1
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Kannan A, Gangadharan Leela S, Branzei D, Gangwani L. Role of senataxin in R-loop-mediated neurodegeneration. Brain Commun 2024; 6:fcae239. [PMID: 39070547 PMCID: PMC11277865 DOI: 10.1093/braincomms/fcae239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 06/14/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024] Open
Abstract
Senataxin is an RNA:DNA helicase that plays an important role in the resolution of RNA:DNA hybrids (R-loops) formed during transcription. R-loops are involved in the regulation of biological processes such as immunoglobulin class switching, gene expression and DNA repair. Excessive accumulation of R-loops results in DNA damage and loss of genomic integrity. Senataxin is critical for maintaining optimal levels of R-loops to prevent DNA damage and acts as a genome guardian. Within the nucleus, senataxin interacts with various RNA processing factors and DNA damage response and repair proteins. Senataxin interactors include survival motor neuron and zinc finger protein 1, with whom it co-localizes in sub-nuclear bodies. Despite its ubiquitous expression, mutations in senataxin specifically affect neurons and result in distinct neurodegenerative diseases such as amyotrophic lateral sclerosis type 4 and ataxia with oculomotor apraxia type 2, which are attributed to the gain-of-function and the loss-of-function mutations in senataxin, respectively. In addition, low levels of senataxin (loss-of-function) in spinal muscular atrophy result in the accumulation of R-loops causing DNA damage and motor neuron degeneration. Senataxin may play multiple functions in diverse cellular processes; however, its emerging role in R-loop resolution and maintenance of genomic integrity is gaining attention in the field of neurodegenerative diseases. In this review, we highlight the role of senataxin in R-loop resolution and its potential as a therapeutic target to treat neurodegenerative diseases.
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Affiliation(s)
| | - Shyni Gangadharan Leela
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
| | - Dana Branzei
- The AIRC Institute of Molecular Oncology Foundation, IFOM ETS, Milan 20139, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), Pavia 27100, Italy
| | - Laxman Gangwani
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA
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2
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Wen X, Xu H, Woolley PR, Conway OM, Yao J, Matouschek A, Lambowitz AM, Paull TT. Senataxin deficiency disrupts proteostasis through nucleolar ncRNA-driven protein aggregation. J Cell Biol 2024; 223:e202309036. [PMID: 38717338 PMCID: PMC11080644 DOI: 10.1083/jcb.202309036] [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: 09/06/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 05/12/2024] Open
Abstract
Senataxin is an evolutionarily conserved RNA-DNA helicase involved in DNA repair and transcription termination that is associated with human neurodegenerative disorders. Here, we investigated whether Senataxin loss affects protein homeostasis based on previous work showing R-loop-driven accumulation of DNA damage and protein aggregates in human cells. We find that Senataxin loss results in the accumulation of insoluble proteins, including many factors known to be prone to aggregation in neurodegenerative disorders. These aggregates are located primarily in the nucleolus and are promoted by upregulation of non-coding RNAs expressed from the intergenic spacer region of ribosomal DNA. We also map sites of R-loop accumulation in human cells lacking Senataxin and find higher RNA-DNA hybrids within the ribosomal DNA, peri-centromeric regions, and other intergenic sites but not at annotated protein-coding genes. These findings indicate that Senataxin loss affects the solubility of the proteome through the regulation of transcription-dependent lesions in the nucleus and the nucleolus.
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Affiliation(s)
- Xuemei Wen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Hengyi Xu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Phillip R. Woolley
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Olivia M. Conway
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jun Yao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Alan M. Lambowitz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - Tanya T. Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
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3
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Xiong Y, Han W, Xu C, Shi J, Wang L, Jin T, Jia Q, Lu Y, Hu S, Dou SX, Lin W, Strick TR, Wang S, Li M. Single-molecule reconstruction of eukaryotic factor-dependent transcription termination. Nat Commun 2024; 15:5113. [PMID: 38879529 PMCID: PMC11180205 DOI: 10.1038/s41467-024-49527-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/09/2024] [Indexed: 06/19/2024] Open
Abstract
Factor-dependent termination uses molecular motors to remodel transcription machineries, but the associated mechanisms, especially in eukaryotes, are poorly understood. Here we use single-molecule fluorescence assays to characterize in real time the composition and the catalytic states of Saccharomyces cerevisiae transcription termination complexes remodeled by Sen1 helicase. We confirm that Sen1 takes the RNA transcript as its substrate and translocates along it by hydrolyzing multiple ATPs to form an intermediate with a stalled RNA polymerase II (Pol II) transcription elongation complex (TEC). We show that this intermediate dissociates upon hydrolysis of a single ATP leading to dissociation of Sen1 and RNA, after which Sen1 remains bound to the RNA. We find that Pol II ends up in a variety of states: dissociating from the DNA substrate, which is facilitated by transcription bubble rewinding, being retained to the DNA substrate, or diffusing along the DNA substrate. Our results provide a complete quantitative framework for understanding the mechanism of Sen1-dependent transcription termination in eukaryotes.
