Category: Standard Studentships

Manipulating the molecular features of long non-coding RNAs to regulate gene expression in an industrial context

Project No. 2346

STANDARD PROJECT

Primary Supervisor

Prof Sarah Newbury – University of Sussex

Co-Supervisor(s)

Prof Tobias von der Haar – University of Kent

Dr Ben Towler – University of Sussex

Summary

Cytoplasmic long non-coding RNAs (lncRNAs) have crucial functions in many cellular processes, including the stress response and cell survival.

Misregulation of lncRNAs is associated with a growing number of human diseases such as cancer and neurodegeneration. Despite their name, lncRNAs can be translated into biologically active peptides and therefore it is likely that their levels within cells are tightly regulated. RNA levels can be regulated by manipulating their stability, however mechanisms whereby lncRNA stability is controlled remain elusive. Our recent experiments have revealed a set of ribosome-associated lncRNAs which show sensitivity to the highly conserved exoribonucleases Dis3L2 and Xrn1/Pacman in Drosophila. These data suggest a novel dimension of lncRNA biology.

This project aims to understand the interplay between lncRNA stability and their ribosome association in the context of industrial applications. Human cell lines generated in our lab that are deficient for the major cytoplasmic exoribonucleases will be used in biochemical experiments to identify lncRNAs which are ribosome-associated and regulated by RNA stability. The identified lncRNAs will then be subjected to further investigation to dissect the molecular mechanisms underpinning their regulation. This will include systems biology analyses to identify specific regulatory features, including determining translation rates and codon optimality within the lncRNA open reading frames. The selected lncRNAs will be mutated (using CRISPR/Cas9) to modify their translation (by deletion of the start codon or manipulation of codon usage) to understand the molecular processes involved. The project will lead to a new understanding of the fundamental mechanisms regulating lncRNAs biology, which has general relevance to cellular metabolism as well as Industrial Biotechnology.