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Khan M, Hou S, Chen M, Lei H. Mechanisms of RNA export and nuclear retention. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1755. [PMID: 35978483 DOI: 10.1002/wrna.1755] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/21/2022] [Accepted: 07/06/2022] [Indexed: 05/13/2023]
Abstract
With the identification of huge amount of noncoding RNAs in recent years, the concept of RNA localization has extended from traditional mRNA export to RNA export of mRNA and ncRNA as well as nuclear retention of ncRNA. This review aims to summarize the recent findings from studies on the mechanisms of export of different RNAs and nuclear retention of some lncRNAs in higher eukaryotes, with a focus on splicing-dependent TREX recruitment for the export of spliced mRNA and the sequence-dependent mechanism of mRNA export in the absence of splicing. In addition, evidence to support the involvement of m6 A modification in RNA export with the coordination between the methylase complex and TREX complex as well as sequence-dependent nuclear retention of lncRNA is recapitulated. Finally, a model of sequence-dependent RNA localization is proposed along with the many questions that remain to be answered. This article is categorized under: RNA Export and Localization > RNA Localization RNA Export and Localization > Nuclear Export/Import.
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Affiliation(s)
- Misbah Khan
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Shuai Hou
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Mo Chen
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Haixin Lei
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
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Kremsdorf D, Lekbaby B, Bablon P, Sotty J, Augustin J, Schnuriger A, Pol J, Soussan P. Alternative splicing of viral transcripts: the dark side of HBV. Gut 2021; 70:2373-2382. [PMID: 34535538 DOI: 10.1136/gutjnl-2021-324554] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 09/06/2021] [Indexed: 02/06/2023]
Abstract
Regulation of alternative splicing is one of the most efficient mechanisms to enlarge the proteomic diversity in eukaryotic organisms. Many viruses hijack the splicing machinery following infection to accomplish their replication cycle. Regarding the HBV, numerous reports have described alternative splicing events of the long viral transcript (pregenomic RNA), which also acts as a template for viral genome replication. Alternative splicing of HBV pregenomic RNAs allows the synthesis of at least 20 spliced variants. In addition, almost all these spliced forms give rise to defective particles, detected in the blood of infected patients. HBV-spliced RNAs have long been unconsidered, probably due to their uneasy detection in comparison to unspliced forms as well as for their dispensable role during viral replication. However, recent data highlighted the relevance of these HBV-spliced variants through (1) the trans-regulation of the alternative splicing of viral transcripts along the course of liver disease; (2) the ability to generate defective particle formation, putative biomarker of the liver disease progression; (3) modulation of viral replication; and (4) their intrinsic propensity to encode for novel viral proteins involved in liver pathogenesis and immune response. Altogether, tricky regulation of HBV alternative splicing may contribute to modulate multiple viral and cellular processes all along the course of HBV-related liver disease.
