Josh Lee

Probing the epitranscriptome with nanopore sequencing (iCASE)


Josh obtained his undergraduate degree (BSc Biochemistry 2014) from the University of Bristol with a placement year in Prof Venugopal Nair’s lab at the Pirbright Institute, studying the role of Chicken anemia virus protein Apoptin in cancer therapy using Marek’s disease lymphoma model. He then worked at the Avon Longitudinal Study of Parents and Children (ALSPAC) Laboratory, before working at Dr David Matthews’s lab at the School of Cellular and Molecular Medicine with a focus on proteomics profiling of interactomes between human host and Middle East respiratory syndrome viral proteins. He is now a PhD student at the University of York working with Dr Dimitris Lagos on probing the immune epitranscriptome using nanopore sequencing technology.

My Project

Epitranscriptomics is an emerging field of RNA research that aims to identify post-transcriptional modifications (PTM) in mRNA transcripts and uncover their functional relevance in biological processes. Whilst over 170 types of RNA modifications have been identified, the functional roles of these modifications remain largely unknown. Nanopore sequencing technology provides a potential unbiased method of mapping RNA modifications. It was previously found that modified bases generate distinct current signatures when compared with unmodified bases. Thus with training sets where RNA modifications are absent, algorithms that helps distinguishing where modification occurs can be developed. This project aims to develop pipeline for generating edited cell lines with defects in N6-Methyl-adenosine (m6A) and 5-methylcytosine (m5C) methylation machinery, and to explore how RNA modifications may shape the immune transcriptome by influencing immune gene functions and responses.