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Series GSE142490 Query DataSets for GSE142490
Status Public on Jun 11, 2020
Title Acetylation of cytidines by NAT10 enhances HIV-1 replication through stabilization of viral RNA
Organism Homo sapiens
Experiment type Other
Summary As obligate parasites, viruses need to navigate a variety of cellular regulatory systems while infecting and replicating in the host cell. Post-transcriptional modifications have recently emerged as an important layer of regulation of viral RNA function. For example, our lab and others have shown that the RNA modification N6-methyladenosine (m6A) can enhance the replication of multiple viruses in cis, including Human Immunodeficiency virus 1 (HIV-1), Influenza A virus, SV40 and Kaposi's sarcoma-associated herpesvirus (KSHV). Recent reports have revealed the presence of another RNA modification, N4-acetylcytidine (ac4C) on cellular mRNAs and have shown that ac4C can enhance mRNA stability and translation. Here, we demonstrate that ac4C is present at multiple sites on HIV-1 mRNAs and on the viral genomic RNA. Through ac4C RNA immunoprecipitation (RNA-IP) and RNA-seq, we found ac4C on HIV-1 mRNAs as well as the virion genomic RNA, with ac4C sites in the coding regions of the pol, env, nef genes, and the trans-activation response (TAR) hairpin. Phenotypically, we observe that increasing the expression level of the ac4C acetyltransferase NAT10 leads to an increase in viral replication that is dependent on the RNA binding and enzymatic domains of NAT10. Moreover, both CRISPR-depletion of NAT10 (Ξ”NAT10) and treatment with the small molecule NAT10 inhibitor Remodelin, diminishes HIV-1 replication in T cells. Lastly, silent mutations introduced to prevent ac4C deposition on the viral genome indeed diminished HIV-1 replication. Our data suggest that HIV-1 has evolved to incorporate ac4C in essential viral gene coding regions and regulatory RNA structures, and that NAT10-dependent ac4C addition enhances HIV-1 replication.
Overall design PA-ac4C-seq on poly(A)+ RNA from mock-infected or HIV-1-infected CEM-SS and CEM cells; PA-ac4C-seq on RNA extracted from HIV-1 infected CEM-SS, SupT1, and CEM cells; PA-ac4C-seq validation of ac4C depletion in virions produced from control or NAT10-depleted CEM cells; GFP (control) or NAT10 PAR-CLIP on HIV-1-infected CEM cells.
Contributor(s) Tsai K, Cullen BR
Citation(s) 32533923
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 DA046111 Epitranscriptomic modification of HIV-1 transcripts: Effects of drugs of abuse DUKE UNIVERSITY BRYAN R. CULLEN
P30 AI064518 Centers for AIDS Research (CFAR) DUKE UNIVERSITY Kent J. Weinhold
Submission date Dec 21, 2019
Last update date Sep 10, 2020
Contact name Bryan R. Cullen
Organization name Duke University Medical Center
Department Molecular Genetics and Microbiology
Street address 213 Research Dr. 420 CARL Bldg.
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (12)
GSM4230371 mock infected CEM-SS mRNA PA-ac4C-seq
GSM4230372 HIV-1 infected CEM-SS mRNA PA-ac4C-seq
GSM4230373 CEM-SS virion RNA PA-ac4C-seq
BioProject PRJNA597154
SRA SRP238484

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Supplementary file Size Download File type/resource
GSE142490_RAW.tar 80.0 Kb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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