101
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Park J, Kang M, Kim M. Unraveling the mechanistic features of RNA polymerase II termination by the 5'-3' exoribonuclease Rat1. Nucleic Acids Res 2015; 43:2625-37. [PMID: 25722373 PMCID: PMC4357727 DOI: 10.1093/nar/gkv133] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Within a complex with Rai1, the 5′-3′ exoribonuclease Rat1 promotes termination of RNA polymerase II (RNAPII) on protein-coding genes, but its underlying molecular mechanism is still poorly understood. Using in vitro transcription termination assays, we have found that RNAPII is prone to more effective termination by Rat1/Rai1 when its catalytic site is disrupted due to NTP misincorporation, implying that paused RNAPII, which is often found in vivo near termination sites, could adopt a similar configuration to Rat1/Rai1 and trigger termination. Intriguingly, yeast Rat1/Rai1 does not terminate Escherichia coli RNAP, implying that a specific interaction between Rat1/Rai1 and RNAPII may be required for termination. Furthermore, the efficiency of termination increases as the RNA transcript undergoing degradation by Rat1 gets longer, which suggests that Rat1 may generate a driving force for dissociating RNAPII from the template while degrading the nascent transcripts to catch up to the polymerase. These results indicate that multiple mechanistic features contribute to Rat1-mediated termination of RNAPII.
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Affiliation(s)
- Jieun Park
- Center for RNA Research, Institute for Basic Science and Department of Biophysics and Chemical Biology, Seoul National University, 1 Gwanak-Ro, Gwanakgu, Seoul, 151-742, South Korea
| | - Myungjin Kang
- Center for RNA Research, Institute for Basic Science and Department of Biophysics and Chemical Biology, Seoul National University, 1 Gwanak-Ro, Gwanakgu, Seoul, 151-742, South Korea
| | - Minkyu Kim
- Center for RNA Research, Institute for Basic Science and Department of Biophysics and Chemical Biology, Seoul National University, 1 Gwanak-Ro, Gwanakgu, Seoul, 151-742, South Korea
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102
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Porrua O, Libri D. Transcription termination and the control of the transcriptome: why, where and how to stop. Nat Rev Mol Cell Biol 2015; 16:190-202. [DOI: 10.1038/nrm3943] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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103
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Gehring AM, Santangelo TJ. Manipulating archaeal systems to permit analyses of transcription elongation-termination decisions in vitro. Methods Mol Biol 2015; 1276:263-79. [PMID: 25665569 DOI: 10.1007/978-1-4939-2392-2_15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcription elongation by multisubunit RNA polymerases (RNAPs) is processive, but neither uniform nor continuous. Regulatory events during elongation include pausing, backtracking, arrest, and transcription termination, and it is critical to determine whether the absence of continued synthesis is transient or permanent. Here we describe mechanisms to generate large quantities of stable archaeal elongation complexes on a solid support to permit (1) single-round transcription, (2) walking of RNAP to any defined template position, and (3) discrimination of transcripts that are associated with RNAP from those that are released to solution. This methodology is based on untagged proteins transcribing biotin- and digoxigenin-labeled DNA templates in association with paramagnetic particles.
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Affiliation(s)
- Alexandra M Gehring
- Department of Biochemistry and Molecular Biology, 383 MRB, Colorado State University, Fort Collins, CO, 80523, USA
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104
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Chen Y, Zhang L, Estarás C, Choi SH, Moreno L, Karn J, Moresco JJ, Yates JR, Jones KA. A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation. Genes Dev 2014; 28:2261-75. [PMID: 25319827 PMCID: PMC4201287 DOI: 10.1101/gad.250449.114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
HIV-1 Tat stimulates transcription elongation by recruiting the P-TEFb (positive transcription elongation factor-b) (CycT1:CDK9) C-terminal domain (CTD) kinase to the HIV-1 promoter. Here we show that Tat transactivation also requires the Ssu72 CTD Ser5P (S5P)-specific phosphatase, which mediates transcription termination and intragenic looping at eukaryotic genes. Importantly, HIV-1 Tat interacts directly with Ssu72 and strongly stimulates its CTD phosphatase activity. We found that Ssu72 is essential for Tat:P-TEFb-mediated phosphorylation of the S5P-CTD in vitro. Interestingly, Ssu72 also stimulates nascent HIV-1 transcription in a phosphatase-dependent manner in vivo. Chromatin immunoprecipitation (ChIP) experiments reveal that Ssu72, like P-TEFb and AFF4, is recruited by Tat to the integrated HIV-1 proviral promoter in TNF-α signaling 2D10 T cells and leaves the elongation complex prior to the termination site. ChIP-seq (ChIP combined with deep sequencing) and GRO-seq (genome-wide nuclear run-on [GRO] combined with deep sequencing) analysis further reveals that Ssu72 predominantly colocalizes with S5P-RNAPII (RNA polymerase II) at promoters in human embryonic stem cells, with a minor peak in the terminator region. A few genes, like NANOG, also have high Ssu72 at the terminator. Ssu72 is not required for transcription at most cellular genes but has a modest effect on cotranscriptional termination. We conclude that Tat alters the cellular function of Ssu72 to stimulate viral gene expression and facilitate the early S5P-S2P transition at the integrated HIV-1 promoter.
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Affiliation(s)
- Yupeng Chen
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Lirong Zhang
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Conchi Estarás
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Seung H Choi
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Luis Moreno
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
| | - James J Moresco
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - John R Yates
- Department of Chemical Physiology and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Katherine A Jones
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;
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105
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Stadelmayer B, Micas G, Gamot A, Martin P, Malirat N, Koval S, Raffel R, Sobhian B, Severac D, Rialle S, Parrinello H, Cuvier O, Benkirane M. Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes. Nat Commun 2014; 5:5531. [PMID: 25410209 PMCID: PMC4263189 DOI: 10.1038/ncomms6531] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 10/10/2014] [Indexed: 12/19/2022] Open
Abstract
RNA polymerase II (RNAPII) pausing/termination shortly after initiation is a hallmark of gene regulation. Here, we show that negative elongation factor (NELF) interacts with Integrator complex subunits (INTScom), RNAPII and Spt5. The interaction between NELF and INTScom subunits is RNA and DNA independent. Using both human immunodeficiency virus type 1 promoter and genome-wide analyses, we demonstrate that Integrator subunits specifically control NELF-mediated RNAPII pause/release at coding genes. The strength of RNAPII pausing is determined by the nature of the NELF-associated INTScom subunits. Interestingly, in addition to controlling RNAPII pause-release INTS11 catalytic subunit of the INTScom is required for RNAPII processivity. Finally, INTScom target genes are enriched in human immunodeficiency virus type 1 transactivation response element/NELF binding element and in a 3' box sequence required for small nuclear RNA biogenesis. Revealing these unexpected functions of INTScom in regulating RNAPII pause-release and completion of mRNA synthesis of NELF-target genes will contribute to our understanding of the gene expression cycle. RNA polymerase II (RNAPII) pausing at transcriptional start sites is an important element of gene transcription regulation. Here, the authors implicate the Integrator complex as a regulator of RNAPII pause-release and completion of mRNA synthesis at a subset of the negative elongation factor target genes.