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Affiliation(s)
- Ying Xiong
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
- School of Physics, University of Chinese Academy of Sciences, Beijing, China
| | - Weijing Han
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Jing Shi
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lisha Wang
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Taoli Jin
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Qi Jia
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Shuxin Hu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- School of Physics, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Lin
- Department of Pathogen Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China.
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Terence R Strick
- Institut de Biologie de l'Ecole Normale Supérieure, PSL Université, INSERM, CNRS, Paris, France.
- Equipe Labellisée de la Ligue Nationale Contre le Cancer, Paris, France.
| | - Shuang Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China.
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, China
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4
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Wang S, Han Z, Strick TR. Single-molecule characterization of Sen1 translocation properties provides insights into eukaryotic factor-dependent transcription termination. Nucleic Acids Res 2024; 52:3249-3261. [PMID: 38261990 PMCID: PMC11013386 DOI: 10.1093/nar/gkae026] [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: 08/09/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
Sen1 is an essential helicase for factor-dependent transcription termination in Saccharomyces cerevisiae, whose molecular-motor mechanism has not been well addressed. Here, we use single-molecule experimentation to better understand the molecular-motor determinants of its action on RNA polymerase II (Pol II) complex. We quantify Sen1 translocation activity on single-stranded DNA (ssDNA), finding elevated translocation rates, high levels of processivity and ATP affinities. Upon deleting the N- and C-terminal domains, or further deleting different parts of the prong subdomain, which is an essential element for transcription termination, Sen1 displays changes in its translocation properties, such as slightly reduced translocation processivities, enhanced translocation rates and statistically identical ATP affinities. Although these parameters fulfil the requirements for Sen1 translocating along the RNA transcript to catch up with a stalled Pol II complex, we observe significant reductions in the termination efficiencies as well as the factions of the formation of the previously described topological intermediate prior to termination, suggesting that the prong may preserve an interaction with Pol II complex during factor-dependent termination. Our results underscore a more detailed rho-like mechanism of Sen1 and a critical interaction between Sen1 and Pol II complex for factor-dependent transcription termination in eukaryotes.
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Affiliation(s)
- Shuang Wang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, 100190 Beijing, China
- Songshan Lake Materials Laboratory, 523808 Dongguan, Guangdong, China
- Molecular Motors and Machines group, Ecole normale supérieure, Institut de Biologie de l’Ecole normale supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France
| | - Zhong Han
- Metabolism and Function of RNA in the Nucleus, Institut Jacques Monod, CNRS, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France
| | - Terence R Strick
- Molecular Motors and Machines group, Ecole normale supérieure, Institut de Biologie de l’Ecole normale supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France
- Programme Equipe Labellisées, Ligue Contre le Cancer, 75013 Paris, France
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5
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Giannini M, Porrua O. Senataxin: A key actor in RNA metabolism, genome integrity and neurodegeneration. Biochimie 2024; 217:10-19. [PMID: 37558082 DOI: 10.1016/j.biochi.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023]
Abstract
The RNA/DNA helicase senataxin (SETX) has been involved in multiple crucial processes related to genome expression and integrity such us transcription termination, the regulation of transcription-replication conflicts and the resolution of R-loops. SETX has been the focus of numerous studies since the discovery that mutations in its coding gene are the root cause of two different neurodegenerative diseases: Ataxia with Oculomotor Apraxia type 2 (AOA2) and a juvenile form of Amyotrophic Lateral Sclerosis (ALS4). A plethora of cellular phenotypes have been described as the result of SETX deficiency, yet the precise molecular function of SETX as well as the molecular pathways leading from SETX mutations to AOA2 and ALS4 pathologies have remained unclear. However, recent data have shed light onto the biochemical activities and biological roles of SETX, thus providing new clues to understand the molecular consequences of SETX mutation. In this review we summarize near two decades of scientific effort to elucidate SETX function, we discuss strengths and limitations of the approaches and models used thus far to investigate SETX-associated diseases and suggest new possible research avenues for the study of AOA2 and ALS4 pathogenesis.
