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Mérida-Cerro JA, Maraver-Cárdenas P, Rondón AG, Aguilera A. Rat1 promotes premature transcription termination at R-loops. Nucleic Acids Res 2024; 52:3623-3635. [PMID: 38281203 DOI: 10.1093/nar/gkae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
Certain DNA sequences can adopt a non-B form in the genome that interfere with DNA-templated processes, including transcription. Among the sequences that are intrinsically difficult to transcribe are those that tend to form R-loops, three-stranded nucleic acid structures formed by a DNA-RNA hybrid and the displaced ssDNA. Here we compared the transcription of an endogenous gene with and without an R-loop-forming sequence inserted. We show that, in agreement with previous in vivo and in vitro analyses, transcription elongation is delayed by R-loops in yeast. Importantly, we demonstrate that the Rat1 transcription terminator factor facilitates transcription throughout such structures by inducing premature termination of arrested RNAPIIs. We propose that RNase H degrades the RNA moiety of the hybrid, providing an entry site for Rat1. Thus, we have uncovered an unanticipated function of Rat1 as a transcription restoring factor opening up the possibility that it may also promote transcription through other genomic DNA structures intrinsically difficult to transcribe. If R-loop-mediated transcriptional stress is not relieved by Rat1, it will cause genomic instability, probably through the increase of transcription-replication conflicts, a deleterious situation that could lead to cancer.
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Affiliation(s)
- José Antonio Mérida-Cerro
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Pablo Maraver-Cárdenas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Ana G Rondón
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
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2
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Dhoondia Z, Elewa H, Malik M, Arif Z, Pique-Regi R, Ansari A. A termination-independent role of Rat1 in cotranscriptional splicing. Nucleic Acids Res 2021; 49:5520-5536. [PMID: 33978753 PMCID: PMC8191773 DOI: 10.1093/nar/gkab339] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 01/18/2023] Open
Abstract
Rat1 is a 5′→3′ exoribonuclease in budding yeast. It is a highly conserved protein with homologs being present in fission yeast, flies, worms, mice and humans. Rat1 and its human homolog Xrn2 have been implicated in multiple nuclear processes. Here we report a novel role of Rat1 in mRNA splicing. We observed an increase in the level of unspliced transcripts in mutants of Rat1. Accumulation of unspliced transcripts was not due to the surveillance role of Rat1 in degrading unspliced mRNA, or an indirect effect of Rat1 function in termination of transcription or on the level of splicing factors in the cell, or due to an increased elongation rate in Rat1 mutants. ChIP-Seq analysis revealed Rat1 crosslinking to the introns of a subset of yeast genes. Mass spectrometry and coimmunoprecipitation revealed an interaction of Rat1 with the Clf1, Isy1, Yju2, Prp43 and Sub2 splicing factors. Furthermore, recruitment of splicing factors on the intron was compromised in the Rat1 mutant. Based on these findings we propose that Rat1 has a novel role in splicing of mRNA in budding yeast. Rat1, however, is not a general splicing factor as it crosslinks to only long introns with an average length of 400 nucleotides.
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Affiliation(s)
- Zuzer Dhoondia
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Hesham Elewa
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Marva Malik
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Zahidur Arif
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 540 East Canfield, Detroit, MI 48201, USA
| | - Athar Ansari
- To whom correspondence should be addressed. Tel: +1 313 577 9251; Fax: +1 313 571 6891;
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3
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Yang L, Zhang Y, Ma Y, Du J, Gu L, Zheng L, Zhang X. Effect of melatonin on EGF- and VEGF-induced monolayer permeability of HUVECs. Am J Physiol Heart Circ Physiol 2018; 316:H1178-H1191. [PMID: 30575440 DOI: 10.1152/ajpheart.00542.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Melatonin is a natural hormone involved in the regulation of circadian rhythm, immunity, and cardiovascular function. In the present study, we focused on the mechanism of melatonin in the regulation of vascular permeability. We found that melatonin could inhibit both VEGF- and EGF-induced monolayer permeability of human umbilical vein endothelial cells (HUVECs) and change the tyrosine phosphorylation of vascular-endothelial (VE-)cadherin, which was related to endothelial barrier function. In addition, phospho-AKT (Ser473) and phospho-ERK(1/2) played significant roles in the regulation of VE-cadherin phosphorylation. Both the phosphatidylinositol 3-kinase/AKT inhibitor LY49002 and MEK/ERK inhibitor U0126 could inhibit the permeability of HUVECs, but with different effects on tyrosine phosphorylation of VE-cadherin. Melatonin can influence the two growth factor-induced phosphorylation of AKT (Ser473) but not ERK(1/2). Our results show that melatonin can inhibit growth factor-induced monolayer permeability of HUVECs by influencing the phosphorylation of AKT and VE-cadherin. Melatonin can be a potential treatment for diseases associated with abnormal vascular permeability. NEW & NOTEWORTHY We found that melatonin could inhibit both EGF- and VEGF-induced monolayer permeability of human umbilical vein endothelial cells, which is related to phosphorylation of vascular-endothelial cadherin. Blockade of phosphatidylinositol 3-kinase/AKT and MEK/ERK pathways could inhibit the permeability of human umbilical vein endothelial cells, and phosphorylation of AKT (Ser473) might be a critical event in the changing of monolayer permeability and likely has cross-talk with the MEK/ERK pathway.
