Investigating the role of RNA cap methyltransferase CMTR1 in regulating gene expression in embryonic stem cells

Abstract

The RNA cap structure is critical to protect RNA polymerase II (RNAPII) transcripts from degradation and promote downstream RNA processing events. In mammals, the N-7 position of the cap guanosine and the O-2 position of the first transcribed nucleotide ribose are methylated by the cap methyltransferases RNMT and CMTR1 respectively, to form the most prevalent cap structure. The co-transcriptional recruitment of cap methyltransferases is essential for the kinetic and spatial coupling between transcription and cap methylation. Previous experimental observations suggest that RNMT and CMTR1 regulate transcription, here we aimed to investigate how these enzymes are recruited to chromatin and further understand the mechanism by which they influence transcription in mouse embryonic stem cells (mESCs).
In this thesis, we identified different chromatin binding patterns of the two cap methyltransferases RNMT and CMTR1. CMTR1 globally bound to the transcription start site (TSS) and colocalised with RNAPII on chromatin while RNMT was not significantly enriched on the majority of genes, which suggested different substrate recruitment mechanisms for these two enzymes. Furthermore, CMTR1 chromatin binding levels globally correlated with the binding of total RNAPII and Serine 5 phosphorylated RNAPII C-terminal domain (Ser5P) near the TSS. In particular histones and ribosomal protein genes were the most CMTR1-enriched gene families in mESCs.

We further investigated the impact of CMTR1 on gene expression in mESCs. We found that CMTR1 had a positive effect in modulating RNAPII binding and thus influencing nascent transcription of its target histone and ribosomal protein genes in the mESCs. During mESC differentiation, CMTR1 expression is upregulated. Our findings indicate that CMTR1 upregulation is important to maintain histone and ribosomal expression to support changes in chromatin structure and proteome and thus promote the cell differentiation process.

Date of Award	2023
Original language	English
Awarding Institution	University of Dundee
Sponsors	China Scholarship Council
Supervisor	Victoria Cowling (Supervisor)