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Affiliation(s)
- Marta Giannini
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Odil Porrua
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.
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6
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Appel CD, Bermek O, Dandey VP, Wood M, Viverette E, Williams JG, Bouvette J, Riccio AA, Krahn JM, Borgnia MJ, Williams RS. Sen1 architecture: RNA-DNA hybrid resolution, autoregulation, and insights into SETX inactivation in AOA2. Mol Cell 2023; 83:3692-3706.e5. [PMID: 37832548 PMCID: PMC10629462 DOI: 10.1016/j.molcel.2023.09.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/25/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
The senataxin (SETX, Sen1 in yeasts) RNA-DNA hybrid resolving helicase regulates multiple nuclear transactions, including DNA replication, transcription, and DNA repair, but the molecular basis for Sen1 activities is ill defined. Here, Sen1 cryoelectron microscopy (cryo-EM) reconstructions reveal an elongated inchworm-like architecture. Sen1 is composed of an amino terminal helical repeat Sen1 N-terminal (Sen1N) regulatory domain that is flexibly linked to its C-terminal SF1B helicase motor core (Sen1Hel) via an intrinsically disordered tether. In an autoinhibited state, the Sen1Sen1N domain regulates substrate engagement by promoting occlusion of the RNA substrate-binding cleft. The X-ray structure of an activated Sen1Hel engaging single-stranded RNA and ADP-SO4 shows that the enzyme encircles RNA and implicates a single-nucleotide power stroke in the Sen1 RNA translocation mechanism. Together, our data unveil dynamic protein-protein and protein-RNA interfaces underpinning helicase regulation and inactivation of human SETX activity by RNA-binding-deficient mutants in ataxia with oculomotor apraxia 2 neurodegenerative disease.
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Affiliation(s)
- C Denise Appel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Oya Bermek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Venkata P Dandey
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Makayla Wood
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Elizabeth Viverette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Jason G Williams
- Epigenetics and Stem Cell Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Jonathan Bouvette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Amanda A Riccio
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.
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7
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Goguen EC, Brow DA. Domains and residues of the Saccharomyces cerevisiae hnRNP protein Hrp1 important for transcriptional autoregulation and noncoding RNA termination. Genetics 2023; 225:iyad134. [PMID: 37467478 PMCID: PMC10471224 DOI: 10.1093/genetics/iyad134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023] Open
Abstract
Proteins that bind the nascent transcript exiting RNA polymerase II can regulate transcription elongation. The essential Saccharomyces cerevisiae hnRNP protein Hrp1 is one such protein and participates in both cleavage and polyadenylation-coupled and Nrd1-Nab3-Sen1-dependent RNA polymerase II termination. Prior evidence that Hrp1 is a positive RNA polymerase II elongation factor suggests that its release from the elongation complex promotes termination. Here we report the effects of deletions and substitutions in Hrp1 on its autoregulation via an Nrd1-Nab3-Sen1-dependent transcription attenuator in the 5'-UTR of its mRNA and on the function of an Hrp1-dependent Nrd1-Nab3-Sen1 terminator in the SNR82 snoRNA gene. Deletion of either of two central RNA recognition motifs or either of the flanking low-sequence complexity domains is lethal. Smaller, viable deletions in the amino-terminal low-sequence complexity domain cause readthrough of both the HRP1 attenuator and SNR82 terminator. Substitutions that cause readthrough localized mostly to the RNA recognition motifs, although not always to the RNA-binding face. We found that autoregulation of Hrp1 mRNA synthesis is surprisingly robust, overcoming the expected lethal effects of the start codon and frameshift mutations via overexpression of the mRNA up to 40-fold. Our results suggest a model in which binding of attenuator or terminator elements in the nascent transcript by RNA recognition motifs 1 and 2 disrupts interactions between RNA recognition motif 2 and the RNA polymerase II elongation complex, increasing its susceptibility to termination.
