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Chapus F, Giraud G, Huchon P, Rodà M, Grand X, Charre C, Goldsmith C, Roca Suarez AA, Martinez MG, Fresquet J, Diederichs A, Locatelli M, Polvèche H, Scholtès C, Chemin I, Vargas HH, Rivoire M, Bourgeois CF, Zoulim F, Testoni B. Helicases DDX5 and DDX17 promote heterogeneity in HBV transcription termination in infected human hepatocytes. J Hepatol 2024:S0168-8278(24)00351-9. [PMID: 38782119 DOI: 10.1016/j.jhep.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/28/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND & AIMS Transcription termination fine tunes gene expression and contributes to specify the function of RNAs in eukaryotic cells. Transcription termination of hepatitis B virus (HBV) is subjected to the recognition of the canonical polyadenylation signal (cPAS) common to all viral transcripts. The regulation of the usage of this cPAS and its impact on viral gene expression and replication is currently unknown. APPROACH & RESULTS To unravel the regulation of HBV transcript termination, we implemented a 3' RACE-PCR assay coupled to single molecule sequencing both in in vitro infected hepatocytes and in chronically infected patients. The detection of a previously unidentified transcriptional readthrough indicated that the cPAS was not systematically recognized during HBV replication in vitro and in vivo. Gene expression downregulation experiments demonstrated a role for the RNA helicases DDX5 and DDX17 in promoting viral transcriptional readthrough, which was, in turn, associated to HBV RNA destabilization and decreased HBx protein expression. RNA and chromatin immunoprecipitation, together with mutation of cPAS sequence, suggested a direct role of DDX5 and DDX17 in functionally linking cPAS recognition to transcriptional readthrough, HBV RNA stability and replication. CONCLUSIONS Our findings identify DDX5 and DDX17 as crucial determinants for HBV transcriptional fidelity and as host restriction factors for HBV replication. IMPACT AND IMPLICATIONS Hepatitis B virus (HBV) covalently closed circular (ccc)DNA degradation or functional inactivation remains the holy grail to be attained to achieve HBV cure. Transcriptional fidelity is a cornerstone in gene expression regulation. Here, we demonstrate that two helicases, DDX5 and DDX17, inhibit the recognition of HBV polyadenylation signal and transcriptional termination, thus decreasing HBV RNA stability and acting as restriction factors for efficient cccDNA transcription and viral replication. The observation that DDX5 and DDX17 are downregulated in HBV chronically infected patients suggests a role for the helicases in HBV persistence in vivo. These results open new perspectives for researchers aiming at identifying new targets to neutralise cccDNA transcription.
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Affiliation(s)
- Fleur Chapus
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon
| | - Guillaume Giraud
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France
| | - Pélagie Huchon
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon
| | - Mélanie Rodà
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France
| | - Xavier Grand
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France
| | - Caroline Charre
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon; Department of Virology, Croix Rousse Hospital, Hospices Civils de Lyon, Lyon, France
| | | | | | - Maria-Guadalupe Martinez
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon
| | - Judith Fresquet
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France
| | - Audrey Diederichs
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon
| | - Maëlle Locatelli
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon
| | - Hélène Polvèche
- CECS/AFM, I-Stem, Corbeil-Essonnes, 91100, France; University Claude Bernard of Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5239, INSERM U1293, Laboratory of Biology and Modelling of the Cell, 69007, Lyon, France
| | - Caroline Scholtès
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon; Department of Virology, Croix Rousse Hospital, Hospices Civils de Lyon, Lyon, France
| | - Isabelle Chemin
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France
| | | | - Michel Rivoire
- Centre Léon Bérard (CLB), INSERM U1032, 69008, Lyon, France
| | - Cyril F Bourgeois
- University Claude Bernard of Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5239, INSERM U1293, Laboratory of Biology and Modelling of the Cell, 69007, Lyon, France
| | - Fabien Zoulim
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France; University of Lyon, UMR_S1052, CRCL, 69008 Lyon; Department of Hepatology, Hospices Civils de Lyon, France.
| | - Barbara Testoni
- INSERM U1052- Cancer Research Center of Lyon (CRCL), 69008 Lyon, France.