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Affiliation(s)
- Bernd Stadelmayer
- 1] Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France [2] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [3] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France [4] IGF, MGX-Montpellier GenomiX, France
| | - Gaël Micas
- LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France
| | - Adrien Gamot
- LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France
| | - Pascal Martin
- 1] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [2] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France
| | - Nathalie Malirat
- Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France
| | - Slavik Koval
- Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France
| | - Raoul Raffel
- LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France
| | - Bijan Sobhian
- Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France
| | | | | | | | - Olivier Cuvier
- 1] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [2] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France [3] IGF, MGX-Montpellier GenomiX, France
| | - Monsef Benkirane
- 1] Institute of Human Genetics, CNRS UPR1142, Laboratory of Molecular Virology; MGX-Montpellier GenomiX, 141 rue de la Cardonille, Montpellier 34396, France [2] LBME-CNRS, Cell Cycle Chromatin Dynamics Laboratory. University Paul Sabatier, Toulouse 31061, France [3] INRA, TOXALIM (Research Centre in Food Toxicology), Toulouse 31300, France [4] IGF, MGX-Montpellier GenomiX, France
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106
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Lemay JF, Larochelle M, Marguerat S, Atkinson S, Bähler J, Bachand F. The RNA exosome promotes transcription termination of backtracked RNA polymerase II. Nat Struct Mol Biol 2014; 21:919-26. [DOI: 10.1038/nsmb.2893] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/26/2014] [Indexed: 11/09/2022]
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107
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Bernard MA, Zhao H, Yue SC, Anandaiah A, Koziel H, Tachado SD. Novel HIV-1 miRNAs stimulate TNFα release in human macrophages via TLR8 signaling pathway. PLoS One 2014; 9:e106006. [PMID: 25191859 PMCID: PMC4156304 DOI: 10.1371/journal.pone.0106006] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 07/25/2014] [Indexed: 12/11/2022] Open
Abstract
Purpose To determine whether HIV-1 produces microRNAs and elucidate whether these miRNAs can induce inflammatory response in macrophages (independent of the conventional miRNA function in RNA interference) leading to chronic immune activation. Methods Using sensitive quantitative Real Time RT-PCR and sequencing, we detected novel HIV-derived miRNAs in the sera of HIV+ persons, and associated with exosomes. Release of TNFα by macrophages challenged with HIV miRNAs was measured by ELISA. Results HIV infection of primary alveolar macrophages produced elevated levels of viral microRNAs vmiR88, vmiR99 and vmiR-TAR in cell extracts and in exosome preparations from conditioned medium. Furthermore, these miRNAs were also detected in exosome fraction of sera from HIV-infected persons. Importantly, vmiR88 and vmiR99 (but not vmiR-TAR) stimulated human macrophage TNFα release, which is dependent on macrophage TLR8 expression. These data support a potential role for HIV-derived vmiRNAs released from infected macrophages as contributing to chronic immune activation in HIV-infected persons, and may represent a novel therapeutic target to limit AIDS pathogenesis. Conclusion Novel HIV vmiR88 and vmiR99 are present in the systemic circulation of HIV+ persons and could exhibit biological function (independent of gene silencing) as ligands for TLR8 signaling that promote macrophage TNFα release, and may contribute to chronic immune activation. Targeting novel HIV-derived miRNAs may represent a therapeutic strategy to limit chronic immune activation and AIDS progression.
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Affiliation(s)
- Mark A. Bernard
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Hui Zhao
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Respiratory Medicine, The Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, PR China
| | - Simon C. Yue
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Asha Anandaiah
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Henry Koziel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Souvenir D. Tachado
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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108
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Vantaggiato C, Cantoni O, Guidarelli A, Romaniello R, Citterio A, Arrigoni F, Doneda C, Castelli M, Airoldi G, Bresolin N, Borgatti R, Bassi MT. Novel SETX variants in a patient with ataxia, neuropathy, and oculomotor apraxia are associated with normal sensitivity to oxidative DNA damaging agents. Brain Dev 2014; 36:682-9. [PMID: 24183476 DOI: 10.1016/j.braindev.2013.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Homozygous and compound heterozygous mutations in SETX are associated with AOA2 disease, a recessive form of ataxia with oculomotor apraxia and neuropathy with onset of ataxia between the first and second decade of life. The majority of the AOA2 mutated cell lines tested show hypersensitivity to oxidative DNA damaging agents, with one exception. RESULTS We describe a patient presenting with early-onset progressive ataxia, oculomotor apraxia, axonal sensory-motor neuropathy, optic atrophy, delayed psychomotor development, and a behavior disorder. The patient carries two novel missense variants in the SETX gene. Based on the hypothesis that the patient's clinical phenotype may represent an atypical form of the AOA2 disease, we tested the patient-derived cell line for hypersensitivity to oxidative DNA damaging agents, with negative results. CONCLUSIONS The lack of hypersensitivity we observed may be explained either by considering the atypical clinical picture of the patient analyzed or, alternatively, by hypothesizing that the variants detected are not the cause of the observed phenotype. Consistent with the first hypothesis of an atypical AOA2 form and based on the multiple functions of senataxin reported so far, it is likely that different sets of SETX mutations/variants may have variable functional effects that still need to be functionally characterized. The possibility that the severe and complicated clinical picture presented by the patient described here represents a clinical entity differing from the known recessive ataxias should be considered as well.
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Affiliation(s)
- Chiara Vantaggiato
- Scientific Institute IRCCS E. Medea, Laboratory of Molecular Biology, 23842 Bosisio Parini, Lecco, Italy
| | - Orazio Cantoni
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Andrea Guidarelli
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Romina Romaniello
- Scientific Institute IRCCS E. Medea, Neuropsychiatry and Neurorehabilitation Unit, Bosisio Parini, Lecco, Italy
| | - Andrea Citterio
- Scientific Institute IRCCS E. Medea, Laboratory of Molecular Biology, 23842 Bosisio Parini, Lecco, Italy
| | - Filippo Arrigoni
- Scientific Institute IRCCS E.Medea, Neuroimaging Unit, Bosisio Parini, Lecco, Italy
| | - Chiara Doneda
- Radiology and Pediatric Neuroradiology, Buzzi Hospital, Milan, Italy
| | - Marianna Castelli
- Scientific Institute IRCCS E. Medea, Laboratory of Molecular Biology, 23842 Bosisio Parini, Lecco, Italy
| | - Giovanni Airoldi
- Scientific Institute IRCCS E. Medea, Laboratory of Molecular Biology, 23842 Bosisio Parini, Lecco, Italy
| | - Nereo Bresolin
- Scientific Institute IRCCS E. Medea, Laboratory of Molecular Biology, 23842 Bosisio Parini, Lecco, Italy; Dino Ferrari Centre, IRCCS Ca' Granda, Ospedale Maggiore Policlinico Foundation, Department of Physiopathology and Transplantation, University of Milan, Italy
| | - Renato Borgatti
- Scientific Institute IRCCS E. Medea, Neuropsychiatry and Neurorehabilitation Unit, Bosisio Parini, Lecco, Italy
| | - Maria Teresa Bassi
- Scientific Institute IRCCS E. Medea, Laboratory of Molecular Biology, 23842 Bosisio Parini, Lecco, Italy.
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109
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Abstract
Eukaryotic mRNAs are extensively processed to generate functional transcripts, which are 5′ capped, spliced and 3′ polyadenylated. Accumulation of unprocessed (aberrant) mRNAs can be deleterious for the cell, hence processing fidelity is closely monitored by QC (quality control) mechanisms that identify erroneous transcripts and initiate their selective removal. Nucleases including Xrn2/Rat1 and the nuclear exosome have been shown to play an important role in the turnover of aberrant mRNAs. Recently, with the growing appreciation that mRNA processing occurs concomitantly with polII (RNA polymerase II) transcription, it has become evident that QC acts at the transcriptional level in addition to degrading aberrant RNAs. In the present review, we discuss mechanisms that allow cells to co-transcriptionally initiate the removal of RNAs as well as down-regulate transcription of transcripts where processing repeatedly fails.
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110
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A source of the single-stranded DNA substrate for activation-induced deaminase during somatic hypermutation. Nat Commun 2014; 5:4137. [PMID: 24923561 PMCID: PMC4154566 DOI: 10.1038/ncomms5137] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 05/16/2014] [Indexed: 11/08/2022] Open
Abstract
During somatic hypermutation (SHM), activation-induced deaminase (AID) mutates deoxycytidine on single-stranded DNA (ssDNA) generated by the transcription machinery, but the detailed mechanism remains unclear. Here we report a higher abundance of RNA polymerase II (Pol II) at the immunoglobulin heavy-chain variable (Igh-V) region compared with the constant region and partially transcribed Igh RNAs, suggesting a slower Pol II progression at Igh-V that could result in some early/premature transcription termination after prolonged pausing/stalling of Pol II. Knocking down RNA-exosome complexes, which could decrease premature transcription termination, leads to decreased SHM. Knocking down Spt5, which can augment premature transcription termination, leads to increase in both, SHM and the abundance of ssDNA substrates. Collectively, our data support the model that, following the reduction of Pol II progression (pausing or stalling) at the Igh-V, additional steps such as premature transcription termination are involved in providing ssDNA substrates for AID during SHM.