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Affiliation(s)
- Dina Kremsdorf
- Institut National de la Santé et de la Recherche Médicale U938, Centre de Recherche de Saint Antoine, Sorbonne Université-Faculté Saint Antoine, Paris, France
| | - Bouchra Lekbaby
- Institut National de la Santé et de la Recherche Médicale U938, Centre de Recherche de Saint Antoine, Sorbonne Université-Faculté Saint Antoine, Paris, France
| | - Pierre Bablon
- Institut National de la Santé et de la Recherche Médicale U938, Centre de Recherche de Saint Antoine, Sorbonne Université-Faculté Saint Antoine, Paris, France
| | - Jules Sotty
- Institut National de la Santé et de la Recherche Médicale U938, Centre de Recherche de Saint Antoine, Sorbonne Université-Faculté Saint Antoine, Paris, France
| | - Jérémy Augustin
- Institut National de la Santé et de la Recherche Médicale U938, Centre de Recherche de Saint Antoine, Sorbonne Université-Faculté Saint Antoine, Paris, France
| | - Aurélie Schnuriger
- Institut National de la Santé et de la Recherche Médicale U938, Centre de Recherche de Saint Antoine, Sorbonne Université-Faculté Saint Antoine, Paris, France.,Assistance Publique - Hôpitaux de Paris, Département de Virologie, GHU Paris-Est, Paris, France
| | - Jonathan Pol
- Institut National de la Santé et de la Recherche Médicale U1138, Centre de Recherche des Cordeliers, Université de Paris, Sorbonne Université, Paris, France.,Metabolomics ann Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France
| | - Patrick Soussan
- Institut National de la Santé et de la Recherche Médicale U938, Centre de Recherche de Saint Antoine, Sorbonne Université-Faculté Saint Antoine, Paris, France .,Assistance Publique - Hôpitaux de Paris, Département de Virologie, GHU Paris-Est, Paris, France
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Zhou T, Block T, Liu F, Kondratowicz AS, Sun L, Rawat S, Branson J, Guo F, Steuer HM, Liang H, Bailey L, Moore C, Wang X, Cuconatti A, Gao M, Lee ACH, Harasym T, Chiu T, Gotchev D, Dorsey B, Rijnbrand R, Sofia MJ. HBsAg mRNA degradation induced by a dihydroquinolizinone compound depends on the HBV posttranscriptional regulatory element. Antiviral Res 2017; 149:191-201. [PMID: 29133129 DOI: 10.1016/j.antiviral.2017.11.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/01/2017] [Accepted: 11/07/2017] [Indexed: 12/23/2022]
Abstract
In pursuit of novel therapeutics targeting the hepatitis B virus (HBV) infection, we evaluated a dihydroquinolizinone compound (DHQ-1) that in the nanomolar range reduced the production of virion and surface protein (HBsAg) in tissue culture. This compound also showed broad HBV genotype coverage, but was inactive against a panel of DNA and RNA viruses of other species. Oral administration of DHQ-1 in the AAV-HBV mouse model resulted in a significant reduction of serum HBsAg as soon as 4 days following the commencement of treatment. Reduction of HBV markers in both in vitro and in vivo experiments was related to the reduced amount of viral RNA including pre-genomic RNA (pgRNA) and 2.4/2.1 kb HBsAg mRNA. Nuclear run-on and subcellular fractionation experiments indicated that DHQ-1 mediated HBV RNA reduction was the result of accelerated viral RNA degradation in the nucleus, rather than the consequence of inhibition of transcription initiation. Through mutagenesis of HBsAg gene sequences, we found induction of HBsAg mRNA decay by DHQ-1 required the presence of the HBV posttranscriptional regulatory element (HPRE), with a 109 nucleotides sequence within the central region of the HPRE alpha sub-element being the most critical. Taken together, the current study shows that a small molecule can reduce the overall levels of HBV RNA, especially the HBsAg mRNA, and viral surface proteins. This may shed light on the development of a new class of HBV therapeutics.
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Affiliation(s)
- Tianlun Zhou
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States.
| | - Timothy Block
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Fei Liu
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Andrew S Kondratowicz
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Liren Sun
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Siddhartha Rawat
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Jeffrey Branson
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Fang Guo
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | | | - Hongyan Liang
- Baruch S. Blumberg Institute, Department of Translational Medicine, Doylestown, PA 18902, United States
| | - Lauren Bailey
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Chris Moore
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Xiaohe Wang
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Andy Cuconatti
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Min Gao
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Amy C H Lee
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Troy Harasym
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Tim Chiu
- Arbutus BioPharma, 100 - 8900 Glenlyon Parkway, Burnaby, British Columbia V5J 5J8, Canada
| | - Dimitar Gotchev
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Bruce Dorsey
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Rene Rijnbrand
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States
| | - Michael J Sofia
- Arbutus BioPharma, 701 Veterans Circle, Warminster, PA 18974, United States.
