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Determination of RNA structural diversity and its role in HIV-1 RNA splicing
- Source :
- Nature
- Publication Year :
- 2020
-
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 factors1,2. 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 elements3. 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 expectation-maximization' (DREEM), which reveals the alternative conformations that are assumed by the same RNA sequence. Contrary to previous models that have analysed population averages4, our results reveal heterogeneous regions of RNA structure across the entire HIV-1 genome. In addition to confirming that in vitro characterized5 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 hypothesis6-8 that heterogeneity in RNA conformation regulates splice-site use and viral gene expression.
- Subjects :
- Gene Expression Regulation, Viral
RNA Folding
Computational biology
Biology
Sulfuric Acid Esters
Primary transcript
Article
03 medical and health sciences
Humans
Nucleic acid structure
Gene
030304 developmental biology
0303 health sciences
Multidisciplinary
Base Sequence
Sequence Analysis, RNA
030302 biochemistry & molecular biology
RNA Conformation
Alternative splicing
RNA
Reproducibility of Results
Alternative Splicing
HEK293 Cells
RNA splicing
Mutation
HIV-1
Nucleic Acid Conformation
RNA, Viral
Thermodynamics
Human genome
RNA Splice Sites
Algorithms
Subjects
Details
- Language :
- English
- ISSN :
- 14764687 and 00280836
- Volume :
- 582
- Issue :
- 7812
- Database :
- OpenAIRE
- Journal :
- Nature
- Accession number :
- edsair.doi.dedup.....ada02574b201f96085c349314b09362f