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111
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Liu H, Luo M, Wen JK. mRNA stability in the nucleus. J Zhejiang Univ Sci B 2014; 15:444-54. [PMID: 24793762 PMCID: PMC4076601 DOI: 10.1631/jzus.b1400088] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 04/11/2014] [Indexed: 01/15/2023]
Abstract
Eukaryotic gene expression is controlled by different levels of biological events, such as transcription factors regulating the timing and strength of transcripts production, alteration of transcription rate by RNA processing, and mRNA stability during RNA processing and translation. RNAs, especially mRNAs, are relatively vulnerable molecules in living cells for ribonucleases (RNases). The maintenance of quality and quantity of transcripts is a key issue for many biological processes. Extensive studies draw the conclusion that the stability of RNAs is dedicated-regulated, occurring co- and post-transcriptionally, and translation-coupled as well, either in the nucleus or cytoplasm. Recently, RNA stability in the nucleus has aroused much research interest, especially the stability of newly-made transcripts. In this article, we summarize recent progresses on mRNA stability in the nucleus, especially focusing on quality control of newly-made RNA by RNA polymerase II in eukaryotes.
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Affiliation(s)
- Han Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Min Luo
- Chongqing Institute of Tuberculosis Prevention and Treatment, Chongqing 400050, China
| | - Ji-kai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
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112
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Harwig A, Das AT, Berkhout B. Retroviral microRNAs. Curr Opin Virol 2014; 7:47-54. [PMID: 24769093 DOI: 10.1016/j.coviro.2014.03.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 03/22/2014] [Accepted: 03/26/2014] [Indexed: 12/18/2022]
Abstract
Eukaryotic cells and several DNA viruses encode miRNAs to regulate the expression of specific target genes. It has been controversial whether RNA viruses can encode such miRNAs as miRNA excision may lead to cleavage of the viral RNA genome. We will focus on the retrovirus family, HIV-1 in particular, and discuss the production of virus-encoded miRNAs and their putative function in the viral replication cycle. An intricate scenario of multi-layer virus-host interactions becomes apparent with small RNAs as the regulatory molecules.
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Affiliation(s)
- Alex Harwig
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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113
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Fogel BL, Cho E, Wahnich A, Gao F, Becherel OJ, Wang X, Fike F, Chen L, Criscuolo C, De Michele G, Filla A, Collins A, Hahn AF, Gatti RA, Konopka G, Perlman S, Lavin MF, Geschwind DH, Coppola G. Mutation of senataxin alters disease-specific transcriptional networks in patients with ataxia with oculomotor apraxia type 2. Hum Mol Genet 2014; 23:4758-69. [PMID: 24760770 DOI: 10.1093/hmg/ddu190] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Senataxin, encoded by the SETX gene, contributes to multiple aspects of gene expression, including transcription and RNA processing. Mutations in SETX cause the recessive disorder ataxia with oculomotor apraxia type 2 (AOA2) and a dominant juvenile form of amyotrophic lateral sclerosis (ALS4). To assess the functional role of senataxin in disease, we examined differential gene expression in AOA2 patient fibroblasts, identifying a core set of genes showing altered expression by microarray and RNA-sequencing. To determine whether AOA2 and ALS4 mutations differentially affect gene expression, we overexpressed disease-specific SETX mutations in senataxin-haploinsufficient fibroblasts and observed changes in distinct sets of genes. This implicates mutation-specific alterations of senataxin function in disease pathogenesis and provides a novel example of allelic neurogenetic disorders with differing gene expression profiles. Weighted gene co-expression network analysis (WGCNA) demonstrated these senataxin-associated genes to be involved in both mutation-specific and shared functional gene networks. To assess this in vivo, we performed gene expression analysis on peripheral blood from members of 12 different AOA2 families and identified an AOA2-specific transcriptional signature. WGCNA identified two gene modules highly enriched for this transcriptional signature in the peripheral blood of all AOA2 patients studied. These modules were disease-specific and preserved in patient fibroblasts and in the cerebellum of Setx knockout mice demonstrating conservation across species and cell types, including neurons. These results identify novel genes and cellular pathways related to senataxin function in normal and disease states, and implicate alterations in gene expression as underlying the phenotypic differences between AOA2 and ALS4.
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Affiliation(s)
- Brent L Fogel
- Program in Neurogenetics, Department of Neurology and
| | - Ellen Cho
- Program in Neurogenetics, Department of Neurology and
| | | | - Fuying Gao
- Department of Psychiatry, Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
| | - Olivier J Becherel
- Radiation Biology and Oncology Laboratory, University of Queensland, UQ Centre for Clinical Research, Herston, Australia
| | - Xizhe Wang
- Program in Neurogenetics, Department of Neurology and
| | | | - Leslie Chen
- Program in Neurogenetics, Department of Neurology and
| | - Chiara Criscuolo
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, Federico II University, Napoli, Italy
| | - Giuseppe De Michele
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, Federico II University, Napoli, Italy
| | - Alessandro Filla
- Department of Neuroscience and Reproductive and Odontostomatological Sciences, Federico II University, Napoli, Italy
| | - Abigail Collins
- Department of Pediatrics and Department of Neurology, Children's Hospital Colorado, University of Colorado, Denver, School of Medicine, Aurora, CO, USA
| | - Angelika F Hahn
- Department of Clinical Neurological Sciences, Western University, London, Ontario, Canada and
| | - Richard A Gatti
- Department of Pathology and Laboratory Medicine and Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
| | - Susan Perlman
- Program in Neurogenetics, Department of Neurology and
| | - Martin F Lavin
- Radiation Biology and Oncology Laboratory, University of Queensland, UQ Centre for Clinical Research, Herston, Australia
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology and Department of Psychiatry, Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Giovanni Coppola
- Program in Neurogenetics, Department of Neurology and Department of Psychiatry, Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
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114
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HIV-1 latency: an update of molecular mechanisms and therapeutic strategies. Viruses 2014; 6:1715-58. [PMID: 24736215 PMCID: PMC4014718 DOI: 10.3390/v6041715] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/18/2014] [Accepted: 03/20/2014] [Indexed: 02/06/2023] Open
Abstract
The major obstacle towards HIV-1 eradication is the life-long persistence of the virus in reservoirs of latently infected cells. In these cells the proviral DNA is integrated in the host’s genome but it does not actively replicate, becoming invisible to the host immune system and unaffected by existing antiviral drugs. Rebound of viremia and recovery of systemic infection that follows interruption of therapy, necessitates life-long treatments with problems of compliance, toxicity, and untenable costs, especially in developing countries where the infection hits worst. Extensive research efforts have led to the proposal and preliminary testing of several anti-latency compounds, however, overall, eradication strategies have had, so far, limited clinical success while posing several risks for patients. This review will briefly summarize the more recent advances in the elucidation of mechanisms that regulates the establishment/maintenance of latency and therapeutic strategies currently under evaluation in order to eradicate HIV persistence.
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Quality control of mRNP biogenesis: networking at the transcription site. Semin Cell Dev Biol 2014; 32:37-46. [PMID: 24713468 DOI: 10.1016/j.semcdb.2014.03.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 03/28/2014] [Indexed: 11/20/2022]
Abstract
Eukaryotic cells carry out quality control (QC) over the processes of RNA biogenesis to inactivate or eliminate defective transcripts, and to avoid their production. In the case of protein-coding transcripts, the quality controls can sense defects in the assembly of mRNA-protein complexes, in the processing of the precursor mRNAs, and in the sequence of open reading frames. Different types of defect are monitored by different specialized mechanisms. Some of them involve dedicated factors whose function is to identify faulty molecules and target them for degradation. Others are the result of a more subtle balance in the kinetics of opposing activities in the mRNA biogenesis pathway. One way or another, all such mechanisms hinder the expression of the defective mRNAs through processes as diverse as rapid degradation, nuclear retention and transcriptional silencing. Three major degradation systems are responsible for the destruction of the defective transcripts: the exosome, the 5'-3' exoribonucleases, and the nonsense-mediated mRNA decay (NMD) machinery. This review summarizes recent findings on the cotranscriptional quality control of mRNA biogenesis, and speculates that a protein-protein interaction network integrates multiple mRNA degradation systems with the transcription machinery.
