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Li R, Sklutuis R, Groebner JL, Romerio F. HIV-1 Natural Antisense Transcription and Its Role in Viral Persistence. Viruses 2021; 13:v13050795. [PMID: 33946840 PMCID: PMC8145503 DOI: 10.3390/v13050795] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
Natural antisense transcripts (NATs) represent a class of RNA molecules that are transcribed from the opposite strand of a protein-coding gene, and that have the ability to regulate the expression of their cognate protein-coding gene via multiple mechanisms. NATs have been described in many prokaryotic and eukaryotic systems, as well as in the viruses that infect them. The human immunodeficiency virus (HIV-1) is no exception, and produces one or more NAT from a promoter within the 3’ long terminal repeat. HIV-1 antisense transcripts have been the focus of several studies spanning over 30 years. However, a complete appreciation of the role that these transcripts play in the virus lifecycle is still lacking. In this review, we cover the current knowledge about HIV-1 NATs, discuss some of the questions that are still open and identify possible areas of future research.
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Affiliation(s)
- Rui Li
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
| | - Rachel Sklutuis
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Jennifer L. Groebner
- HIV Dynamics and Replication Program, Host-Virus Interaction Branch, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA; (R.S.); (J.L.G.)
| | - Fabio Romerio
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA;
- Correspondence:
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Mutzel V, Okamoto I, Dunkel I, Saitou M, Giorgetti L, Heard E, Schulz EG. A symmetric toggle switch explains the onset of random X inactivation in different mammals. Nat Struct Mol Biol 2019; 26:350-360. [PMID: 30962582 PMCID: PMC6558282 DOI: 10.1038/s41594-019-0214-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/07/2019] [Indexed: 12/31/2022]
Abstract
Gene-regulatory networks control establishment and maintenance of alternative gene expression states during development. A particular challenge is the acquisition of opposing states by two copies of the same gene, as it is the case in mammals for Xist at the onset of random X-chromosome inactivation (XCI). The regulatory principles that lead to stable mono-allelic expression of Xist remain unknown. Here, we uncovered the minimal Xist regulatory network, by combining mathematical modeling and experimental validation of central model predictions. We identified a symmetric toggle switch as the basis for random mono-allelic Xist up-regulation, which reproduces data from several mutant, aneuploid and polyploid murine cell lines with various Xist expression patterns. Moreover, this toggle switch explains the diversity of strategies employed by different species at the onset of XCI. In addition to providing a unifying conceptual framework to explore X-chromosome inactivation across mammals, our study sets the stage for identifying the molecular mechanisms required to initiate random XCI.
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Affiliation(s)
- Verena Mutzel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ikuhiro Okamoto
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Japan Science and Technology (JST), Exploratory Research for Advanced Technology (ERATO), Kyoto, Japan
| | - Ilona Dunkel
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.,Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Edith Heard
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France.,European Molecular Biology Laboratory (EMBL), Directors' research unit, Heidelberg, Germany
| | - Edda G Schulz
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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Anguera MC, Sun BK, Xu N, Lee JT. X-chromosome kiss and tell: how the Xs go their separate ways. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:429-37. [PMID: 17381325 DOI: 10.1101/sqb.2006.71.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Loci associated with noncoding RNAs have important roles in X-chromosome inactivation (XCI), the dosage compensation mechanism by which one of two X chromosomes in female cells becomes transcriptionally silenced. The Xs start out as epigenetically equivalent chromosomes, but XCI requires a cell to treat two identical X chromosomes in completely different ways: One X chromosome must remain transcriptionally active while the other becomes repressed. In the embryo of eutherian mammals, the choice to inactivate the maternal or paternal X chromosome is random. The fact that the Xs always adopt opposite fates hints at the existence of a trans-sensing mechanism to ensure the mutually exclusive silencing of one of the two Xs. This paper highlights recent evidence supporting a model for mutually exclusive choice that involves homologous chromosome pairing and the placement of asymmetric chromatin marks on the two Xs.
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Affiliation(s)
- M C Anguera
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
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Tufarelli C. The silence RNA keeps: cis mechanisms of RNA mediated epigenetic silencing in mammals. Philos Trans R Soc Lond B Biol Sci 2006; 361:67-79. [PMID: 16553309 PMCID: PMC1626536 DOI: 10.1098/rstb.2005.1732] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
One of the fundamental questions of modern biology is to unravel how genes are switched on and off at the right time and in the correct tissues. It is well recognized that gene regulation depends on a dynamic balance between activating and repressing forces, and multiple mechanisms are involved in both gene silencing and activation. Work over the last decade has revealed that in some cases transcriptional silencing of specific genes is mediated by RNAs that specifically recruit repressing complexes to homologous DNA sequences. Examples of both cis and trans RNA driven transcriptional silencing have been reported. This review focuses on those examples of transcriptional gene silencing in which the RNA component seems to act uniquely in cis. Speculative models of how such cis acting transcripts may trigger transcriptional silencing are proposed. Future experimental testing of these and other mechanisms is important to gain a fuller understanding of how genes are regulated and to identify instances in which such mechanisms are defective, leading to disease. Understanding the basic molecular basis of these phenomena will provide us with invaluable tools for the future development of targeted therapies and drugs for those diseases in which they are faulty.
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Affiliation(s)
- Cristina Tufarelli
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK.
