTD phosphorylation patterns are functionally linked to histone modification patterns. We are deciphering how the CTDs, CTD-binding proteins, and CTD kinases dictate patterns of co-transcriptional histone modifications using the model eukaryote fission yeast (Schizosaccharomyces pombe).

From Mbogning et al NAR 2015

Functions of co-transcriptional histone modifications

The significance of co-transcriptional histone modification patterns for gene expression is not yet understood. We study co-transcriptional histone H2B monoubiquitylation (H2Bub1), a modification associated with the elongation phase of RNAPII transcription, to better understand these mechanisms. H2Bub1 does not lead to H2B degradation by the proteasome, but instead seems to function as a regulatory signal. We use genomics, genetics, and biochemistry approaches in fission yeast to define how this regulatory pathway works. We have found an important connection between H2Bub1 and Cdk9, a subunit of the essential RNAPII elongation factor positive transcription elongation factor b (P-TEFb). We have also identified shared function with H3K36 methylation, another prominent co-transcriptional histone modification, in regulating antisense transcription. Our current efforts focus on working out the molecular details of these pathways.

Targeting transcription elongation and histone modifications in human disease

Cdk9 is a potential drug target in cancer and in heart disease, but its role in co-transcriptional histone modification pathways in the context of disease has not been studied. In collaboration with the lab of Terry Hébert (McGill Pharmacology), we are investigating the roles of Cdk9, its regulators, and downstream effectors (including histone modifications) on the hypertrophic response in cardiac myocytes. Cardiac hypertrophy (an enlargement of the heart muscle caused by increase in the size of individual myocytes) occurs in healthy individuals in response to exercise, but can also occur as a compensatory response in individuals with heart disease and atherosclerosis. This pathological form of cardiac hypertrophy turns out to be maladaptive and is associated with negative clinical outcomes. The activity of Cdk9 is required for the pathological hypertrophic response. We are interested in learning more about how Cdk9 (and potentially co-transcriptional histone modifications) drives gene expression changes associated with this response. We have also recently found a novel signaling pathway that regulates the Cdk9 partner Brd4 in cardiomyocytes and which may be relevant for Brd4 activation in other cell types. Ultimately, we hope to build on these findings to develop new therapeutic strategies for treatment of disease.

Figure 10.tif

From Martin et al MCB 2020