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116
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Intestinal epithelial barrier disruption through altered mucosal microRNA expression in human immunodeficiency virus and simian immunodeficiency virus infections. J Virol 2014; 88:6268-80. [PMID: 24672033 DOI: 10.1128/jvi.00097-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED Epithelial barrier dysfunction during human immunodeficiency virus (HIV) infection has largely been attributed to the rapid and severe depletion of CD4(+) T cells in the gastrointestinal (GI) tract. Although it is known that changes in mucosal gene expression contribute to intestinal enteropathy, the role of small noncoding RNAs, specifically microRNA (miRNA), has not been investigated. Using the simian immunodeficiency virus (SIV)-infected nonhuman primate model of HIV pathogenesis, we investigated the effect of viral infection on miRNA expression in intestinal mucosa. SIV infection led to a striking decrease in the expression of mucosal miRNA compared to that in uninfected controls. This decrease coincided with an increase in 5'-3'-exoribonuclease 2 protein and alterations in DICER1 and Argonaute 2 expression. Targets of depleted miRNA belonged to molecular pathways involved in epithelial proliferation, differentiation, and immune response. Decreased expression of several miRNA involved in maintaining epithelial homeostasis in the gut was localized to the proliferative crypt region of the intestinal epithelium. Our findings suggest that SIV-induced decreased expression of miRNA involved in epithelial homeostasis, disrupted expression of miRNA biogenesis machinery, and increased expression of XRN2 are involved in the development of epithelial barrier dysfunction and gastroenteropathy. IMPORTANCE MicroRNA (miRNA) regulate the development and function of intestinal epithelial cells, and many viruses disrupt normal host miRNA expression. In this study, we demonstrate that SIV and HIV disrupt expression of miRNA in the small intestine during infection. The depletion of several key miRNA is localized to the proliferative crypt region of the gut epithelium. These miRNA are known to control expression of genes involved in inflammation, cell death, and epithelial maturation. Our data indicate that this disruption might be caused by altered expression of miRNA biogenesis machinery during infection. These findings suggest that the disruption of miRNA in the small intestine likely plays a role in intestinal enteropathy during HIV infection.
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Negative elongation factor is required for the maintenance of proviral latency but does not induce promoter-proximal pausing of RNA polymerase II on the HIV long terminal repeat. Mol Cell Biol 2014; 34:1911-28. [PMID: 24636995 DOI: 10.1128/mcb.01013-13] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The role of the negative elongation factor (NELF) in maintaining HIV latency was investigated following small hairpin RNA (shRNA) knockdown of the NELF-E subunit, a condition that induced high levels of proviral transcription in latently infected Jurkat T cells. Chromatin immunoprecipitation (ChIP) assays showed that latent proviruses accumulate RNA polymerase II (RNAP II) on the 5' long terminal repeat (LTR) but not on the 3' LTR. NELF colocalizes with RNAP II, and its level increases following proviral induction. RNAP II pause sites on the HIV provirus were mapped to high resolution by ChIP with high-throughput sequencing (ChIP-Seq). Like cellular promoters, RNAP II accumulates at around position +30, but HIV also shows additional pausing at +90, which is immediately downstream of a transactivation response (TAR) element and other distal sites on the HIV LTR. Following NELF-E knockdown or tumor necrosis factor alpha (TNF-α) stimulation, promoter-proximal RNAP II levels increase up to 3-fold, and there is a dramatic increase in RNAP II levels within the HIV genome. These data support a kinetic model for proviral transcription based on continuous replacement of paused RNAP II during both latency and productive transcription. In contrast to most cellular genes, HIV is highly activated by the combined effects of NELF-E depletion and activation of initiation by TNF-α, suggesting that opportunities exist to selectively activate latent HIV proviruses.
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118
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Heras SR, Macias S, Cáceres JF, Garcia-Perez JL. Control of mammalian retrotransposons by cellular RNA processing activities. Mob Genet Elements 2014; 4:e28439. [PMID: 25346866 PMCID: PMC4203495 DOI: 10.4161/mge.28439] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 03/02/2014] [Accepted: 03/05/2014] [Indexed: 01/27/2023] Open
Abstract
Retrotransposons make up roughly 50% of the mammalian genome and have played an important role in genome evolution. A small fraction of non-LTR retrotransposons, LINE-1 and SINE elements, is currently active in the human genome. These elements move in our genome using an intermediate RNA and a reverse transcriptase activity by a copy and paste mechanism. Their ongoing mobilization can impact the human genome leading to several human disorders. However, how the cell controls the activity of these elements minimizing their mutagenic effect is not fully understood. Recent studies have highlighted that the intermediate RNA of retrotransposons is a target of different mechanisms that limit the mobilization of endogenous retrotransposons in mammals. Here, we provide an overview of recent discoveries that show how RNA processing events can act to control the activity of mammalian retrotransposons and discuss several arising questions that remain to be answered.
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Affiliation(s)
- Sara R Heras
- GENYO; Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government; Granada, Spain
| | - Sara Macias
- Medical Research Council Human Genetics Unit; Institute of Genetics and Molecular Medicine; University of Edinburgh; Western General Hospital; Edinburgh, UK
| | - Javier F Cáceres
- Medical Research Council Human Genetics Unit; Institute of Genetics and Molecular Medicine; University of Edinburgh; Western General Hospital; Edinburgh, UK
| | - Jose L Garcia-Perez
- GENYO; Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government; Granada, Spain
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Morales JC, Richard P, Rommel A, Fattah FJ, Motea EA, Patidar PL, Xiao L, Leskov K, Wu SY, Hittelman WN, Chiang CM, Manley JL, Boothman DA. Kub5-Hera, the human Rtt103 homolog, plays dual functional roles in transcription termination and DNA repair. Nucleic Acids Res 2014; 42:4996-5006. [PMID: 24589584 PMCID: PMC4005673 DOI: 10.1093/nar/gku160] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Functions of Kub5-Hera (In Greek Mythology Hera controlled Artemis) (K-H), the human homolog of the yeast transcription termination factor Rtt103, remain undefined. Here, we show that K-H has functions in both transcription termination and DNA double-strand break (DSB) repair. K-H forms distinct protein complexes with factors that repair DSBs (e.g. Ku70, Ku86, Artemis) and terminate transcription (e.g. RNA polymerase II). K-H loss resulted in increased basal R-loop levels, DSBs, activated DNA-damage responses and enhanced genomic instability. Significantly lowered Artemis protein levels were detected in K-H knockdown cells, which were restored with specific K-H cDNA re-expression. K-H deficient cells were hypersensitive to cytotoxic agents that induce DSBs, unable to reseal complex DSB ends, and showed significantly delayed γ-H2AX and 53BP1 repair-related foci regression. Artemis re-expression in K-H-deficient cells restored DNA-repair function and resistance to DSB-inducing agents. However, R loops persisted consistent with dual roles of K-H in transcription termination and DSB repair.
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Affiliation(s)
- Julio C Morales
- Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390-8807, USA, Department of Biological Sciences, Columbia University, New York, NY 10027, USA, Laboratory of Genetics, Salk Institute of Biological Studies, La Jolla, CA 92037, USA, Department of Radiation Oncology, Case Western Reserve University, Cleveland, OH 44106, USA and Department of Experimental Therapeutics, M.D. Anderson Cancer Center, Houston, TX 77030, USA
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Mbonye U, Karn J. Transcriptional control of HIV latency: cellular signaling pathways, epigenetics, happenstance and the hope for a cure. Virology 2014; 454-455:328-39. [PMID: 24565118 DOI: 10.1016/j.virol.2014.02.008] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 01/23/2014] [Accepted: 02/07/2014] [Indexed: 02/06/2023]
Abstract
Replication-competent latent HIV-1 proviruses that persist in the genomes of a very small subset of resting memory T cells in infected individuals under life-long antiretroviral therapy present a major barrier towards viral eradication. Multiple molecular mechanisms are required to repress the viral trans-activating factor Tat and disrupt the regulatory Tat feedback circuit leading to the establishment of the latent viral reservoir. In particular, latency is due to a combination of transcriptional silencing of proviruses via host epigenetic mechanisms and restrictions on the expression of P-TEFb, an essential co-factor for Tat. Induction of latent proviruses in the presence of antiretroviral therapy is expected to enable clearance of latently infected cells by viral cytopathic effects and host antiviral immune responses. An in-depth comprehensive understanding of the molecular control of HIV-1 transcription should inform the development of optimal combinatorial reactivation strategies that are intended to purge the latent viral reservoir.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States.