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Affiliation(s)
- Emma C Goguen
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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8
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Lee SY, Miller KM, Kim JJ. Clinical and Mechanistic Implications of R-Loops in Human Leukemias. Int J Mol Sci 2023; 24:ijms24065966. [PMID: 36983041 PMCID: PMC10052022 DOI: 10.3390/ijms24065966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/17/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Genetic mutations or environmental agents are major contributors to leukemia and are associated with genomic instability. R-loops are three-stranded nucleic acid structures consisting of an RNA-DNA hybrid and a non-template single-stranded DNA. These structures regulate various cellular processes, including transcription, replication, and DSB repair. However, unregulated R-loop formation can cause DNA damage and genomic instability, which are potential drivers of cancer including leukemia. In this review, we discuss the current understanding of aberrant R-loop formation and how it influences genomic instability and leukemia development. We also consider the possibility of R-loops as therapeutic targets for cancer treatment.
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Affiliation(s)
- Seo-Yun Lee
- Department of Life Science and Multidisciplinary, Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jae-Jin Kim
- Department of Life Science and Multidisciplinary, Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
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9
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Villa T, Porrua O. Pervasive transcription: a controlled risk. FEBS J 2022. [PMID: 35587776 DOI: 10.1111/febs.16530] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/26/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022]
Abstract
Transcriptome-wide interrogation of eukaryotic genomes has unveiled the pervasive nature of RNA polymerase II transcription. Virtually, any DNA region with an accessible chromatin structure can be transcribed, resulting in a mass production of noncoding RNAs (ncRNAs) with the potential of interfering with gene expression programs. Budding yeast has proved to be a powerful model organism to understand the mechanisms at play to control pervasive transcription and overcome the risks of hazardous disruption of cellular functions. In this review, we focus on the actors and strategies yeasts employ to govern ncRNA production, and we discuss recent findings highlighting the dangers of losing control over pervasive transcription.
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Affiliation(s)
- Tommaso Villa
- Institut Jacques Monod CNRS, Université de Paris Cité France
| | - Odil Porrua
- Institut Jacques Monod CNRS, Université de Paris Cité France
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10
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Zardoni L, Nardini E, Brambati A, Lucca C, Choudhary R, Loperfido F, Sabbioneda S, Liberi G. Elongating RNA polymerase II and RNA:DNA hybrids hinder fork progression and gene expression at sites of head-on replication-transcription collisions. Nucleic Acids Res 2021; 49:12769-12784. [PMID: 34878142 PMCID: PMC8682787 DOI: 10.1093/nar/gkab1146] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/20/2022] Open
Abstract
Uncoordinated clashes between replication forks and transcription cause replication stress and genome instability, which are hallmarks of cancer and neurodegeneration. Here, we investigate the outcomes of head-on replication-transcription collisions, using as a model system budding yeast mutants for the helicase Sen1, the ortholog of human Senataxin. We found that RNA Polymerase II accumulates together with RNA:DNA hybrids at sites of head-on collisions. The replication fork and RNA Polymerase II are both arrested during the clash, leading to DNA damage and, in the long run, the inhibition of gene expression. The inactivation of RNA Polymerase II elongation factors, such as the HMG-like protein Spt2 and the DISF and PAF complexes, but not alterations in chromatin structure, allows replication fork progression through transcribed regions. Attenuation of RNA Polymerase II elongation rescues RNA:DNA hybrid accumulation and DNA damage sensitivity caused by the absence of Sen1, but not of RNase H proteins, suggesting that such enzymes counteract toxic RNA:DNA hybrids at different stages of the cell cycle with Sen1 mainly acting in replication. We suggest that the main obstacle to replication fork progression is the elongating RNA Polymerase II engaged in an R-loop, rather than RNA:DNA hybrids per se or hybrid-associated chromatin modifications.
