Bioinformatics Seminar
Time:
Venue: Na
11 February 2020
NaMoving beyond RNA sequence: uncovering the functional role of RNA structure
Vincent CorbinWEHI Bioinformatics
Previous work in RNA analysis has focused on RNA sequencing and expression ; however RNA actually derives much of its functionality from structure. An aspect that has been poorly studied is the capacity of a given RNA sequence to assume more than one secondary structure ; and how crucial this is for RNA function.
We have used DMS-MaPseq to probe the structure of RNA in cells ; developing an algorithm called "Detection of RNA folding Ensembles using Expectation-Maximization" (DREEM) ; which can reveal dominant and alternative conformations assumed by the same RNA sequence. Previous attempts to analyse RNA structure were limited to the derivation of a population average ; whereas our method is capable of revealing the widespread heterogeneous nature of RNA structure ; revealing the assumption of a single average structure as incorrect.
Human immunodeficiency virus-1 (HIV-1) is a retrovirus with a 10-kb single-stranded RNA genome. HIV-1 must express all of its gene products from the same primary transcript ; which undergoes alternative splicing to produce diverse protein products ; including structural proteins (Gag ; Pol ;and Env) and regulatory factors (Tat ; Rev ; Vif ; Vpu ; Nef and Vpr). Despite the critical role of alternative splicing ; the mechanisms driving splice-site choice are poorly understood ; as HIV-1 does not encode any of its own splicing factors. Synonymous RNA mutations that lead to severe defects in splicing and viral replication indicate the presence of unknown cis-regulatory elements.
In addition to confirming that in vitro characterized alternative structures for the HIV-1 Rev Responsive Element (RRE) exists in cells ; we discovered alternative splice site conformations which influence the ratio of transcript isoforms. Our simultaneous measurement of splicing and intracellular RNA structure provides conclusive evidence for the long-standing hypothesis that RNA folding regulates splice site usage ; and of most significance ; uncovers a major role for RNA conformation heterogeneity in regulating RNA gene expression.;;;