Determination of RNA structural diversity and its role in HIV-1 RNA splicing
Top Cited Papers
- 18 June 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature
- Vol. 582 (7812), 438-+
- https://doi.org/10.1038/s41586-020-2253-5
Abstract
Human immunodeficiency virus 1 (HIV-1) is a retrovirus with a ten-kilobase single-stranded RNA genome. HIV-1 must express all of its gene products from a single primary transcript, which undergoes alternative splicing to produce diverse protein products that include structural proteins and regulatory factors(1,2). Despite the critical role of alternative splicing, the mechanisms that drive the choice of splice site are poorly understood. Synonymous RNA mutations that lead to severe defects in splicing and viral replication indicate the presence of unknown cis-regulatory elements(3). Here we use dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to investigate the structure of HIV-1 RNA in cells, and develop an algorithm that we name `detection of RNA folding ensembles using expectationmaximization' (DREEM), which reveals the alternative conformations that are assumed by the same RNA sequence. Contrary to previous models that have analysed population averages(4), our results reveal heterogeneous regions of RNA structure across the entire HIV-1 genome. In addition to confirming that in vitro characterized(5) alternative structures for the HIV-1 Rev responsive element also exist in cells, we discover alternative conformations at critical splice sites that influence the ratio of transcript isoforms. Our simultaneous measurement of splicing and intracellular RNA structure provides evidence for the long-standing hypothesis(6-8) that heterogeneity in RNA conformation regulates splice-site use and viral gene expression.This publication has 36 references indexed in Scilit:
- Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencingNucleic Acids Research, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory MechanismsPLoS Genetics, 2011
- Disease-Associated Mutations That Alter the RNA Structural EnsemblePLoS Genetics, 2010
- Role of RNA structure in regulating pre-mRNA splicingTrends in Biochemical Sciences, 2010
- RNAstructure: software for RNA secondary structure prediction and analysisBMC Bioinformatics, 2010
- Architecture and secondary structure of an entire HIV-1 RNA genomeNature, 2009
- VARNA: Interactive drawing and editing of the RNA secondary structureBioinformatics, 2009
- Conserved RNA secondary structures promote alternative splicingRNA, 2008
- Estimating the Dimension of a ModelThe Annals of Statistics, 1978