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Affiliation(s)
- Ling Yang
- Department of Cardiology, The Third Affiliated Hospital of Soochow University , Changzhou, Jiangsu , China
| | - Yujie Zhang
- Department of Physiology, Nanjing Medical University , Nanjing, Jiangsu , China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , Nanjing, Jiangsu , China
| | - Yadong Ma
- Department of Physiology, Nanjing Medical University , Nanjing, Jiangsu , China
| | - Jun Du
- Department of Physiology, Nanjing Medical University , Nanjing, Jiangsu , China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , Nanjing, Jiangsu , China
| | - Luo Gu
- Department of Physiology, Nanjing Medical University , Nanjing, Jiangsu , China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University , Nanjing, Jiangsu , China
| | - Lu Zheng
- General Laboratory, The Third Affiliated Hospital of Soochow University , Changzhou, Jiangsu , China
| | - Xiaoying Zhang
- Department of Cardiothoracic surgery and the General Laboratory, The Third Affiliated Hospital of Soochow University , Changzhou, Jiangsu , China
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4
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Larochelle M, Robert MA, Hébert JN, Liu X, Matteau D, Rodrigue S, Tian B, Jacques PÉ, Bachand F. Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast. Nat Commun 2018; 9:4364. [PMID: 30341288 PMCID: PMC6195540 DOI: 10.1038/s41467-018-06546-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 08/30/2018] [Indexed: 11/09/2022] Open
Abstract
Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that is critical for determining the borders between genes. In budding yeast, termination at protein-coding genes is initiated by the cleavage/polyadenylation machinery, whereas termination of most noncoding RNA (ncRNA) genes occurs via the Nrd1-Nab3-Sen1 (NNS) pathway. Here, we find that NNS-like transcription termination is not conserved in fission yeast. Rather, genome-wide analyses show global recruitment of mRNA 3' end processing factors at the end of ncRNA genes, including snoRNAs and snRNAs, and that this recruitment coincides with high levels of Ser2 and Tyr1 phosphorylation on the RNAPII C-terminal domain. We also find that termination of mRNA and ncRNA transcription requires the conserved Ysh1/CPSF-73 and Dhp1/XRN2 nucleases, supporting widespread cleavage-dependent transcription termination in fission yeast. Our findings thus reveal that a common mode of transcription termination can produce functionally and structurally distinct types of polyadenylated and non-polyadenylated RNAs.
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Affiliation(s)
- Marc Larochelle
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, J1E4K8, Canada
| | - Marc-Antoine Robert
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada
| | - Jean-Nicolas Hébert
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, J1E4K8, Canada
| | - Xiaochuan Liu
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School and Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Dominick Matteau
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada
| | - Sébastien Rodrigue
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School and Rutgers Cancer Institute of New Jersey, Newark, NJ, 07103, USA
| | - Pierre-Étienne Jacques
- Départment de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K2R1, Canada.
- Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, J1H5N4, Canada.
| | - François Bachand
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, J1E4K8, Canada.
- Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, J1H5N4, Canada.
