Investigation into factors involved in the transcriptional regulation of snRNA genes

Thesis

The human pol II-dependent small nuclear (sn)RNAs are non-coding RNAs which function as small nuclear ribonucleoproteins (snRNPs) and play key roles in the processing of other RNAs, including splicing of pre-mRNA. Unlike most mRNAs, these snRNAs are not spliced or polyadenylated, and 3’ end formation is directed by a gene-specific 3’ box rather than a poly(A) site. Cleavage by the Integrator complex upstream of the 3’ box produces pre-snRNAs that are further processed in the cytoplasm. In addition, these snRNA genes have a specialised promoter comprising an enhancer-like DSE and an essential PSE that functions as the core promoter. The enzymatic activity of several transcriptional cyclin-dependent kinases (CDKs) regulates the transcription of protein-coding genes and the processing of the transcripts. CDK9 has been shown to regulate the processing of snRNA gene transcripts by ensuring the recruitment of the Integrator complex. However, the role of other CDKs is not yet clear. I have used analog-sensitive CDK cell lines, RT-qPCR, and chromatin immunoprecipitation to investigate the role of other transcriptional CDKs in the expression of human snRNA genes. I have found that the activity of either CDK12 or CDK13 is required for the 3’ end processing of snRNA gene transcripts, and inhibition of both CDK12 and CDK13 causes failure to recognise the 3’ box. In addition, CDK12 and CDK13, as well as the elongation factor, SPT6, help to recruit Integrator subunits to snRNA genes. Using ChIP-qPCR, I have demonstrated that inhibition of CDK12 or CDK13 affects phosphorylation of CTD residues other than Ser2 and Ser 5 during the transcription of U2 snRNA genes. This work provides new insights into factors that regulate the 3’ end processing of snRNA genes and the potential mechanisms underlying their function.

Authors: Fagbemi, MO

• DOI: 10.5287/ora-qrokyndk2
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: transcription; CDKs; snRNA 3' end misprocessing; CDK12/13; RNA Pol II; U2 snRNA; snRNA; cyclin-dependent kinases; CDK13/12; snRNA 3' end processing; CDK12; RNA Polymerase II; CDK13; 3' Box
• Subjects: Molecular biology; Cyclin-dependent kinases; Transcription