Category: Standard Studentships

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

Project No.2242

Primary Supervisor

Prof Sarah Newbury – University of Sussex

Co-Supervisor(s)

Dr 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 remains elusive. Our recent polyriboseq experiments have revealed a set of ribosome-associated lncRNAs which show sensitivity to the highly conserved exoribonucleases of Dis3L2 and Xrn1 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 an industrial context. The project will be complementary to another being carried out by Hope Haime, a Cohort2020 SocoBioDTP student, which aims to generate DIS3L2-deficient human cell lines to produce bioactive proteins under nutrient-poor conditions. In the current project, the student will use these cells and produce cell lines deficient for the other major cytoplasmic exoribonuclease, XRN1. These cells will be used in polyriboseq experiments to identify lncRNAs which are ribosome-associated and regulated by RNA stability. The identified lncRNAs will then be subject to further investigation to dissect the molecular mechanisms underpinning their regulation. This will include systems biology analyses to identify specific regulatory features, including 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.