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Affiliation(s)
- Luca Zardoni
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy.,Scuola Universitaria Superiore IUSS, 27100 Pavia, Italy
| | - Eleonora Nardini
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Alessandra Brambati
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | | | | | - Federica Loperfido
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy
| | - Giordano Liberi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza", CNR, 27100 Pavia, Italy.,IFOM Foundation, 20139 Milan, Italy
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11
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San Martin-Alonso M, Soler-Oliva ME, García-Rubio M, García-Muse T, Aguilera A. Harmful R-loops are prevented via different cell cycle-specific mechanisms. Nat Commun 2021; 12:4451. [PMID: 34294712 PMCID: PMC8298424 DOI: 10.1038/s41467-021-24737-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 07/01/2021] [Indexed: 12/13/2022] Open
Abstract
Identifying how R-loops are generated is crucial to know how transcription compromises genome integrity. We show by genome-wide analysis of conditional yeast mutants that the THO transcription complex, prevents R-loop formation in G1 and S-phase, whereas the Sen1 DNA-RNA helicase prevents them only in S-phase. Interestingly, damage accumulates asymmetrically downstream of the replication fork in sen1 cells but symmetrically in the hpr1 THO mutant. Our results indicate that: R-loops form co-transcriptionally independently of DNA replication; that THO is a general and cell-cycle independent safeguard against R-loops, and that Sen1, in contrast to previously believed, is an S-phase-specific R-loop resolvase. These conclusions have important implications for the mechanism of R-loop formation and the role of other factors reported to affect on R-loop homeostasis.
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Affiliation(s)
- Marta San Martin-Alonso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-UPO, Seville, Spain
| | - María E Soler-Oliva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-UPO, Seville, Spain
| | - María García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-UPO, Seville, Spain
| | - Tatiana García-Muse
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-UPO, Seville, Spain.
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-UPO, Seville, Spain.
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12
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Dutta M, Moin M, Saha A, Dutta D, Bakshi A, Kirti PB. Gain-of-function mutagenesis through activation tagging identifies XPB2 and SEN1 helicase genes as potential targets for drought stress tolerance in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2253-2272. [PMID: 33821294 DOI: 10.1007/s00122-021-03823-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 03/23/2021] [Indexed: 05/13/2023]
Abstract
XPB2 and SEN1 helicases were identified through activation tagging as potential candidate genes in rice for inducing high water-use efficiency (WUE) and maintaining sustainable yield under drought stress. As a follow-up on the high-water-use-efficiency screening and physiological analyses of the activation-tagged gain-of-function mutant lines that were developed in an indica rice variety, BPT-5204 (Moin et al. in Plant Cell Environ 39:2440-2459, 2016a, https://doi.org/10.1111/pce.12796 ), we have identified two gain-of-function mutant lines (XM3 and SM4), which evidenced the activation of two helicases, ATP-dependent DNA helicase (XPB2) and RNA helicase (SEN1), respectively. We performed the transcript profiling of XPB2 and SEN1 upon exposure to various stress conditions and found their significant upregulation, particularly in ABA and PEG treatments. Extensive morpho-physiological and biochemical analyses based on 24 metrics were performed under dehydration stress (PEG) and phytohormone (ABA) treatments for the wild-type and the two mutant lines. Principal component analysis (PCA) performed on the dataset captured 72.73% of the cumulative variance using the parameters influencing the first two principal components. The tagged mutants exhibited reduced leaf wilting, improved revival efficiency, constant amylose:amylopectin ratio, high chlorophyll and proline contents, profuse tillering, high quantum efficiency and yield-related traits with respect to their controls. These observations were further validated under greenhouse conditions by the periodic withdrawal of water at the pot level. Germination of the seeds of these mutant lines indicated their insensitivity to high ABA concentration. The associated upregulation of stress-specific genes further suggests that their drought tolerance might be because of the coordinated expression of several stress-responsive genes in these two mutants. Altogether, our results provided a firm basis for SEN1 and XPB2 as potential candidates for manipulation of drought tolerance and improving rice performance and yield under limited water conditions.
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Affiliation(s)
- Mouboni Dutta
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Mazahar Moin
- Biotechnology Division, Indian Institute of Rice Research, Hyderabad, 500030, India.
| | - Anusree Saha
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Dibyendu Dutta
- Department of Chemical Engineering, Indian Institute of Technology, Bombay, Mumbai, 400076, India
| | - Achala Bakshi
- Biotechnology Division, Indian Institute of Rice Research, Hyderabad, 500030, India
| | - P B Kirti
- Agri Biotech Foundation, PJTS Agricultural University Campus, Hyderabad, 500030, India.