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121
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Witwer KW, Hirschi KD. Transfer and functional consequences of dietary microRNAs in vertebrates: concepts in search of corroboration: negative results challenge the hypothesis that dietary xenomiRs cross the gut and regulate genes in ingesting vertebrates, but important questions persist. Bioessays 2014; 36:394-406. [PMID: 24436255 PMCID: PMC4109825 DOI: 10.1002/bies.201300150] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
If validated, diet-derived foreign microRNA absorption and function in consuming vertebrates would drastically alter our understanding of nutrition and ecology. RNA interference (RNAi) mechanisms of Caenorhabditis elegans are enhanced by uptake of environmental RNA and amplification and systemic distribution of RNAi effectors. Therapeutic exploitation of RNAi in treating human disease is difficult because these accessory processes are absent or diminished in most animals. A recent report challenged multiple paradigms, suggesting that ingested microRNAs (miRNAs) are transferred to blood, accumulate in tissues, and exert canonical regulation of endogenous transcripts. Independent replication of these findings has been elusive, and multiple disconfirmatory findings have been published. In the face of mounting negative results, any additional positive reports must provide the proverbial “extraordinary proof” to support such claims. In this article, we review the evidence for and against a significant role for dietary miRNAs in influencing gene expression, and make recommendations for future studies.
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Affiliation(s)
- Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University, Baltimore, MD, USA
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122
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Contreras X, Benkirane M, Kiernan R. Premature termination of transcription by RNAP II: the beginning of the end. Transcription 2013; 4:72-6. [PMID: 23714697 DOI: 10.4161/trns.24148] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Transcription elongation is now recognized as an important mechanism of gene regulation in eukaryotes. A large number of genes undergo an early step in transcription that is rate limiting for expression. Genome-wide studies showing that RNA polymerase II accumulates to high densities near the promoters of many genes has led to the idea that promoter-proximal pausing of transcription is a widespread, rate-limiting step in early elongation. Recent evidence suggests that much of this paused RNA polymerase II is competent for transcription elongation. Here, we discuss recent studies suggesting that RNA polymerase II that accumulates nearby the promoter of a subset of genes is undergoing premature termination of transcription.
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Affiliation(s)
- Xavier Contreras
- Institut de Génétique Humaine; CNRS UPR1142, Laboratoire de Régulation des Gènes, Montpellier, France
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123
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Gromak N, Dienstbier M, Macias S, Plass M, Eyras E, Cáceres JF, Proudfoot NJ. Drosha regulates gene expression independently of RNA cleavage function. Cell Rep 2013; 5:1499-510. [PMID: 24360955 PMCID: PMC3898267 DOI: 10.1016/j.celrep.2013.11.032] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 09/13/2013] [Accepted: 11/15/2013] [Indexed: 12/21/2022] Open
Abstract
Drosha is the main RNase III-like enzyme involved in the process of microRNA (miRNA) biogenesis in the nucleus. Using whole-genome ChIP-on-chip analysis, we demonstrate that, in addition to miRNA sequences, Drosha specifically binds promoter-proximal regions of many human genes in a transcription-dependent manner. This binding is not associated with miRNA production or RNA cleavage. Drosha knockdown in HeLa cells downregulated nascent gene transcription, resulting in a reduction of polyadenylated mRNA produced from these gene regions. Furthermore, we show that this function of Drosha is dependent on its N-terminal protein-interaction domain, which associates with the RNA-binding protein CBP80 and RNA Polymerase II. Consequently, we uncover a previously unsuspected RNA cleavage-independent function of Drosha in the regulation of human gene expression. Drosha binds promoter-proximal regions of transcribed human genes Drosha binding is not associated with RNA cleavage or miRNA processing Drosha regulates nascent gene transcription Drosha interacts with CBP80 and RNA Pol II through its N-terminal domain
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Affiliation(s)
- Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Martin Dienstbier
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Sara Macias
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Mireya Plass
- Computational Genomics Group, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain; The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Eduardo Eyras
- Computational Genomics Group, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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124
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Abstract
Different classes of RNA function in various cellular processes, and their biogenesis and turnover involve diverse RNases for processing and degradation. XRN2 is a 5'→3' exoribonuclease that is evolutionarily conserved in eukaryotes. It is predominantly localized in the nucleus and recognizes single-stranded RNA with a 5'-terminal monophosphate to degrade it processively to mononucleotides. In the present paper, we review functions of XRN2 and its cofactors in maturation, surveillance and activity control of several classes of RNA such as pre-mRNA (precursor mRNA), rRNA and snoRNA (small nucleolar RNA).
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125
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Tuck AC, Tollervey D. A transcriptome-wide atlas of RNP composition reveals diverse classes of mRNAs and lncRNAs. Cell 2013; 154:996-1009. [PMID: 23993093 PMCID: PMC3778888 DOI: 10.1016/j.cell.2013.07.047] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/25/2013] [Accepted: 07/31/2013] [Indexed: 01/30/2023]
Abstract
Eukaryotic genomes generate a heterogeneous ensemble of mRNAs and long noncoding RNAs (lncRNAs). LncRNAs and mRNAs are both transcribed by Pol II and acquire 5′ caps and poly(A) tails, but only mRNAs are translated into proteins. To address how these classes are distinguished, we identified the transcriptome-wide targets of 13 RNA processing, export, and turnover factors in budding yeast. Comparing the maturation pathways of mRNAs and lncRNAs revealed that transcript fate is largely determined during 3′ end formation. Most lncRNAs are targeted for nuclear RNA surveillance, but a subset with 3′ cleavage and polyadenylation features resembling the mRNA consensus can be exported to the cytoplasm. The Hrp1 and Nab2 proteins act at this decision point, with dual roles in mRNA cleavage/polyadenylation and lncRNA surveillance. Our data also reveal the dynamic and heterogeneous nature of mRNA maturation, and highlight a subset of “lncRNA-like” mRNAs regulated by the nuclear surveillance machinery. Transcriptome-wide analysis shows dynamic assembly of ribonucleoprotein particles LncRNA and mRNA subclasses undergo distinct maturation and turnover pathways Transcript fate is determined during 3′ end formation Transcript classes overlap, with many “mRNA-like” lncRNAs and “lncRNA-like” mRNAs
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Affiliation(s)
- Alex Charles Tuck
- The University of Edinburgh, Wellcome Trust Centre for Cell Biology, Michael Swann Building, Kings Buildings, Edinburgh EH9 3JR, UK
| | - David Tollervey
- The University of Edinburgh, Wellcome Trust Centre for Cell Biology, Michael Swann Building, Kings Buildings, Edinburgh EH9 3JR, UK.
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126
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Bennett CL, Chen Y, Vignali M, Lo RS, Mason AG, Unal A, Huq Saifee NP, Fields S, La Spada AR. Protein interaction analysis of senataxin and the ALS4 L389S mutant yields insights into senataxin post-translational modification and uncovers mutant-specific binding with a brain cytoplasmic RNA-encoded peptide. PLoS One 2013; 8:e78837. [PMID: 24244371 PMCID: PMC3823977 DOI: 10.1371/journal.pone.0078837] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/24/2013] [Indexed: 12/12/2022] Open
Abstract
Senataxin is a large 303 kDa protein linked to neuron survival, as recessive mutations cause Ataxia with Oculomotor Apraxia type 2 (AOA2), and dominant mutations cause amyotrophic lateral sclerosis type 4 (ALS4). Senataxin contains an amino-terminal protein-interaction domain and a carboxy-terminal DNA/RNA helicase domain. In this study, we focused upon the common ALS4 mutation, L389S, by performing yeast two-hybrid screens of a human brain expression library with control senataxin or L389S senataxin as bait. Interacting clones identified from the two screens were collated, and redundant hits and false positives subtracted to yield a set of 13 protein interactors. Among these hits, we discovered a highly specific and reproducible interaction of L389S senataxin with a peptide encoded by the antisense sequence of a brain-specific non-coding RNA, known as BCYRN1. We further found that L389S senataxin interacts with other proteins containing regions of conserved homology with the BCYRN1 reverse complement-encoded peptide, suggesting that such aberrant protein interactions may contribute to L389S ALS4 disease pathogenesis. As the yeast two-hybrid screen also demonstrated senataxin self-association, we confirmed senataxin dimerization via its amino-terminal binding domain and determined that the L389S mutation does not abrogate senataxin self-association. Finally, based upon detection of interactions between senataxin and ubiquitin-SUMO pathway modification enzymes, we examined senataxin for the presence of ubiquitin and SUMO monomers, and observed this post-translational modification. Our senataxin protein interaction study reveals a number of features of senataxin biology that shed light on senataxin normal function and likely on senataxin molecular pathology in ALS4.
