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.
N1 - Funding Information:
This work was supported by NIH grants U54GM103297 (the Center for HIV RNA Studies, to P.D.B., S.B.K., and R.I.S.), K22 AI116258 (to S.B.K.), R01 AI50111 (to P.D.B.), GM101979 (to B.S.T.), and F31 AI116406 (to A.E.). The work was also supported by the UNC Center for AIDS Research (NIH award P30 AI50410) and the UNC Lineberger Comprehensive Cancer Center (NIH award P30 CA16068).
Publisher Copyright:
© 2019 American Society for Microbiology. All Rights Reserved.
PY - 2019
Y1 - 2019
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.
AB - 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.
KW - HIV-1
KW - HnRNP
KW - Splicing
UR - http://www.scopus.com/inward/record.url?scp=85073304814&partnerID=8YFLogxK
U2 - 10.1128/JVI.01048-19
DO - 10.1128/JVI.01048-19
M3 - Article
C2 - 31413137
AN - SCOPUS:85073304814
VL - 93
JO - Journal of Virology
JF - Journal of Virology
SN - 0022-538X
IS - 21
M1 - e01048-19
ER -