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Jowhar Z, Xu A, Venkataramanan S, Dossena F, Hoye ML, Silver DL, Floor SN, Calviello L. A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. Mol Syst Biol 2024; 20:276-290. [PMID: 38273160 PMCID: PMC10912769 DOI: 10.1038/s44320-024-00013-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
The road from transcription to protein synthesis is paved with many obstacles, allowing for several modes of post-transcriptional regulation of gene expression. A fundamental player in mRNA biology is DDX3X, an RNA binding protein that canonically regulates mRNA translation. By monitoring dynamics of mRNA abundance and translation following DDX3X depletion, we observe stabilization of translationally suppressed mRNAs. We use interpretable statistical learning models to uncover GC content in the coding sequence as the major feature underlying RNA stabilization. This result corroborates GC content-related mRNA regulation detectable in other studies, including hundreds of ENCODE datasets and recent work focusing on mRNA dynamics in the cell cycle. We provide further evidence for mRNA stabilization by detailed analysis of RNA-seq profiles in hundreds of samples, including a Ddx3x conditional knockout mouse model exhibiting cell cycle and neurogenesis defects. Our study identifies a ubiquitous feature underlying mRNA regulation and highlights the importance of quantifying multiple steps of the gene expression cascade, where RNA abundance and protein production are often uncoupled.
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Affiliation(s)
- Ziad Jowhar
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Albert Xu
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, 94158, USA
| | | | | | - Mariah L Hoye
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, USA
- Department of Cell Biology, Duke University Medical Center, Durham, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, USA
- Department of Neurobiology, Duke University Medical Center, Durham, USA
- Duke Institute for Brain Sciences, Duke University Medical Center, Durham, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, UCSF, San Francisco, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, USA.
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Bacchus-Souffan C, Fitch M, Symons J, Abdel-Mohsen M, Reeves DB, Hoh R, Stone M, Hiatt J, Kim P, Chopra A, Ahn H, York VA, Cameron DL, Hecht FM, Martin JN, Yukl SA, Mallal S, Cameron PU, Deeks SG, Schiffer JT, Lewin SR, Hellerstein MK, McCune JM, Hunt PW. Relationship between CD4 T cell turnover, cellular differentiation and HIV persistence during ART. PLoS Pathog 2021; 17:e1009214. [PMID: 33465157 PMCID: PMC7846027 DOI: 10.1371/journal.ppat.1009214] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/29/2021] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
The precise role of CD4 T cell turnover in maintaining HIV persistence during antiretroviral therapy (ART) has not yet been well characterized. In resting CD4 T cell subpopulations from 24 HIV-infected ART-suppressed and 6 HIV-uninfected individuals, we directly measured cellular turnover by heavy water labeling, HIV reservoir size by integrated HIV-DNA (intDNA) and cell-associated HIV-RNA (caRNA), and HIV reservoir clonality by proviral integration site sequencing. Compared to HIV-negatives, ART-suppressed individuals had similar fractional replacement rates in all subpopulations, but lower absolute proliferation rates of all subpopulations other than effector memory (TEM) cells, and lower plasma IL-7 levels (p = 0.0004). Median CD4 T cell half-lives decreased with cell differentiation from naïve to TEM cells (3 years to 3 months, p<0.001). TEM had the fastest replacement rates, were most highly enriched for intDNA and caRNA, and contained the most clonal proviral expansion. Clonal proviruses detected in less mature subpopulations were more expanded in TEM, suggesting that they were maintained through cell differentiation. Earlier ART initiation was associated with lower levels of intDNA, caRNA and fractional replacement rates. In conclusion, circulating integrated HIV proviruses appear to be maintained both by slow turnover of immature CD4 subpopulations, and by clonal expansion as well as cell differentiation into effector cells with faster replacement rates.
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Affiliation(s)
- Charline Bacchus-Souffan
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Mark Fitch
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, United States of America
| | - Jori Symons
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | | | - Daniel B. Reeves
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Mars Stone
- Vitalant Research Institute and Department of Laboratory Medicine at the University of California, San Francisco, California, United States of America
| | - Joseph Hiatt
- Medical Scientist Training Program & Biomedical Sciences Graduate Program, University of California, San Francisco, California, United States of America
| | - Peggy Kim
- Infectious Diseases Section, Medical Service, San Francisco Veterans Affairs Medical Center, California, United States of America
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
- Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Haelee Ahn
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Vanessa A. York
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
| | - Daniel L. Cameron
- Division of Bioinformatics, Walter & Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Frederick M. Hecht
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Jeffrey N. Martin
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Steven A. Yukl
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
- Infectious Diseases Section, Medical Service, San Francisco Veterans Affairs Medical Center, California, United States of America
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Australia
- Center for Translational Immunology and Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Paul U. Cameron
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Steven G. Deeks
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California, United States of America
| | - Joshua T. Schiffer
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Sharon R. Lewin
- The Peter Doherty Institute for Infection and Immunity, University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
| | - Marc K. Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, United States of America
| | - Joseph M. McCune
- Global Health Innovative Technology Solutions/HIV Frontiers, Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Peter W. Hunt
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, California, United States of America
- * E-mail:
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