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Studying RNA methylation and splicing in cancer with direct RNA nanopore sequencing

PhD/Masters/Honours project

RNA methylation and splicing have outsize effects on RNA production, metabolism and function and contribute to the pathogenesis of multiple diseases, including cancer. The molecular mechanisms underlying RNA methylation and splicing in cancer contexts remain poorly characterised, at least partially because RNA methylation and splicing is exceedingly difficult to assay using standard RNA-sequencing technologies. In this collaborative project with colleagues at the Peter MacCallum Cancer Centre, we will use Oxford Nanopore's direct RNA-sequencing technology to assay full-length RNA transcripts from which we can detect RNA modifications and distinct isoforms that lead to different protein structures. As a cutting edge technology, the computational tools needed for these analyses are lacking. We will develop bioinformatic and statistical tools for the calling of RNA methylation and splicing isoforms from direct RNA-sequencing data and apply them to answer outstanding questions about the roles of RNA methylation and splicing in cancer.

Supervised by:

  • Dr Davis McCarthy
  • Disease Focus:

  • Cancer
  • Research Unit:

  • Bioinformatics & cellular genomics
  • For further information about this project, contact: [email protected]