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Affiliation(s)
- Craig L. Bennett
- Comparative Genomics Centre, School of Pharmacy and Molecular Sciences, James Cook University, Townsville, Queensland, Australia
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Yingzhang Chen
- Department of Pediatrics, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Marissa Vignali
- Department of Genome Sciences, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Russell S. Lo
- Department of Genome Sciences, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Amanda G. Mason
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Asli Unal
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Nabiha P. Huq Saifee
- Department of Pharmacology, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Stanley Fields
- Department of Genome Sciences, University of Washington Medical Center, Seattle, Washington, United States of America
| | - Albert R. La Spada
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
- Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Neurosciences, University of California San Diego, La Jolla, California, United States of America
- Rady Children’s Hospital, La Jolla, California, United States of America
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127
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Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals. Mol Cell 2013; 52:517-28. [PMID: 24184211 DOI: 10.1016/j.molcel.2013.10.001] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/03/2013] [Accepted: 09/26/2013] [Indexed: 01/17/2023]
Abstract
Metazoan gene expression is often regulated after the recruitment of RNA polymerase II (Pol II) to promoters, through the controlled release of promoter-proximally paused Pol II into productive RNA synthesis. Despite the prevalence of paused Pol II, very little is known about the dynamics of these early elongation complexes or the fate of the short transcription start site-associated (tss) RNAs they produce. Here, we demonstrate that paused elongation complexes can be remarkably stable, with half-lives exceeding 15 min at genes with inefficient pause release. Promoter-proximal termination by Pol II is infrequent, and released tssRNAs are targeted for rapid degradation. Further, we provide evidence that the predominant tssRNA species observed are nascent RNAs held within early elongation complexes. We propose that stable pausing of polymerase provides a temporal window of opportunity for recruitment of factors to modulate gene expression and that the nascent tssRNA represents an appealing target for these interactions.
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128
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Coiras M, Montes M, Montanuy I, López-Huertas MR, Mateos E, Le Sommer C, Garcia-Blanco MA, Hernández-Munain C, Alcamí J, Suñé C. Transcription elongation regulator 1 (TCERG1) regulates competent RNA polymerase II-mediated elongation of HIV-1 transcription and facilitates efficient viral replication. Retrovirology 2013; 10:124. [PMID: 24165037 PMCID: PMC3874760 DOI: 10.1186/1742-4690-10-124] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 10/18/2013] [Indexed: 12/30/2022] Open
Abstract
Background Control of RNA polymerase II (RNAPII) release from pausing has been proposed as a checkpoint mechanism to ensure optimal RNAPII activity, especially in large, highly regulated genes. HIV-1 gene expression is highly regulated at the level of elongation, which includes transcriptional pausing that is mediated by both viral and cellular factors. Here, we present evidence for a specific role of the elongation-related factor TCERG1 in regulating the extent of HIV-1 elongation and viral replication in vivo. Results We show that TCERG1 depletion diminishes the basal and viral Tat-activated transcription from the HIV-1 LTR. In support of a role for an elongation mechanism in the transcriptional control of HIV-1, we found that TCERG1 modifies the levels of pre-mRNAs generated at distal regions of HIV-1. Most importantly, TCERG1 directly affects the elongation rate of RNAPII transcription in vivo. Furthermore, our data demonstrate that TCERG1 regulates HIV-1 transcription by increasing the rate of RNAPII elongation through the phosphorylation of serine 2 within the carboxyl-terminal domain (CTD) of RNAPII and suggest a mechanism for the involvement of TCERG1 in relieving pausing. Finally, we show that TCERG1 is required for HIV-1 replication. Conclusions Our study reveals that TCERG1 regulates HIV-1 transcriptional elongation by increasing the elongation rate of RNAPII and phosphorylation of Ser 2 within the CTD. Based on our data, we propose a general mechanism for TCERG1 acting on genes that are regulated at the level of elongation by increasing the rate of RNAPII transcription through the phosphorylation of Ser2. In the case of HIV-1, our evidence provides the basis for further investigation of TCERG1 as a potential therapeutic target for the inhibition of HIV-1 replication
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Carlos Suñé
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina "López Neyra" (IPBLN-CSIC), Armilla, Granada 18016, Spain.
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129
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Abstract
Elongation is becoming increasingly recognized as a critical step in eukaryotic transcriptional regulation. Although traditional genetic and biochemical studies have identified major players of transcriptional elongation, our understanding of the importance and roles of these factors is evolving rapidly through the recent advances in genome-wide and single-molecule technologies. Here, we focus on how elongation can modulate the transcriptional outcome through the rate-liming step of RNA polymerase II (Pol II) pausing near promoters and how the participating factors were identified. Among the factors we describe are the pausing factors--NELF (negative elongation factor) and DSIF (DRB sensitivity-inducing factor)--and P-TEFb (positive elongation factor b), which is the key player in pause release. We also describe the high-resolution view of Pol II pausing and propose nonexclusive models for how pausing is achieved. We then discuss Pol II elongation through the bodies of genes and the roles of FACT and SPT6, factors that allow Pol II to move through nucleosomes.
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Affiliation(s)
- Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703; ,
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130
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Ouellet DL, Vigneault-Edwards J, Létourneau K, Gobeil LA, Plante I, Burnett JC, Rossi JJ, Provost P. Regulation of host gene expression by HIV-1 TAR microRNAs. Retrovirology 2013; 10:86. [PMID: 23938024 PMCID: PMC3751525 DOI: 10.1186/1742-4690-10-86] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Accepted: 08/06/2013] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The transactivating response (TAR) element of human immunodeficiency virus type 1 (HIV-1) is the source of two functional microRNAs (miRNAs), miR-TAR-5p and miR-TAR-3p. The objective of this study was to characterize the post-transcriptional regulation of host messenger RNAs (mRNAs) relevant to HIV-1 pathogenesis by HIV-1 TAR miRNAs. RESULTS We demonstrated that TAR miRNAs derived from HIV-1 can incorporate into host effector Argonaute protein complexes, which is required if these miRNAs are to regulate host mRNA expression. Bioinformatic predictions and reporter gene activity assays identified regulatory elements complementary and responsive to miR-TAR-5p and miR-TAR-3p in the 3' untranslated region (UTR) of several candidate genes involved in apoptosis and cell survival. These include Caspase 8, Aiolos, Ikaros and Nucleophosmin (NPM)/B23. Analyses of Jurkat cells that stably expressed HIV-1 TAR or contained a full-length latent HIV provirus suggested that HIV-1 TAR miRNAs could regulate the expression of genes in T cells that affect the balance between apoptosis and cell survival. CONCLUSIONS HIV-1 TAR miRNAs may contribute to the replication cycle and pathogenesis of HIV-1, by regulating host genes involved in the intricate balance between apoptosis and infected cell, to induce conditions that promote HIV-1 propagation and survival.
