RNA Modifications & Epitranscriptome

In Simple Terms

After a genetic message is copied out, the cell can still decorate it with tiny chemical marks. These marks do not change the underlying letters, but they change how the message behaves: how long it survives, how it is folded, and how readily it is turned into protein. This extra layer of information is called the epitranscriptome. It is one way a cell fine tunes itself without rewriting its genes, and it shifts during development, stress and disease. The marks are small and were long invisible, so we build methods that can read them, one molecule at a time, across an entire transcriptome.

The Science

We detect and interpret RNA modifications directly from Oxford Nanopore direct RNA sequencing, which reads native RNA molecules whole rather than as short reconstructed fragments. Using deep-learning detectors such as CHEUI we call m6A and m5C at single-molecule resolution and measure their co-occurrence across the transcriptome, while SWARM resolves signal interference between different modification types so that overlapping marks can be told apart. This lets us map modifications to individual isoforms, relate them to splicing and to translational output, and follow how the modification landscape is remodelled between conditions and across evolution.

Team

• Dr Nikolay ShirokikhLead
• Prof Alice CleynenLead
• Orlane RossiniPhD student
• Shafi MahmudStaff
• Bac DaoPhD student
• Xin HoMasters student
• Ben ChungMasters student
• Siyun ChenMasters student
• Agin RavindranGuest Scientist
• Pratosh SathishkumarGuest Scientist

Tools & Methods

Key Publications

All publications