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

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.

Post-translational modifications of hnRNP A1 differentially modulate retroviral IRES-mediated translation initiation

“…HnRNP A1 interacts with the HIV-1 full-length mRNA ( 61–64 ), participating in different stages of its metabolism, including splicing ( 62 , 65 , 66 ), trafficking ( 23 , 67 ), and translation ( 10 , 23 , 36 ). HnRNP A1 interacts with the HIV-1 5′UTR and promotes its IRES activity ( 23 , 64 ).…”

Alternative splicing events implicated in carcinogenesis and prognosis of thyroid gland cancer

“…The BCL2L1 pre-mRNA related to greater tumor cell survival in various cancer types, including human lymphoma, breast cancer, prostate cancer and human hepatocellular carcinoma 34 − 35 . AS even found in AIDS, study found AS of HIV-1 mRNAs increases viral coding potential and controls the levels and timing of gene expression 36 . While the role of AS in the thyroid cancer as yet missing, therefore, it was necessary to carry out this study to provide more information about the combination of splicing and clinical parameters, as well as potential mechanism of the survival-related ASEs in TC.…”

Filgotinib suppresses HIV-1–driven gene transcription by inhibiting HIV-1 splicing and T cell activation

“…We found that genes harboring retained introns upon filgotinib treatment were enriched in RNA processing and splicing pathways (Supplemental Figure 7, B-H, and Figure 6B). In particular, filgotinib induced intron retention in key RNA processing-related genes in HIV-1 transcription, such as HNRNPH1 (101) and DDX41 (ref. 102 and Figure 6, C-F, blue arrowheads).…”