Determination of RNA structural diversity and its role in HIV-1 RNA splicing.

Autor: Tomezsko PJ; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Program in Virology, Harvard Medical School, Boston, MA, USA.; Brigham and Women's Hospital, Boston, MA, USA., Corbin VDA; Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia., Gupta P; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Swaminathan H; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Glasgow M; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Massachusetts Institute of Technology, Cambridge, MA, USA., Persad S; Whitehead Institute for Biomedical Research, Cambridge, MA, USA.; Massachusetts Institute of Technology, Cambridge, MA, USA., Edwards MD; Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA., Mcintosh L; Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.; Department of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia., Papenfuss AT; Bioinformatics Division, Walter and Eliza Hall Institute, Parkville, Victoria, Australia.; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia.; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.; Department of Mathematics and Statistics, University of Melbourne, Melbourne, Victoria, Australia.; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia., Emery A; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Swanstrom R; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA., Zang T; Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA., Lan TCT; Whitehead Institute for Biomedical Research, Cambridge, MA, USA., Bieniasz P; Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA., Kuritzkes DR; Brigham and Women's Hospital, Boston, MA, USA.; Department of Medicine, Harvard Medical School, Boston, MA, USA., Tsibris A; Brigham and Women's Hospital, Boston, MA, USA.; Department of Medicine, Harvard Medical School, Boston, MA, USA., Rouskin S; Whitehead Institute for Biomedical Research, Cambridge, MA, USA. srouskin@wi.mit.edu.
Jazyk: angličtina
Zdroj: Nature [Nature] 2020 Jun; Vol. 582 (7812), pp. 438-442. Date of Electronic Publication: 2020 May 06.
DOI: 10.1038/s41586-020-2253-5
Abstrakt: 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 expectation-maximization' (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.
Databáze: MEDLINE