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5
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Malik I, Qiu C, Snavely T, Kaplan CD. Wide-ranging and unexpected consequences of altered Pol II catalytic activity in vivo. Nucleic Acids Res 2017; 45:4431-4451. [PMID: 28119420 PMCID: PMC5416818 DOI: 10.1093/nar/gkx037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/13/2017] [Indexed: 01/28/2023] Open
Abstract
Here we employ a set of RNA Polymerase II (Pol II) activity mutants to determine the consequences of increased or decreased Pol II catalysis on gene expression in Saccharomyces cerevisiae. We find that alteration of Pol II catalytic rate, either fast or slow, leads to decreased Pol II occupancy and apparent reduction in elongation rate in vivo. However, we also find that determination of elongation rate in vivo by chromatin immunoprecipitation can be confounded by the kinetics and conditions of transcriptional shutoff in the assay. We identify promoter and template-specific effects on severity of gene expression defects for both fast and slow Pol II mutants. We show that mRNA half-lives for a reporter gene are increased in both fast and slow Pol II mutant strains and the magnitude of half-life changes correlate both with mutants' growth and reporter expression defects. Finally, we tested a model that altered Pol II activity sensitizes cells to nucleotide depletion. In contrast to model predictions, mutated Pol II retains normal sensitivity to altered nucleotide levels. Our experiments establish a framework for understanding the diversity of transcription defects derived from altered Pol II activity mutants, essential for their use as probes of transcription mechanisms.
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Affiliation(s)
- Indranil Malik
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Chenxi Qiu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Thomas Snavely
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Craig D Kaplan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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6
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Fong N, Saldi T, Sheridan RM, Cortazar MA, Bentley DL. RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction. Mol Cell 2017; 66:546-557.e3. [PMID: 28506463 DOI: 10.1016/j.molcel.2017.04.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 01/11/2017] [Accepted: 04/19/2017] [Indexed: 10/19/2022]
Abstract
Eukaryotic genes are marked by conserved post-translational modifications on the RNA pol II C-terminal domain (CTD) and the chromatin template. How the 5'-3' profiles of these marks are established is poorly understood. Using pol II mutants in human cells, we found that slow transcription repositioned specific co-transcriptionally deposited chromatin modifications; histone H3 lysine 36 trimethyl (H3K36me3) shifted within genes toward 5' ends, and histone H3 lysine 4 dimethyl (H3K4me2) extended farther upstream of start sites. Slow transcription also evoked a hyperphosphorylation of CTD Ser2 residues at 5' ends of genes that is conserved in yeast. We propose a "dwell time in the target zone" model to explain the effects of transcriptional dynamics on the establishment of co-transcriptionally deposited protein modifications. Promoter-proximal Ser2 phosphorylation is associated with a longer pol II dwell time at start sites and reduced transcriptional polarity because of strongly enhanced divergent antisense transcription at promoters. These results demonstrate that pol II dynamics help govern the decision between sense and divergent antisense transcription.
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Affiliation(s)
- Nova Fong
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Tassa Saldi
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Ryan M Sheridan
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Michael A Cortazar
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
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7
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Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization. Mol Cell 2016; 63:433-44. [PMID: 27477907 DOI: 10.1016/j.molcel.2016.06.036] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 05/09/2016] [Accepted: 06/23/2016] [Indexed: 12/25/2022]
Abstract
During transcription initiation, the TFIIH-kinase Kin28/Cdk7 marks RNA polymerase II (Pol II) by phosphorylating the C-terminal domain (CTD) of its largest subunit. Here we describe a structure-guided chemical approach to covalently and specifically inactivate Kin28 kinase activity in vivo. This method of irreversible inactivation recapitulates both the lethal phenotype and the key molecular signatures that result from genetically disrupting Kin28 function in vivo. Inactivating Kin28 impacts promoter release to differing degrees and reveals a "checkpoint" during the transition to productive elongation. While promoter-proximal pausing is not observed in budding yeast, inhibition of Kin28 attenuates elongation-licensing signals, resulting in Pol II accumulation at the +2 nucleosome and reduced transition to productive elongation. Furthermore, upon inhibition, global stabilization of mRNA masks different degrees of reduction in nascent transcription. This study resolves long-standing controversies on the role of Kin28 in transcription and provides a rational approach to irreversibly inhibit other kinases in vivo.
