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Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing.
J Virol. 2019 11 01; 93(21)JV

Abstract

Alternative splicing of HIV-1 mRNAs increases viral coding potential and controls the levels and timing of gene expression. HIV-1 splicing is regulated in part by heterogeneous nuclear ribonucleoproteins (hnRNPs) and their viral target sequences, which typically repress splicing when studied outside their native viral context. Here, we determined the location and extent of hnRNP binding to HIV-1 mRNAs and their impact on splicing in a native viral context. Notably, hnRNP A1, hnRNP A2, and hnRNP B1 bound to many dispersed sites across viral mRNAs. Conversely, hnRNP H1 bound to a few discrete purine-rich sequences, a finding that was mirrored in vitro hnRNP H1 depletion and mutation of a prominent viral RNA hnRNP H1 binding site decreased the use of splice acceptor A1, causing a deficit in Vif expression and replicative fitness. This quantitative framework for determining the regulatory inputs governing alternative HIV-1 splicing revealed an unexpected splicing enhancer role for hnRNP H1 through binding to its target element.IMPORTANCE Alternative splicing of HIV-1 mRNAs is an essential yet quite poorly understood step of virus replication that enhances the coding potential of the viral genome and allows the temporal regulation of viral gene expression. Although HIV-1 constitutes an important model system for general studies of the regulation of alternative splicing, the inputs that determine the efficiency with which splice sites are utilized remain poorly defined. Our studies provide an experimental framework to study an essential step of HIV-1 replication more comprehensively and in much greater detail than was previously possible and reveal novel cis-acting elements regulating HIV-1 splicing.

Authors+Show Affiliations

Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA kutluay@wustl.edu pbieniasz@rockefeller.edu.Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA.Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA.Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA.Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA.Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, Missouri, USA.Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA.Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA.Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA.Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA. UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA kutluay@wustl.edu pbieniasz@rockefeller.edu. Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA.

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural

Language

eng

PubMed ID

31413137

Citation

Kutluay, Sebla B., et al. "Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing." Journal of Virology, vol. 93, no. 21, 2019.
Kutluay SB, Emery A, Penumutchu SR, et al. Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing. J Virol. 2019;93(21).
Kutluay, S. B., Emery, A., Penumutchu, S. R., Townsend, D., Tenneti, K., Madison, M. K., Stukenbroeker, A. M., Powell, C., Jannain, D., Tolbert, B. S., Swanstrom, R. I., & Bieniasz, P. D. (2019). Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing. Journal of Virology, 93(21). https://doi.org/10.1128/JVI.01048-19
Kutluay SB, et al. Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing. J Virol. 2019 11 1;93(21) PubMed PMID: 31413137.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-Wide Analysis of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) Binding to HIV-1 RNA Reveals a Key Role for hnRNP H1 in Alternative Viral mRNA Splicing. AU - Kutluay,Sebla B, AU - Emery,Ann, AU - Penumutchu,Srinivasa R, AU - Townsend,Dana, AU - Tenneti,Kasyap, AU - Madison,Michaela K, AU - Stukenbroeker,Amanda M, AU - Powell,Chelsea, AU - Jannain,David, AU - Tolbert,Blanton S, AU - Swanstrom,Ronald I, AU - Bieniasz,Paul D, Y1 - 2019/10/15/ PY - 2019/06/23/received PY - 2019/07/23/accepted PY - 2019/8/16/pubmed PY - 2020/6/11/medline PY - 2019/8/16/entrez KW - HIV-1 KW - hnRNP KW - splicing JF - Journal of virology JO - J. Virol. VL - 93 IS - 21 N2 - Alternative splicing of HIV-1 mRNAs increases viral coding potential and controls the levels and timing of gene expression. HIV-1 splicing is regulated in part by heterogeneous nuclear ribonucleoproteins (hnRNPs) and their viral target sequences, which typically repress splicing when studied outside their native viral context. Here, we determined the location and extent of hnRNP binding to HIV-1 mRNAs and their impact on splicing in a native viral context. Notably, hnRNP A1, hnRNP A2, and hnRNP B1 bound to many dispersed sites across viral mRNAs. Conversely, hnRNP H1 bound to a few discrete purine-rich sequences, a finding that was mirrored in vitro hnRNP H1 depletion and mutation of a prominent viral RNA hnRNP H1 binding site decreased the use of splice acceptor A1, causing a deficit in Vif expression and replicative fitness. This quantitative framework for determining the regulatory inputs governing alternative HIV-1 splicing revealed an unexpected splicing enhancer role for hnRNP H1 through binding to its target element.IMPORTANCE Alternative splicing of HIV-1 mRNAs is an essential yet quite poorly understood step of virus replication that enhances the coding potential of the viral genome and allows the temporal regulation of viral gene expression. Although HIV-1 constitutes an important model system for general studies of the regulation of alternative splicing, the inputs that determine the efficiency with which splice sites are utilized remain poorly defined. Our studies provide an experimental framework to study an essential step of HIV-1 replication more comprehensively and in much greater detail than was previously possible and reveal novel cis-acting elements regulating HIV-1 splicing. SN - 1098-5514 UR - https://www.unboundmedicine.com/medline/citation/31413137/Genome_Wide_Analysis_of_Heterogeneous_Nuclear_Ribonucleoprotein__hnRNP__Binding_to_HIV_1_RNA_Reveals_a_Key_Role_for_hnRNP_H1_in_Alternative_Viral_mRNA_Splicing_ L2 - https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/31413137/ DB - PRIME DP - Unbound Medicine ER -