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Affiliation(s)
- Dominique L Ouellet
- Department of Molecular and Cellular Biology, Beckman Research Institute at City of Hope, 1500 E Duarte Road, Duarte, CA 91010, USA
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131
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Roth BM, Ishimaru D, Hennig M. The core microprocessor component DiGeorge syndrome critical region 8 (DGCR8) is a nonspecific RNA-binding protein. J Biol Chem 2013; 288:26785-99. [PMID: 23893406 DOI: 10.1074/jbc.m112.446880] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MicroRNA (miRNA) biogenesis follows a conserved succession of processing steps, beginning with the recognition and liberation of an miRNA-containing precursor miRNA hairpin from a large primary miRNA transcript (pri-miRNA) by the Microprocessor, which consists of the nuclear RNase III Drosha and the double-stranded RNA-binding domain protein DGCR8 (DiGeorge syndrome critical region protein 8). Current models suggest that specific recognition is driven by DGCR8 detection of single-stranded elements of the pri-miRNA stem-loop followed by Drosha recruitment and pri-miRNA cleavage. Because countless RNA transcripts feature single-stranded-dsRNA junctions and DGCR8 can bind hundreds of mRNAs, we explored correlations between RNA binding properties of DGCR8 and specific pri-miRNA substrate processing. We found that DGCR8 bound single-stranded, double-stranded, and random hairpin transcripts with similar affinity. Further investigation of DGCR8/pri-mir-16 interactions by NMR detected intermediate exchange regimes over a wide range of stoichiometric ratios. Diffusion analysis of DGCR8/pri-mir-16 interactions by pulsed field gradient NMR lent further support to dynamic complex formation involving free components in exchange with complexes of varying stoichiometry, although in vitro processing assays showed exclusive cleavage of pri-mir-16 variants bearing single-stranded flanking regions. Our results indicate that DGCR8 binds RNA nonspecifically. Therefore, a sequential model of DGCR8 recognition followed by Drosha recruitment is unlikely. Known RNA substrate requirements are broad and include 70-nucleotide hairpins with unpaired flanking regions. Thus, specific RNA processing is likely facilitated by preformed DGCR8-Drosha heterodimers that can discriminate between authentic substrates and other hairpins.
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Affiliation(s)
- Braden M Roth
- From the Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425
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132
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Smith E, Shilatifard A. Transcriptional elongation checkpoint control in development and disease. Genes Dev 2013; 27:1079-88. [PMID: 23699407 DOI: 10.1101/gad.215137.113] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transcriptional elongation control by RNA polymerase II and its associated factors has taken center stage as a process essential for the regulation of gene expression throughout development. In this review, we analyze recent findings on the identification of factors functioning in the regulation of the transcriptional elongation checkpoint control (TECC) stage of gene expression and how the factors' misregulation is associated with disease pathogenesis, including cancer.
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Affiliation(s)
- Edwin Smith
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
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133
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Abstract
The microprocessor is a complex comprising the RNase III enzyme Drosha and the double-stranded RNA-binding protein DGCR8 (DiGeorge syndrome critical region 8 gene) that catalyses the nuclear step of miRNA (microRNA) biogenesis. DGCR8 recognizes the RNA substrate, whereas Drosha functions as an endonuclease. Recent global analyses of microprocessor and Dicer proteins have suggested novel functions for these components independent of their role in miRNA biogenesis. A HITS-CLIP (high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation) experiment designed to identify novel substrates of the microprocessor revealed that this complex binds and regulates a large variety of cellular RNAs. The microprocessor-mediated cleavage of several classes of RNAs not only regulates transcript levels, but also modulates alternative splicing events, independently of miRNA function. Importantly, DGCR8 can also associate with other nucleases, suggesting the existence of alternative DGCR8 complexes that may regulate the fate of a subset of cellular RNAs. The aim of the present review is to provide an overview of the diverse functional roles of the microprocessor.
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134
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Van Lint C, Bouchat S, Marcello A. HIV-1 transcription and latency: an update. Retrovirology 2013; 10:67. [PMID: 23803414 PMCID: PMC3699421 DOI: 10.1186/1742-4690-10-67] [Citation(s) in RCA: 246] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 05/29/2013] [Indexed: 12/11/2022] Open
Abstract
Combination antiretroviral therapy, despite being potent and life-prolonging, is not curative and does not eradicate HIV-1 infection since interruption of treatment inevitably results in a rapid rebound of viremia. Reactivation of latently infected cells harboring transcriptionally silent but replication-competent proviruses is a potential source of persistent residual viremia in cART-treated patients. Although multiple reservoirs may exist, the persistence of resting CD4+ T cells carrying a latent infection represents a major barrier to eradication. In this review, we will discuss the latest reports on the molecular mechanisms that may regulate HIV-1 latency at the transcriptional level, including transcriptional interference, the role of cellular factors, chromatin organization and epigenetic modifications, the viral Tat trans-activator and its cellular cofactors. Since latency mechanisms may also operate at the post-transcriptional level, we will consider inhibition of nuclear RNA export and inhibition of translation by microRNAs as potential barriers to HIV-1 gene expression. Finally, we will review the therapeutic approaches and clinical studies aimed at achieving either a sterilizing cure or a functional cure of HIV-1 infection, with a special emphasis on the most recent pharmacological strategies to reactivate the latent viruses and decrease the pool of viral reservoirs.
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Affiliation(s)
- Carine Van Lint
- Université Libre de Bruxelles (ULB), Service of Molecular Virology, Institute of Molecular Biology and Medicine, 12, Rue des Profs Jeener et Brachet, 6041, Gosselies, Belgium.
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135
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Porrua O, Libri D. A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast. Nat Struct Mol Biol 2013; 20:884-91. [PMID: 23748379 DOI: 10.1038/nsmb.2592] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/22/2013] [Indexed: 12/25/2022]
Abstract
Transcription termination is essential to generate functional RNAs and to prevent disruptive polymerase collisions resulting from concurrent transcription. The yeast Sen1p helicase is involved in termination of most noncoding RNAs transcribed by RNA polymerase II (RNAPII). However, the mechanism of termination and the role of this protein have remained enigmatic. Here we address the mechanism of Sen1p-dependent termination by using a highly purified in vitro system. We show that Sen1p is the key enzyme of the termination reaction and reveal features of the termination mechanism. Like the bacterial termination factor Rho, Sen1p recognizes the nascent RNA and hydrolyzes ATP to dissociate the elongation complex. Sen1p-dependent termination is highly specific and, notably, does not require the C-terminal domain of RNAPII. We also show that termination is inhibited by RNA-DNA hybrids. Our results elucidate the role of Sen1p in controlling pervasive transcription.
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Affiliation(s)
- Odil Porrua
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, Gif sur Yvette, France.
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136
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Nagarajan VK, Jones CI, Newbury SF, Green PJ. XRN 5'→3' exoribonucleases: structure, mechanisms and functions. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1829:590-603. [PMID: 23517755 PMCID: PMC3742305 DOI: 10.1016/j.bbagrm.2013.03.005] [Citation(s) in RCA: 247] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2012] [Revised: 03/08/2013] [Accepted: 03/11/2013] [Indexed: 01/11/2023]
Abstract
The XRN family of 5'→3' exoribonucleases is critical for ensuring the fidelity of cellular RNA turnover in eukaryotes. Highly conserved across species, the family is typically represented by one cytoplasmic enzyme (XRN1/PACMAN or XRN4) and one or more nuclear enzymes (XRN2/RAT1 and XRN3). Cytoplasmic and/or nuclear XRNs have proven to be essential in all organisms tested, and deficiencies can have severe developmental phenotypes, demonstrating that XRNs are indispensable in fungi, plants and animals. XRNs degrade diverse RNA substrates during general RNA decay and function in specialized processes integral to RNA metabolism, such as nonsense-mediated decay (NMD), gene silencing, rRNA maturation, and transcription termination. Here, we review current knowledge of XRNs, highlighting recent work of high impact and future potential. One example is the breakthrough in our understanding of how XRN1 processively degrades 5' monophosphorylated RNA, revealed by its crystal structure and mutational analysis. The expanding knowledge of XRN substrates and interacting partners is outlined and the functions of XRNs are interpreted at the organismal level using available mutant phenotypes. Finally, three case studies are discussed in more detail to underscore a few of the most exciting areas of research on XRN function: XRN4 involvement in small RNA-associated processes in plants, the roles of XRN1/PACMAN in Drosophila development, and the function of human XRN2 in nuclear transcriptional quality control. This article is part of a Special Issue entitled: RNA Decay mechanisms.