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Sun S, Nakashima K, Ito M, Li Y, Chida T, Takahashi H, Watashi K, Sawasaki T, Wakita T, Suzuki T. Involvement of PUF60 in Transcriptional and Post-transcriptional Regulation of Hepatitis B Virus Pregenomic RNA Expression. Sci Rep 2017; 7:12874. [PMID: 28993636 PMCID: PMC5634508 DOI: 10.1038/s41598-017-12497-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 09/11/2017] [Indexed: 02/06/2023] Open
Abstract
Here we identified PUF60, a splicing factor and a U2 small nuclear ribonucleoprotein auxiliary factor, as a versatile regulator of transcriptional and post-transcriptional steps in expression of hepatitis B virus (HBV) 3.5 kb, precore plus pregenomic RNA. We demonstrate that PUF60 is involved in: 1) up-regulation of core promoter activity through its interaction with transcription factor TCF7L2, 2) promotion of 3.5 kb RNA degradation and 3) suppression of 3.5 kb RNA splicing. When the 1.24-fold HBV genome was introduced into cells with the PUF60-expression plasmid, the 3.5 kb RNA level was higher at days 1–2 post-transfection but declined thereafter in PUF60-expressing cells compared to viral replication control cells. Deletion analyses showed that the second and first RNA recognition motifs (RRMs) within PUF60 are responsible for core promoter activation and RNA degradation, respectively. Expression of PUF60 mutant deleting the first RRM led to higher HBV production. To our knowledge, this is the first to identify a host factor involved in not only positively regulating viral gene expression but also negative regulation of the same viral life cycle. Functional linkage between transcriptional and post-transcriptional controls during viral replication might be involved in mechanisms for intracellular antiviral defense and viral persistence.
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Affiliation(s)
- Suofeng Sun
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka, 431-3192, Japan
| | - Kenji Nakashima
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka, 431-3192, Japan
| | - Masahiko Ito
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka, 431-3192, Japan
| | - Yuan Li
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka, 431-3192, Japan
| | - Takeshi Chida
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka, 431-3192, Japan
| | | | - Koichi Watashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | | | - Takaji Wakita
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Tetsuro Suzuki
- Department of Virology and Parasitology, Hamamatsu University School of Medicine, Shizuoka, 431-3192, Japan.
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Lim CS, Brown CM. Hepatitis B virus nuclear export elements: RNA stem-loop α and β, key parts of the HBV post-transcriptional regulatory element. RNA Biol 2016; 13:743-7. [PMID: 27031749 DOI: 10.1080/15476286.2016.1166330] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Many viruses contain RNA elements that modulate splicing and/or promote nuclear export of their RNAs. The RNAs of the major human pathogen, hepatitis B virus (HBV) contain a large (~600 bases) composite cis-acting 'post-transcriptional regulatory element' (PRE). This element promotes expression from these naturally intronless transcripts. Indeed, the related woodchuck hepadnavirus PRE (WPRE) is used to enhance expression in gene therapy and other expression vectors. These PRE are likely to act through a combination of mechanisms, including promotion of RNA nuclear export. Functional components of both the HBV PRE and WPRE are 2 conserved RNA cis-acting stem-loop (SL) structures, SLα and SLβ. They are within the coding regions of polymerase (P) gene, and both P and X genes, respectively. Based on previous studies using mutagenesis and/or nuclear magnetic resonance (NMR), here we propose 2 covariance models for SLα and SLβ. The model for the 30-nucleotide SLα contains a G-bulge and a CNGG(U) apical loop of which the first and the fourth loop residues form a CG pair and the fifth loop residue is bulged out, as observed in the NMR structure. The model for the 23-nucleotide SLβ contains a 7-base-pair stem and a 9-nucleotide loop. Comparison of the models with other RNA structural elements, as well as similarity searches of human transcriptome and viral genomes demonstrate that SLα and SLβ are specific to HBV transcripts. However, they are well conserved among the hepadnaviruses of non-human primates, the woodchuck and ground squirrel.
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Affiliation(s)
- Chun Shen Lim
- a Biochemistry and Genetics Otago , University of Otago , Dunedin , New Zealand
| | - Chris M Brown
- a Biochemistry and Genetics Otago , University of Otago , Dunedin , New Zealand
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