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Giraud G, El Achi K, Zoulim F, Testoni B. Co-Transcriptional Regulation of HBV Replication: RNA Quality Also Matters. Viruses 2024; 16:615. [PMID: 38675956 PMCID: PMC11053573 DOI: 10.3390/v16040615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Chronic hepatitis B (CHB) virus infection is a major public health burden and the leading cause of hepatocellular carcinoma. Despite the efficacy of current treatments, hepatitis B virus (HBV) cannot be fully eradicated due to the persistence of its minichromosome, or covalently closed circular DNA (cccDNA). The HBV community is investing large human and financial resources to develop new therapeutic strategies that either silence or ideally degrade cccDNA, to cure HBV completely or functionally. cccDNA transcription is considered to be the key step for HBV replication. Transcription not only influences the levels of viral RNA produced, but also directly impacts their quality, generating multiple variants. Growing evidence advocates for the role of the co-transcriptional regulation of HBV RNAs during CHB and viral replication, paving the way for the development of novel therapies targeting these processes. This review focuses on the mechanisms controlling the different co-transcriptional processes that HBV RNAs undergo, and their contribution to both viral replication and HBV-induced liver pathogenesis.
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Affiliation(s)
- Guillaume Giraud
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
| | - Khadija El Achi
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
| | - Fabien Zoulim
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
- Hospices Civils de Lyon, Hôpital Croix Rousse, Service d’Hépato-Gastroentérologie, 69004 Lyon, France
| | - Barbara Testoni
- INSERM U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université Claude Bernard Lyon 1, 69008 Lyon, France (F.Z.)
- The Lyon Hepatology Institute EVEREST, 69003 Lyon, France
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Yan AP, Salnikov PA, Gridina MM, Belokopytova PS, Fishman VS. Towards Development of the 4C-Based Method Detecting Interactions of Plasmid DNA with Host Genome. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:653-662. [PMID: 38831502 DOI: 10.1134/s0006297924040059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/01/2024] [Accepted: 03/02/2024] [Indexed: 06/05/2024]
Abstract
Chromosome conformation capture techniques have revolutionized our understanding of chromatin architecture and dynamics at the genome-wide scale. In recent years, these methods have been applied to a diverse array of species, revealing fundamental principles of chromosomal organization. However, structural organization of the extrachromosomal entities, like viral genomes or plasmids, and their interactions with the host genome, remain relatively underexplored. In this work, we introduce an enhanced 4C-protocol tailored for probing plasmid DNA interactions. We design specific plasmid vector and optimize protocol to allow high detection rate of contacts between the plasmid and host DNA.
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Affiliation(s)
- Alexandra P Yan
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Paul A Salnikov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Maria M Gridina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Polina S Belokopytova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Veniamin S Fishman
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
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Giraud G, Testoni B. [cccDNA phase separates in a G-quadruplex-dependent manner to facilitate its transcription and HBV replication]. Med Sci (Paris) 2024; 40:338-341. [PMID: 38651958 DOI: 10.1051/medsci/2024035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Affiliation(s)
- Guillaume Giraud
- Inserm U1052, CNRS UMR5286, Centre de recherche en cancérologie de Lyon, Institut d'hépatologie de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Barbara Testoni
- Inserm U1052, CNRS UMR5286, Centre de recherche en cancérologie de Lyon, Institut d'hépatologie de Lyon, Université Claude Bernard Lyon 1, Lyon, France
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Marie P, Bazire M, Ladet J, Ameur LB, Chahar S, Fontrodona N, Sexton T, Auboeuf D, Bourgeois CF, Mortreux F. Gene-to-gene coordinated regulation of transcription and alternative splicing by 3D chromatin remodeling upon NF-κB activation. Nucleic Acids Res 2024; 52:1527-1543. [PMID: 38272542 PMCID: PMC10899780 DOI: 10.1093/nar/gkae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
The NF-κB protein p65/RelA plays a pivotal role in coordinating gene expression in response to diverse stimuli, including viral infections. At the chromatin level, p65/RelA regulates gene transcription and alternative splicing through promoter enrichment and genomic exon occupancy, respectively. The intricate ways in which p65/RelA simultaneously governs these functions across various genes remain to be fully elucidated. In this study, we employed the HTLV-1 Tax oncoprotein, a potent activator of NF-κB, to investigate its influence on the three-dimensional organization of the genome, a key factor in gene regulation. We discovered that Tax restructures the 3D genomic landscape, bringing together genes based on their regulation and splicing patterns. Notably, we found that the Tax-induced gene-gene contact between the two master genes NFKBIA and RELA is associated with their respective changes in gene expression and alternative splicing. Through dCas9-mediated approaches, we demonstrated that NFKBIA-RELA interaction is required for alternative splicing regulation and is caused by an intragenic enrichment of p65/RelA on RELA. Our findings shed light on new regulatory mechanisms upon HTLV-1 Tax and underscore the integral role of p65/RelA in coordinated regulation of NF-κB-responsive genes at both transcriptional and splicing levels in the context of the 3D genome.
