Investigating the significance of PRMT1 methylation for chromatin biology

Secondary Supervisor(s): TBC

University of Registration: University of Birmingham

BBSRC Research Themes: Understanding the Rules of Life (Structural Biology, Systems Biology)

Project Outline

Arginine methylation is a post-translational modification that regulates many cellular processes including gene expression, genome stability, signalling and RNA metabolism. PRMT1 is the main symmetric dimethyltransferase responsible for 85% of all arginine methylation events within the cell, however the mechanism by which PRMT1 regulates specific cellular events in the cell is still largely unknown. This knowledge is important because PRMT1 is upregulated in many cancer types and is currently being investigated as a potential drug target. A lack of understanding into the biology of PRMT1 will most likely result in the failure of these drugs within the clinic.

To address this, we have identified a novel PRMT1 substrate (Protein X) that is a known regulator of chromatin biology, including epigenetic gene expression and genome stability, through its ability to read methyl-lysine and methyl-arginine histone marks. This protein shares many cellular roles with that of PRMT1, implying a functional interplay. Indeed, our preliminary data suggest that methylation of Protein X is required for S-phase progression and that Protein X can also “read” non-histone methyl-arginine containing proteins. How this occurs and the biological significance of these events is currently unknown.

This studentship will therefore address the following objectives:

1) Is methylation of Protein X regulating epigenetic gene expression of cell cycle genes, checkpoint control and/or the DNA repair in response to replication stress?

2) Does methylation of Protein X regulate its ability to be recruited to chromatin and read methylated histone?

3) Is there a separation of function between arginine-methyl dependent events and histone-lysine reading?

4) What is the interactome of methylated-Protein X during S-phase and replication stress

5) Which non-histone methyl-arginine proteins does Protein X “read”, and is this influenced by its own methylation?

Methods used during the project

• Molecular cloning, cell culture and cell line generation by lentiviral infection
• DNA fibre assay
• FACS and BrdU proliferation assays
• Microscopy to detect DNA damage and repair foci
• PLA and iPOND
• Mass Spectrometry
• RNA sequencing
• ChIP-Sequencing
• Bioinformatics (proteomics and genomics)
• Structural modelling (Alphafold3)

Outcomes

This studentship will use a variety of molecular, biochemical, cellular and ‘omics approaches to address important questions on how PRMT1-mediated methylation of a chromatin regulator influences fundamental cellular processes such as gene expression and genome stability. Given that that both PRMT1 and Protein X has been linked with cancer and that aberrant gene expression and genome instability are hallmarks of cancer, our results understanding fundamental processes may reveal new mechanism that can be exploited therapeutically.

Suggested reading

Protein arginine methyltransferase 1, a major regulator of biological processes.

Sudhakar SRN, Khan SN, Clark A, Hendrickson-Rebizant T, Patel S, Lakowski TM, Davie JR. Biochem Cell Biol. 2024 Apr 1;102(2):106-126. doi: 10.1139/bcb-2023-0212. Epub 2023 Nov 3.