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8
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Jeronimo C, Collin P, Robert F. The RNA Polymerase II CTD: The Increasing Complexity of a Low-Complexity Protein Domain. J Mol Biol 2016; 428:2607-2622. [DOI: 10.1016/j.jmb.2016.02.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/27/2016] [Accepted: 02/02/2016] [Indexed: 01/18/2023]
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9
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Tucker JF, Ohle C, Schermann G, Bendrin K, Zhang W, Fischer T, Zhang K. A Novel Epigenetic Silencing Pathway Involving the Highly Conserved 5'-3' Exoribonuclease Dhp1/Rat1/Xrn2 in Schizosaccharomyces pombe. PLoS Genet 2016; 12:e1005873. [PMID: 26889830 PMCID: PMC4758730 DOI: 10.1371/journal.pgen.1005873] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 01/26/2016] [Indexed: 01/09/2023] Open
Abstract
Epigenetic gene silencing plays a critical role in regulating gene expression and contributes to organismal development and cell fate acquisition in eukaryotes. In fission yeast, Schizosaccharomyces pombe, heterochromatin-associated gene silencing is known to be mediated by RNA processing pathways including RNA interference (RNAi) and a 3’-5’ exoribonuclease complex, the exosome. Here, we report a new RNA-processing pathway that contributes to epigenetic gene silencing and assembly of heterochromatin mediated by 5’-3’ exoribonuclease Dhp1/Rat1/Xrn2. Dhp1 mutation causes defective gene silencing both at peri-centromeric regions and at the silent mating type locus. Intriguingly, mutation in either of the two well-characterized Dhp1-interacting proteins, the Din1 pyrophosphohydrolase or the Rhn1 transcription termination factor, does not result in silencing defects at the main heterochromatic regions. We demonstrate that Dhp1 interacts with heterochromatic factors and is essential in the sequential steps of establishing silencing in a manner independent of both RNAi and the exosome. Genomic and genetic analyses suggest that Dhp1 is involved in post-transcriptional silencing of repetitive regions through its RNA processing activity. The results describe the unexpected role of Dhp1/Rat1/Xrn2 in chromatin-based silencing and elucidate how various RNA-processing pathways, acting together or independently, contribute to epigenetic regulation of the eukaryotic genome. Epigenetic mechanisms regulate when, where, and how an organism uses the genetic information stored in its genome. They are essential to many cellular processes, such as the regulation of gene expression, genome organization, and cell-fate determination. They also govern growth, development, and ultimately human health. Heterochromatin constitutes silenced chromatic domains, in which gene silencing occurs through epigenetic mechanisms. RNA processing pathways, such as RNA interference (RNAi) and the exosome, are known to mediate the silencing of genes via degradation of unwanted or aberrant transcripts. In this study, we describe a new RNA processing mechanism in epigenetic silencing using fission yeast, a premier model for studying these processes. With genetic, cell biology, and genomic approaches, we uncovered a previously unrecognized function of Dhp1, a highly conserved 5’-3’ exoribonuclease and ortholog of budding yeast Rat1 and metazoan Xrn2. We show that Dhp1 mediates a novel RNA processing mechanism in epigenetic silencing which occurs independently of both RNAi and the exosome. Our results clarify how multiple RNA processing pathways are involved in the regulation of eukaryotic gene expression and chromatin organization.
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Affiliation(s)
- James Franklin Tucker
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Corina Ohle
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Géza Schermann
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Katja Bendrin
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Wei Zhang
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Tamás Fischer
- Biochemistry Center (BZH), Heidelberg University, Heidelberg, Germany
| | - Ke Zhang
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
- * E-mail:
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10
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Schmid M, Olszewski P, Pelechano V, Gupta I, Steinmetz LM, Jensen TH. The Nuclear PolyA-Binding Protein Nab2p Is Essential for mRNA Production. Cell Rep 2015; 12:128-139. [PMID: 26119729 DOI: 10.1016/j.celrep.2015.06.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/13/2015] [Accepted: 06/01/2015] [Indexed: 10/23/2022] Open
Abstract
Polyadenylation of mRNA is a key step in eukaryotic gene expression. However, despite the major impact of poly(A) tails on mRNA metabolism, the precise roles of poly(A)-binding proteins (PABPs) in nuclear mRNA biogenesis remain elusive. Here, we demonstrate that rapid nuclear depletion of the S. cerevisiae PABP Nab2p leads to a global loss of cellular mRNA, but not of RNA lacking poly(A) tails. Disappearance of mRNA is a nuclear event, but not due to decreased transcription. Instead, the absence of Nab2p results in robust nuclear mRNA decay by the ribonucleolytic RNA exosome in a polyadenylation-dependent process. We conclude that Nab2p is required to protect early mRNA and therefore constitutes a crucial nuclear mRNA biogenesis factor.
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Affiliation(s)
- Manfred Schmid
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus C., Denmark.
| | - Pawel Olszewski
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus C., Denmark
| | - Vicent Pelechano
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Ishaan Gupta
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Lars M Steinmetz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany; Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Torben Heick Jensen
- Centre for mRNP Biogenesis and Metabolism, Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Alle 3, Building 1130, 8000 Aarhus C., Denmark.
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11
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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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12
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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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