The long noncoding RNA HEAL regulates HIV-1 replication through epigenetic Regulation of the HIV-1 promoter

Ti Chun Chao, Qiong Zhang, Zhonghan Li, Shashi Kant Tiwari, Yue Qin, Edwin Yau, Ana Sanchez, Gatikrushna Singh, Kungyen Chang, Marcus Kaul, Maile Ann Young Karris, Tariq M. Ranaa

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

Abstract

A major challenge in finding a cure for HIV-1/AIDS is the difficulty in identifying and eradicating persistent reservoirs of replication-competent provirus. Long noncoding RNAs (lncRNAs, 200 nucleotides) are increasingly recognized to play important roles in pathophysiology. Here, we report the first genome-wide expression analysis of lncRNAs in HIV-1-infected primary monocyte-derived macrophages (MDMs). We identified an lncRNA, which we named HIV-1-enhanced lncRNA (HEAL), that is upregulated by HIV-1 infection of MDMs, microglia, and T lymphocytes. Peripheral blood mononuclear cells of HIV-1-infected individuals show elevated levels of HEAL. Importantly, HEAL is a broad enhancer of multiple HIV-1 strains because depletion of HEAL inhibited X4, R5, and dual-tropic HIV replications and the inhibition was rescued by HEAL overexpression. HEAL forms a complex with the RNA-binding protein FUS, which facilitates HIV replication through at least two mechanisms: (i) HEAL-FUS complex binds the HIV promoter and enhances recruitment of the histone acetyltransferase p300, which positively regulates HIV transcription by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclindependent kinase 2 gene, CDK2, to enhance CDK2 expression. Notably, HEAL knockdown and knockout mediated by RNA interference (RNAi) and CRISPR-Cas9, respectively, prevent HIV-1 recrudescence in T cells and microglia upon cessation of azidothymidine treatment in vitro. Our results suggest that silencing of HEAL or perturbation of the HEAL-FUS ribonucleoprotein complex could provide a new epigenetic silencing strategy to eradicate viral reservoirs and effect a cure for HIV-1/AIDS. IMPORTANCE Despite our increased understanding of the functions of lncRNAs, their potential to develop HIV/AIDS cure strategies remains unexplored. A genomewide analysis of lncRNAs in HIV-1-infected primary monocyte-derived macrophages (MDMs) was performed, and 1,145 differentially expressed lncRNAs were identified. An lncRNA named HIV-1-enhanced lncRNA (HEAL) is upregulated by HIV-1 infection and promotes HIV replication in T cells and macrophages. HEAL forms a complex with the RNA-binding protein FUS to enhance transcriptional coactivator p300 recruitment to the HIV promoter. Furthermore, HEAL knockdown and knockout prevent HIV-1 recrudescence in T cells and microglia upon cessation of azidothymidine treatment, suggesting HEAL as a potential therapeutic target to cure HIV-1/AIDS.

Original languageEnglish (US)
Article numbere02016-19
JournalmBio
Volume10
Issue number5
DOIs
StatePublished - Sep 24 2019

Bibliographical note

Funding Information:
We thank Jonathan Karn for kindly providing E4 and human cell lines and for advice. We thank Steve Head at The Scripps Research Institute and Kristen Jepsen at the UCSD Institute for Genomic Medicine for help with the high-throughput sequencing and data analysis. We thank Jason Dang for his help with preparation of the artwork and members of the Rana lab for helpful discussions and advice. This work was supported in part by grants from the National Institutes of Health. Access to retrospectively collected blood samples from HIV-1-infected individuals was made possible by the University of California, San Diego, Center for AIDS Research, an NIH-funded program (P30 AI036214), which is supported by the following NIH Institutes and Centers: NIAID, NCI, NIMH, NIDA, NICHD, NHLBI, NIA, NIGMS, and NIDDK. T.-C.C. and Q.Z. designed and performed the experiments, analyzed the data, and wrote the manuscript; Z.L., S.K.T., E.Y., A.S., and G.S. performed the experiments; S.K.T., Y.Q., and K.C. analyzed the data; M.K. contributed to the experimental design and analyzed and interpreted the data; M.A.Y.K. provided materials and contributed to the experimental design; and T.M.R. contributed to the experimental design, analyzed and interpreted the data, and wrote the manuscript. We declare that we have no conflicts of interest.

Funding Information:
This work was supported in part by grants from the National Institutes of Health. Access to retrospectively collected blood samples from HIV-1-infected individuals was made possible by the University of California, San Diego, Center for AIDS Research, an NIH-funded program (P30 AI036214), which is supported by the following NIH Institutes and Centers: NIAID, NCI, NIMH, NIDA, NICHD, NHLBI, NIA, NIGMS, and NIDDK.

Publisher Copyright:
© 2019 Ivey et al.

Keywords

  • Epigenetic regulation
  • HIV promoter
  • Long noncoding RNAs
  • Prevention of HIV-1 recrudescence
  • Ribonucleoprotein complexes

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