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Osato N, Yamada H, Satoh K, Ooka H, Yamamoto M, Suzuki K, Kawai J, Carninci P, Ohtomo Y, Murakami K, Matsubara K, Kikuchi S, Hayashizaki Y. Antisense transcripts with rice full-length cDNAs. Genome Biol 2003; 5:R5. [PMID: 14709177 PMCID: PMC395737 DOI: 10.1186/gb-2003-5-1-r5] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2003] [Revised: 10/22/2003] [Accepted: 11/07/2003] [Indexed: 11/29/2022] Open
Abstract
In this study, 687 sense-antisense transcript pairs from 32,127 full-length rice cDNA sequences were identified by aligning the cDNA sequences with rice genome sequences. The large number of pairs suggests that gene regulation by antisense transcripts occurs in plants and not only in animals. Background Natural antisense transcripts control gene expression through post-transcriptional gene silencing by annealing to the complementary sequence of the sense transcript. Because many genome and mRNA sequences have become available recently, genome-wide searches for sense-antisense transcripts have been reported, but few plant sense-antisense transcript pairs have been studied. The Rice Full-Length cDNA Sequencing Project has enabled computational searching of a large number of plant sense-antisense transcript pairs. Results We identified sense-antisense transcript pairs from 32,127 full-length rice cDNA sequences produced by this project and public rice mRNA sequences by aligning the cDNA sequences with rice genome sequences. We discovered 687 bidirectional transcript pairs in rice, including sense-antisense transcript pairs. Both sense and antisense strands of 342 pairs (50%) showed homology to at least one expressed sequence tag other than that of the pair. Microarray analysis showed 82 pairs (32%) out of 258 pairs on the microarray were more highly expressed than the median expression intensity of 21,938 rice transcriptional units. Both sense and antisense strands of 594 pairs (86%) had coding potential. Conclusions The large number of plant sense-antisense transcript pairs suggests that gene regulation by antisense transcripts occurs in plants and not only in animals. On the basis of our results, experiments should be carried out to analyze the function of plant antisense transcripts.
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MESH Headings
- DNA, Antisense/chemistry
- DNA, Antisense/classification
- DNA, Antisense/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/classification
- DNA, Complementary/genetics
- DNA, Plant/chemistry
- DNA, Plant/classification
- DNA, Plant/genetics
- Gene Expression Profiling/methods
- Gene Expression Regulation, Plant/genetics
- Oligonucleotide Array Sequence Analysis/methods
- Oryza/genetics
- RNA Interference/physiology
- RNA, Antisense/classification
- RNA, Antisense/genetics
- RNA, Messenger/chemistry
- RNA, Messenger/classification
- RNA, Messenger/genetics
- RNA, Plant/chemistry
- RNA, Plant/classification
- RNA, Plant/genetics
- Sequence Homology, Nucleic Acid
- Transcription, Genetic/physiology
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Affiliation(s)
- Naoki Osato
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045
| | - Hitomi Yamada
- Department of Molecular Biology, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan 305-8602
| | - Kouji Satoh
- Department of Molecular Biology, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan 305-8602
| | - Hisako Ooka
- Department of Molecular Biology, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan 305-8602
| | - Makoto Yamamoto
- Hitachi Software Engineering Company Ltd, Naka-ku, Yokohama, Kanagawa, Japan 231-0015
| | - Kohji Suzuki
- Hitachi Software Engineering Company Ltd, Naka-ku, Yokohama, Kanagawa, Japan 231-0015
| | - Jun Kawai
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045
- Genome Science Laboratory, RIKEN Wako Main Campus, Wako, Saitama, Japan 351-0198
| | - Piero Carninci
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045
- Genome Science Laboratory, RIKEN Wako Main Campus, Wako, Saitama, Japan 351-0198
| | - Yasuhiro Ohtomo
- Laboratory of Genome Sequencing and Analysis Group, Foundation of Advancement of International Science (FAIS), Tsukuba, Ibaraki, Japan 305-0062
| | - Kazuo Murakami
- Laboratory of Genome Sequencing and Analysis Group, Foundation of Advancement of International Science (FAIS), Tsukuba, Ibaraki, Japan 305-0062
| | - Kenichi Matsubara
- Laboratory of Genome Sequencing and Analysis Group, Foundation of Advancement of International Science (FAIS), Tsukuba, Ibaraki, Japan 305-0062
| | - Shoshi Kikuchi
- Department of Molecular Biology, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki, Japan 305-8602
| | - Yoshihide Hayashizaki
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Science Center (GSC), RIKEN Yokohama Institute, Tsurumi-ku, Yokohama, Kanagawa, Japan 230-0045
- Genome Science Laboratory, RIKEN Wako Main Campus, Wako, Saitama, Japan 351-0198
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Abstract
X-chromosome inactivation leads to divergent fates for two homologous chromosomes. Whether one X remains active or becomes silenced depends on the activity of Xist, a gene expressed only from the inactive X and whose RNA product 'paints' the X in cis. Recent work argues that Xist RNA itself is the acting agent for initiating the silencing step. Xist RNA contains separable domains for RNA localization and chromosome silencing. While no Xist RNA-interacting factors have been identified, a growing collection of chromatin alterations have been identified on the inactive X, including variant histone H2A composition and histone H3 methylation. Some or all of these changes may be critical for chromosome-wide silencing. As none of the silencing proteins identified so far is unique to X chromosome inactivation, the specificity must partly reside in Xist RNA whose spread along the X orchestrates general silencing factors for this specific task.
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Affiliation(s)
- Dena E Cohen
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, Massachusetts 02114, USA
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