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Affiliation(s)
- Paul Marie
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Matéo Bazire
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Julien Ladet
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Lamya Ben Ameur
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Sanjay Chahar
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Nicolas Fontrodona
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Didier Auboeuf
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Cyril F Bourgeois
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
| | - Franck Mortreux
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, Laboratory of Biology and Modelling of the Cell, 46 Allée d’Italie Site Jacques Monod, F-69007 Lyon, France
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Liang W, Wang S, Wang H, Li X, Meng Q, Zhao Y, Zheng C. When 3D genome technology meets viral infection, including SARS-CoV-2. J Med Virol 2022; 94:5627-5639. [PMID: 35916043 PMCID: PMC9538846 DOI: 10.1002/jmv.28040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/09/2022] [Accepted: 07/30/2022] [Indexed: 01/06/2023]
Abstract
Mammalian chromosomes undergo varying degrees of compression to form three-dimensional genome structures. These three-dimensional structures undergo dynamic and precise chromatin interactions to achieve precise spatial and temporal regulation of gene expression. Most eukaryotic DNA viruses can invade their genomes into the nucleus. However, it is still poorly understood how the viral genome is precisely positioned after entering the host cell nucleus to find the most suitable location and whether it can specifically interact with the host genome to hijack the host transcriptional factories or even integrate into the host genome to complete its transcription and replication rapidly. Chromosome conformation capture technology can reveal long-range chromatin interactions between different chromosomal sites in the nucleus, potentially providing a reference for viral DNA-host chromatin interactions. This review summarized the research progress on the three-dimensional interaction between virus and host genome and the impact of virus integration into the host genome on gene transcription regulation, aiming to provide new insights into chromatin interaction and viral gene transcription regulation, laying the foundation for the treatment of infectious diseases.
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Affiliation(s)
- Weizheng Liang
- Central LaboratoryThe First Affiliated Hospital of Hebei North UniversityZhangjiakouChina
- Department of Immunology, School of Basic Medical SciencesFujian Medical UniversityFuzhouChina
| | - Shuangqing Wang
- Department of NeurologyShenzhen University General Hospital, Shenzhen UniversityShenzhen, Guangdong ProvinceChina
| | - Hao Wang
- Department of Obstetrics and GynecologyShenzhen University General HospitalShenzhen, GuangdongChina
| | - Xiushen Li
- Department of Obstetrics and GynecologyShenzhen University General HospitalShenzhen, GuangdongChina
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical EngineeringShenzhen University Health Science CenterShenzhen, GuangdongChina
- Shenzhen Key LaboratoryShenzhen University General HospitalShenzhen, GuangdongChina
| | - Qingxue Meng
- Central LaboratoryThe First Affiliated Hospital of Hebei North UniversityZhangjiakouChina
| | - Yan Zhao
- Department of Mathematics and Computer ScienceFree University BerlinBerlinGermany
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical SciencesFujian Medical UniversityFuzhouChina
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryAlbertaCanada
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
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Linden N, Jones RB. Potential multi-modal effects of provirus integration on HIV-1 persistence: lessons from other viruses. Trends Immunol 2022; 43:617-629. [PMID: 35817699 PMCID: PMC9429957 DOI: 10.1016/j.it.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/29/2022]
Abstract
Despite antiretroviral therapy (ART), HIV-1 persists as proviruses integrated into the genomic DNA of CD4+ T cells. The mechanisms underlying the persistence and clonal expansion of these cells remain incompletely understood. Cases have been described in which proviral integration can alter host gene expression to drive cellular proliferation. Here, we review observations from other genome-integrating human viruses to propose additional putative modalities by which HIV-1 integration may alter cellular function to favor persistence, such as by altering susceptibility to cytotoxicity in virus-expressing cells. We propose that signals implicating such mechanisms may have been masked thus far by the preponderance of defective and/or nonreactivatable HIV-1 proviruses, but could be revealed by focusing on the integration sites of intact proviruses with expression potential.
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Affiliation(s)
- Noemi Linden
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA.
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