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Polenkowski M, Allister AB, Burbano de Lara S, Pierce A, Geary B, El Bounkari O, Wiehlmann L, Hoffmann A, Whetton AD, Tamura T, Tran DDH. THOC5 complexes with DDX5, DDX17, and CDK12 to regulate R loop structures and transcription elongation rate. iScience 2022; 26:105784. [PMID: 36590164 PMCID: PMC9800341 DOI: 10.1016/j.isci.2022.105784] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/10/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
THOC5, a member of the THO complex, is essential for the 3'processing of some inducible genes, the export of a subset of mRNAs and stem cell survival. Here we show that THOC5 depletion results in altered 3'cleavage of >50% of mRNAs and changes in RNA polymerase II binding across genes. THOC5 is recruited close to high-density polymerase II sites, suggesting that THOC5 is involved in transcriptional elongation. Indeed, measurement of elongation rates in vivo demonstrated decreased rates in THOC5-depleted cells. Furthermore, THOC5 is preferentially recruited to its target genes in slow polymerase II cells compared with fast polymerase II cells. Importantly chromatin-associated THOC5 interacts with CDK12 (a modulator of transcription elongation) and RNA helicases DDX5, DDX17, and THOC6 only in slow polymerase II cells. The CDK12/THOC5 interaction promotes CDK12 recruitment to R-loops in a THOC6-dependent manner. These data demonstrate a novel function of THOC5 in transcription elongation.
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Affiliation(s)
- Mareike Polenkowski
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | - Aldrige Bernardus Allister
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Humangenetik, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | | | - Andrew Pierce
- Stem Cell and Leukemia Protoemics Laboratory, University of Manchester, Manchester M20 3LJ, UK
| | - Bethany Geary
- Stem Cell and Leukemia Protoemics Laboratory, University of Manchester, Manchester M20 3LJ, UK
| | - Omar El Bounkari
- Institute for Stroke and Dementia Research, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Lutz Wiehlmann
- Pädiatrische Pneumologie Hannover Medical School, Hannover D-30623, Germany
| | - Andrea Hoffmann
- Department of Orthopedic Surgery, Hannover Medical School, Hannover D-30623, Germany
| | - Anthony D. Whetton
- Stoller Biomarker Discovery Centre, University of Manchester, Manchester M13 9PL, UK
| | - Teruko Tamura
- Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | - Doan Duy Hai Tran
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany,Corresponding author
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Terrone S, Valat J, Fontrodona N, Giraud G, Claude JB, Combe E, Lapendry A, Polvèche H, Ameur LB, Duvermy A, Modolo L, Bernard P, Mortreux F, Auboeuf D, Bourgeois C. RNA helicase-dependent gene looping impacts messenger RNA processing. Nucleic Acids Res 2022; 50:9226-9246. [PMID: 36039747 PMCID: PMC9458439 DOI: 10.1093/nar/gkac717] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022] Open
Abstract
DDX5 and DDX17 are DEAD-box RNA helicase paralogs which regulate several aspects of gene expression, especially transcription and splicing, through incompletely understood mechanisms. A transcriptome analysis of DDX5/DDX17-depleted human cells confirmed the large impact of these RNA helicases on splicing and revealed a widespread deregulation of 3' end processing. In silico analyses and experiments in cultured cells showed the binding and functional contribution of the genome organizing factor CTCF to chromatin sites at or near a subset of DDX5/DDX17-dependent exons that are characterized by a high GC content and a high density of RNA Polymerase II. We propose the existence of an RNA helicase-dependent relationship between CTCF and the dynamics of transcription across DNA and/or RNA structured regions, that contributes to the processing of internal and terminal exons. Moreover, local DDX5/DDX17-dependent chromatin loops spatially connect RNA helicase-regulated exons with their cognate promoter, and we provide the first direct evidence that de novo gene looping modifies alternative splicing and polyadenylation. Overall our findings uncover the impact of DDX5/DDX17-dependent chromatin folding on pre-messenger RNA processing.
