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To understand the mechanisms of HIV latency, we employed an integrated single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin with sequencing (scATAC-seq) approach to simultaneously profile the transcriptomic and epigenomic characteristics of \u223c 125,000 latently infected primary CD4+ T cells after reactivation using three different latency reversing agents. Differentially expressed genes and differentially accessible motifs were used to examine transcriptional pathways and transcription factor (TF) activities across the cell population. We identified cellular transcripts and TFs whose expression\/activity was correlated with viral reactivation and demonstrated that a machine learning model trained on these data was 75%\u201379% accurate at predicting viral reactivation. Finally, we validated the role of two candidate HIV-regulating factors, FOXP1 and GATA3, in viral transcription. These data demonstrate the power of integrated multimodal single-cell analysis to uncover novel relationships between host cell factors and HIV latency.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzae003","type":"journal-article","created":{"date-parts":[[2024,1,11]],"date-time":"2024-01-11T04:31:45Z","timestamp":1704947505000},"source":"Crossref","is-referenced-by-count":21,"title":["Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7880-9497","authenticated-orcid":false,"given":"Manickam","family":"Ashokkumar","sequence":"first","affiliation":[{"name":"Department of Medicine, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"},{"name":"HIV Cure Center, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-3671-8417","authenticated-orcid":false,"given":"Wenwen","family":"Mei","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9562-2109","authenticated-orcid":false,"given":"Jackson J","family":"Peterson","sequence":"additional","affiliation":[{"name":"HIV Cure Center, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"},{"name":"Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1879-5214","authenticated-orcid":false,"given":"Yuriko","family":"Harigaya","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7201-7950","authenticated-orcid":false,"given":"David M","family":"Murdoch","sequence":"additional","affiliation":[{"name":"Department of Medicine, Duke University , Durham, NC 27708, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5714-0002","authenticated-orcid":false,"given":"David M","family":"Margolis","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"},{"name":"HIV Cure Center, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"},{"name":"Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6796-331X","authenticated-orcid":false,"given":"Caleb","family":"Kornfein","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Duke University , Durham, NC 27708, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8546-0089","authenticated-orcid":false,"given":"Alex","family":"Oesterling","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Duke University , Durham, NC 27708, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3510-5358","authenticated-orcid":false,"given":"Zhicheng","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Duke University , Durham, NC 27708, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4283-2780","authenticated-orcid":false,"given":"Cynthia D","family":"Rudin","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Duke University , Durham, NC 27708, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6905-6377","authenticated-orcid":false,"given":"Yuchao","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Statistics, Texas A&M University , College Station, TX 77843, USA"},{"name":"Department of Biology, Texas A&M University , College Station, TX 77843, USA"},{"name":"Department of Biomedical Engineering, Texas A&M University , College Station, TX 77843, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9070-7015","authenticated-orcid":false,"given":"Edward P","family":"Browne","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"},{"name":"HIV Cure Center, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"},{"name":"Department of Microbiology and Immunology, University of North Carolina at Chapel Hill , Chapel Hill , NC 27599, USA"}]}],"member":"286","published-online":{"date-parts":[[2024,6,20]]},"reference":[{"key":"2024070607342395300_qzae003-B1","doi-asserted-by":"crossref","first-page":"8869","DOI":"10.1073\/pnas.95.15.8869","article-title":"Early establishment of a pool of latently infected, resting CD4+\u00a0T cells during primary HIV-1 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transcription","volume":"86","author":"Henderson","year":"2012","journal-title":"J Virol"},{"key":"2024070607342395300_qzae003-B52","doi-asserted-by":"crossref","first-page":"11159","DOI":"10.1128\/JVI.76.21.11159-11165.2002","article-title":"Evidence for regulation of long terminal repeat transcription by Wnt transcription factor TCF-4 in human astrocytic cells","volume":"76","author":"Wortman","year":"2002","journal-title":"J Virol"},{"key":"2024070607342395300_qzae003-B53","doi-asserted-by":"crossref","first-page":"1333","DOI":"10.1038\/s41592-021-01282-5","article-title":"Single-cell chromatin state analysis with Signac","volume":"18","author":"Stuart","year":"2021","journal-title":"Nat Methods"},{"key":"2024070607342395300_qzae003-B54","author":"Lin","year":"2022"},{"key":"2024070607342395300_qzae003-B55","doi-asserted-by":"crossref","DOI":"10.1609\/aaai.v36i9.21194","article-title":"Fast sparse decision tree optimization via reference 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