Regulation of Pol II transcriptional response to DNA damage by RBM7 and P-TEFb

Abstract

DNA damage response (DDR) is a cascade of events within the cells, which is initiated by DNA lesions and results in DNA repair and cell survival. Alternatively, DDR could lead to apoptosis - elimination of cells, in which genetic integrity is impossible to restore. Despite the commonly accepted paradigm that RNA synthesis is shut down following DNA damage, recent studies suggest that transcription of DDR genes is activated. The aim of my dissertation is to shed new light on the molecular mechanisms of the transcriptional response to DNA damage.

Gene transcription is the process of transfer of genetic information from DNA to RNA. There are three major steps of transcription: initiation, elongation, and termination. Pausing in early elongation is a key control point of RNA polymerase II (Pol II)-mediated transcription. Negative transcription elongation factors (N-TEFs) interact with Pol II to mediate promoter-proximal pausing. Cyclin-dependent kinase 9 (CDK9) of the positive transcription elongation factor b (P-TEFb) phosphorylates N-TEFs and the C-terminal domain (CTD) of Pol II to resume transcription of paused genes. Small nuclear ribonucleoprotein complex containing 7SK RNA (7SK snRNP) regulates P-TEFb, offering a possibility for the rapid transcription of DDR genes following genotoxic stress.

Here I provided new insight into the molecular mechanism of the transcriptional response to DNA damage. Using high-throughput protein-RNA interactome mapping by UV crosslinking and immunoprecipitation (iCLIP), nascent RNA sequencing, quantitative PCR, and RNA interference experiments I showed that, following genotoxic stress, RNA-binding motif protein 7 (RBM7) stimulated Pol II pause release by activating the P-TEFb via its release from the inhibitory 7SK snRNP. This was mediated by activation of p38 MAPK, which triggered enhanced binding of RBM7 with core subunits of 7SK snRNP. In turn, P-TEFb relocated to chromatin to induce transcription of short units, including key DDR genes and multiple classes of non-coding RNAs (ncRNA). Inhibition of the CDK9 subunit of P-TEFb or depletion of RBM7 provoked cellular hypersensitivity to DNA-damage-inducing agents via activation of apoptosis. In sum, my work suggests that RBM7 controls transcriptional response to DNA damage through P-TEFb. Moreover, it uncovers the importance of stress-dependent stimulation of the Pol II pause release, which enables a pro-survival transcriptional response that is crucial for cell fate upon genotoxic insult.