Project Reference: TRG27-BIO-EM1

Project title: Does chemistry change shape? How RNA modifications tune RNA folding to rewire gene regulation.

Project outline

RNA is not just a string of nucleotides. It folds into complex shapes that control how genes are regulated: how much messenger RNA a cell holds and for how long, where it is transported, and how much protein it gives rise to. Intriguingly, RNA is also decorated with a plethora of chemical modifications on its bases, adding a further layer of regulation.

For a handful of specific cases, we know they two work together, a chemical mark altering a fold and the fold altering gene expression. What we do not know is whether there are general rules, or what they are.

This project looks for them systematically. The host lab is generating a library of 12,000 synthetic RNA sequences sampling defined structural families, each linked to a fluorescent reporter in two different positions, to track their regulatory functions. The student will put the same library into cells depleted of well-characterised writer enzymes (METTL3 (m6A), METTL1 (m7G) and NAT10 (ac4C)) to see how the missing chemistry changes structure and function.

Objectives: 1 Map RNA structure in modification-depleted versus normal cells with two orthogonal methods: COMRADES, capturing long-range and intermolecular interactions, and SHAPE-MaP, detecting nucleotide-level accessibility. 2 Link structural change to function, measuring RNA abundance, stability, localisation and translation. 3 Use the resulting datasets to test and improve computational folding models, which currently treat every nucleotide as chemically identical.

The outcome will be the first multimodal map of how RNA modifications and structure cooperate in shaping biological function.

The student will be trained in mammalian cell culture, library-based screenings, RNA structure probing, long- and short-read sequencing and machine learning, including a 10-week rotation with Prof Pietro Liò (Computer Science and Technology).

Principal Supervisor

Professor Eric Miska

Email address: eam29@cam.ac.uk

Department / Partner Institute: Biochemistry

Website: https://www.ericmiskalab.org

BBSRC strategic theme

Understanding the rules of life