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Affiliation(s)
| | | | - Nicolas Fontrodona
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | | | - Jean-Baptiste Claude
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | | | - Audrey Lapendry
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Hélène Polvèche
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France,CECS/AFM, I-STEM, 28 rue Henri Desbruères, F-91100, Corbeil-Essonnes, France
| | - Lamya Ben Ameur
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Arnaud Duvermy
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Laurent Modolo
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Pascal Bernard
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Franck Mortreux
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 allee d'Italie, F-69364 Lyon, France
| | - Cyril F Bourgeois
- To whom correspondence should be addressed. Tel: +33 47272 8663; Fax: +33 47272 8674;
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Sharma M, Wente SR. Nucleocytoplasmic shuttling of Gle1 impacts DDX1 at transcription termination sites. Mol Biol Cell 2020; 31:2398-2408. [PMID: 32755435 PMCID: PMC7851961 DOI: 10.1091/mbc.e20-03-0215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Gle1 is a nucleocytoplasmic shuttling protein with well-documented cytoplasmic roles as a modulator of ATP-dependent DEAD-box RNA helicases involved in messenger (m)RNA export, translation initiation and termination, and stress granule dynamics. Here, we identify a novel nuclear role for Gle1 during transcription termination. In HeLa cells treated with a peptide that disrupts Gle1 nucleocytoplasmic shuttling, we detected nuclear accumulation of specific mRNAs with elongated 3′-UTR (untranslated region). Enriched mRNAs were nascently transcribed and accumulated in the nucleus due to a change in transcription state and not due to altered nuclear export. Whereas Gle1 shuttling inhibition did not appear to perturb nuclear DDX19 functions, it did result in increased DDX1 nucleoplasmic localization and decreased DDX1 interactions with Gle1 and the pre-mRNA cleavage stimulation factor CstF-64. An increase in nuclear R-loop signal intensity was also observed with diminished Gle1 shuttling, as well as colocalization of Gle1 at R-loops. Taken together, these studies reveal a nuclear role for Gle1 in coordinating DDX1 function in transcription termination complexes.
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Affiliation(s)
- Manisha Sharma
- Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, TN 37240
| | - Susan R Wente
- Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, TN 37240
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Katahira J, Senokuchi K, Hieda M. Human THO maintains the stability of repetitive DNA. Genes Cells 2020; 25:334-342. [PMID: 32065701 DOI: 10.1111/gtc.12760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/31/2023]
Abstract
The evolutionarily conserved multiprotein complex THO/TREX is required for pre-mRNA processing, mRNA export and the maintenance of genome stability. In this study, we analyzed the genome-wide distribution of human THOC7, a component of human THO, by chromatin immunoprecipitation sequencing. The analysis revealed that human THOC7 occupies repetitive sequences, which include microsatellite repeats in genic and intergenic regions and telomeric repeats. The majority of the THOC7 ChIP peaks overlapped with those of the elongating form of RNA polymerase II and R-loops, indicating that THOC7 accumulates in transcriptionally active repeat regions. Knocking down THOC5, an RNA-binding component of human THO, by siRNA induced the accumulation of γH2AX in the repeat regions. We also observed an aberration in the telomeres in the THOC5-depleted condition. These results suggest that human THO restrains the transcription-associated instability of repeat regions in the human genome.
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Affiliation(s)
- Jun Katahira
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Kohei Senokuchi
- Laboratory of Cellular and Molecular Biology, Department of Veterinary Sciences, Osaka Prefecture University, Izumisano, Japan
| | - Miki Hieda
- Graduate School of Health Sciences, Ehime Prefectural University of Health Sciences, Iyo-gun, Japan
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