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Affiliation(s)
- Vinay K. Nagarajan
- Delaware Biotechnology Institute, Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Christopher I. Jones
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK
| | - Sarah F. Newbury
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK
| | - Pamela J. Green
- Delaware Biotechnology Institute, Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
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137
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Eilebrecht S, Schwartz C, Rohr O. Non-coding RNAs: novel players in chromatin-regulation during viral latency. Curr Opin Virol 2013; 3:387-93. [PMID: 23660570 DOI: 10.1016/j.coviro.2013.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 04/01/2013] [Indexed: 10/26/2022]
Abstract
Chromatin structure plays an essential role during gene expression regulation not only in the case of the host cellular genome, but also during the viral life cycle. Epigenetic chromatin marks thereby define, whether a gene promoter is accessible for the transcription machinery or whether a repressive heterochromatin state is established. The heterochromatin-mediated repression of lytic viral genes results in viral latency, enabling the virus to persist dormant without being recognized by the host immune system, but keeping the potential for reactivation. Arising new systems biology approaches are starting to uncover an unexpected multiplicity and variety of non-coding (nc)RNAs playing important roles during chromatin structure control, likely constituting a novel layer in epigenetic regulation. In this review we give an overview of chromatin-regulatory viral and host cellular ncRNAs and their links to viral latency.
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Affiliation(s)
- Sebastian Eilebrecht
- Vaccine Research Institute, INSERM U955, 8 rue du Général Sarrail, 94010 Créteil, France.
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138
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Berkhout B, Lever A, Wainberg M, Fassati A, Borrow P, Fujii M. Monsef Benkirane awarded 2013 Ming K. Jeang Foundation Retrovirology Prize: landmark HIV-1 research honoured. Retrovirology 2013; 10:38. [PMID: 23561838 PMCID: PMC3635955 DOI: 10.1186/1742-4690-10-38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 03/23/2013] [Indexed: 11/26/2022] Open
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139
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Abstract
Argonaute proteins are the mediators of small RNA-guided gene silencing pathways. In this issue, Couvillion and coworkers (Couvillion et al., 2012) found an unexpected function for a Tetrahymena Argonaute protein: It forms a complex with tRNA fragments and is required for nuclear Xrn2 localization and function.
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Affiliation(s)
- Daniele Hasler
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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140
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Eilebrecht S, Wilhelm E, Benecke BJ, Bell B, Benecke AG. HMGA1 directly interacts with TAR to modulate basal and Tat-dependent HIV transcription. RNA Biol 2013; 10:436-44. [PMID: 23392246 DOI: 10.4161/rna.23686] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The transactivating response element (TAR) of human immunodeficiency virus 1 (HIV-1) is essential for promoter transactivation by the viral transactivator of transcription (Tat). The Tat-TAR interaction thereby recruits active positive transcription elongation factor b (P-TEFb) from its inactive, 7SK/HEXIM1-bound form, leading to efficient viral transcription. Here, we show that the 7SK RNA-associating chromatin regulator HMGA1 can specifically bind to the HIV-1 TAR element and that 7SK RNA can thereby compete with TAR. The HMGA1-binding interface of TAR is located within the binding site for Tat and other cellular activators, and we further provide evidence for competition between HMGA1 and Tat for TAR-binding. HMGA1 negatively influences the expression of a HIV-1 promoter-driven reporter in a TAR-dependent manner, both in the presence and in the absence of Tat. The overexpression of the HMGA1-binding substructure of 7SK RNA results in a TAR-dependent gain of HIV-1 promoter activity similar to the effect of the shRNA-mediated knockdown of HMGA1. Our results support a model in which the HMGA1/TAR interaction prevents the binding of transcription-activating cellular co-factors and Tat, subsequently leading to reduced HIV-1 transcription.
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Affiliation(s)
- Sebastian Eilebrecht
- Institut des Hautes Études Scientifiques - Centre National de la Recherche Scientifique; Bures sur Yvette; France & Vaccine Research Institute; Institut Mondor de Recherche Biomédicale; Créteil, France
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141
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Klase ZA, Sampey GC, Kashanchi F. Retrovirus infected cells contain viral microRNAs. Retrovirology 2013; 10:15. [PMID: 23391025 PMCID: PMC3571942 DOI: 10.1186/1742-4690-10-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 02/01/2013] [Indexed: 11/17/2022] Open
Abstract
The encoding of microRNAs in retroviral genomes has remained a controversial hypothesis despite significant supporting evidence in recent years. A recent publication demonstrating the production of functional miRNAs from the retrovirus bovine leukemia virus adds further credence to the fact that retroviruses do indeed encode their own miRNAs. Here we comment on the importance of this paper to the field, as well as examine the other known examples of miRNAs encoded by RNA viruses.
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Affiliation(s)
- Zachary A Klase
- Molecular Virology Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, 9000 Rockville Pike, Bethesda, MD 20810, USA
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142
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Castelo-Branco G, Amaral PP, Engström PG, Robson SC, Marques SC, Bertone P, Kouzarides T. The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells. Genome Biol 2013; 14:R98. [PMID: 24044525 PMCID: PMC4053805 DOI: 10.1186/gb-2013-14-9-r98] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/10/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pluripotency is characterized by a unique transcriptional state, in which lineage-specification genes are poised for transcription upon exposure to appropriate stimuli, via a bivalency mechanism involving the simultaneous presence of activating and repressive methylation marks at promoter-associated histones. Recent evidence suggests that other mechanisms, such as RNA polymerase II pausing, might be operational in this process, but their regulation remains poorly understood. RESULTS Here we identify the non-coding snRNA 7SK as a multifaceted regulator of transcription in embryonic stem cells. We find that 7SK represses a specific cohort of transcriptionally poised genes with bivalent or activating chromatin marks in these cells, suggesting a novel poising mechanism independent of Polycomb activity. Genome-wide analysis shows that 7SK also prevents transcription downstream of polyadenylation sites at several active genes, indicating that 7SK is required for normal transcriptional termination or control of 3′-UTR length. In addition, 7SK suppresses divergent upstream antisense transcription at more than 2,600 loci, including many that encode divergent long non-coding RNAs, a finding that implicates the 7SK snRNA in the control of transcriptional bidirectionality. CONCLUSIONS Our study indicates that a single non-coding RNA, the snRNA 7SK, is a gatekeeper of transcriptional termination and bidirectional transcription in embryonic stem cells and mediates transcriptional poising through a mechanism independent of chromatin bivalency.
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Affiliation(s)
- Gonçalo Castelo-Branco
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet,SE-17177 Stockholm, Sweden
| | - Paulo P Amaral
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Pär G Engström
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
- Present address: Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Box 1031, SE-17121 Solna, Sweden
| | - Samuel C Robson
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Sueli C Marques
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet,SE-17177 Stockholm, Sweden
| | - Paul Bertone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
- Genome Biology and Developmental Biology Units, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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143
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Abstract
MicroRNAs (miRNAs) are small RNAs that play important roles in the regulation of gene expression. First described as posttranscriptional gene regulators in eukaryotic hosts, virus-encoded miRNAs were later uncovered. It is now apparent that diverse virus families, most with DNA genomes, but at least some with RNA genomes, encode miRNAs. While deciphering the functions of viral miRNAs has lagged behind their discovery, recent functional studies are bringing into focus these roles. Some of the best characterized viral miRNA functions include subtle roles in prolonging the longevity of infected cells, evading the immune response, and regulating the switch to lytic infection. Notably, all of these functions are particularly important during persistent infections. Furthermore, an emerging view of viral miRNAs suggests two distinct groups exist. In the first group, viral miRNAs mimic host miRNAs and take advantage of conserved networks of host miRNA target sites. In the larger second group, viral miRNAs do not share common target sites conserved for host miRNAs, and it remains unclear what fraction of these targeted transcripts are beneficial to the virus. Recent insights from multiple virus families have revealed new ways of interacting with the host miRNA machinery including noncanonical miRNA biogenesis and new mechanisms of posttranscriptional cis gene regulation. Exciting challenges await the field, including determining the most relevant miRNA targets and parlaying our current understanding of viral miRNAs into new therapeutic strategies. To accomplish these goals and to better grasp miRNA function, new in vivo models that recapitulate persistent infections associated with viral pathogens are required.
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Affiliation(s)
- Rodney P. Kincaid
- The University of Texas at Austin, Molecular Genetics & Microbiology, Austin, Texas, United States of America
| | - Christopher S. Sullivan
- The University of Texas at Austin, Molecular Genetics & Microbiology, Austin, Texas, United States of America
- * E-mail:
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