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13
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Ramachandran S, Ma TS, Griffin J, Ng N, Foskolou IP, Hwang MS, Victori P, Cheng WC, Buffa FM, Leszczynska KB, El-Khamisy SF, Gromak N, Hammond EM. Hypoxia-induced SETX links replication stress with the unfolded protein response. Nat Commun 2021; 12:3686. [PMID: 34140498 PMCID: PMC8211819 DOI: 10.1038/s41467-021-24066-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 05/31/2021] [Indexed: 02/07/2023] Open
Abstract
Tumour hypoxia is associated with poor patient prognosis and therapy resistance. A unique transcriptional response is initiated by hypoxia which includes the rapid activation of numerous transcription factors in a background of reduced global transcription. Here, we show that the biological response to hypoxia includes the accumulation of R-loops and the induction of the RNA/DNA helicase SETX. In the absence of hypoxia-induced SETX, R-loop levels increase, DNA damage accumulates, and DNA replication rates decrease. Therefore, suggesting that, SETX plays a role in protecting cells from DNA damage induced during transcription in hypoxia. Importantly, we propose that the mechanism of SETX induction in hypoxia is reliant on the PERK/ATF4 arm of the unfolded protein response. These data not only highlight the unique cellular response to hypoxia, which includes both a replication stress-dependent DNA damage response and an unfolded protein response but uncover a novel link between these two distinct pathways.
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Affiliation(s)
- Shaliny Ramachandran
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Tiffany S Ma
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Jon Griffin
- Department of Molecular Biology and Biotechnology, Healthy Lifespan and Neuroscience Institute, Firth Court, University of Sheffield, Sheffield, UK
- Department of Histopathology, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Natalie Ng
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Iosifina P Foskolou
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Ming-Shih Hwang
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Pedro Victori
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Wei-Chen Cheng
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Francesca M Buffa
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
| | - Katarzyna B Leszczynska
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK
- Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Sherif F El-Khamisy
- Department of Molecular Biology and Biotechnology, Healthy Lifespan and Neuroscience Institute, Firth Court, University of Sheffield, Sheffield, UK
- Institute of Cancer Therapeutics, University of Bradford, Bradford, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ester M Hammond
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, UK.
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14
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San Martin Alonso M, Noordermeer S. Untangling the crosstalk between BRCA1 and R-loops during DNA repair. Nucleic Acids Res 2021; 49:4848-4863. [PMID: 33755171 PMCID: PMC8136775 DOI: 10.1093/nar/gkab178] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/25/2021] [Accepted: 03/04/2021] [Indexed: 01/13/2023] Open
Abstract
R-loops are RNA:DNA hybrids assembled during biological processes but are also linked to genetic instability when formed out of their natural context. Emerging evidence suggests that the repair of DNA double-strand breaks requires the formation of a transient R-loop, which eventually must be removed to guarantee a correct repair process. The multifaceted BRCA1 protein has been shown to be recruited at this specific break-induced R-loop, and it facilitates mechanisms in order to regulate R-loop removal. In this review, we discuss the different potential roles of BRCA1 in R-loop homeostasis during DNA repair and how these processes ensure faithful DSB repair.
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Affiliation(s)
- Marta San Martin Alonso
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Sylvie M Noordermeer
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
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15
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Klaric JA, Wüst S, Panier S. New Faces of old Friends: Emerging new Roles of RNA-Binding Proteins in the DNA Double-Strand Break Response. Front Mol Biosci 2021; 8:668821. [PMID: 34026839 PMCID: PMC8138124 DOI: 10.3389/fmolb.2021.668821] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/22/2021] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions. To protect genomic stability and ensure cell homeostasis, cells mount a complex signaling-based response that not only coordinates the repair of the broken DNA strand but also activates cell cycle checkpoints and, if necessary, induces cell death. The last decade has seen a flurry of studies that have identified RNA-binding proteins (RBPs) as novel regulators of the DSB response. While many of these RBPs have well-characterized roles in gene expression, it is becoming increasingly clear that they also have non-canonical functions in the DSB response that go well beyond transcription, splicing and mRNA processing. Here, we review the current understanding of how RBPs are integrated into the cellular response to DSBs and describe how these proteins directly participate in signal transduction, amplification and repair at damaged chromatin. In addition, we discuss the implications of an RBP-mediated DSB response for genome instability and age-associated diseases such as cancer and neurodegeneration.
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Affiliation(s)
- Julie A Klaric
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stas Wüst
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Stephanie Panier
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD) Research Center, University of Cologne, Cologne, Germany
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16
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Dhar S, Datta A, Brosh RM. DNA helicases and their roles in cancer. DNA Repair (Amst) 2020; 96:102994. [PMID: 33137625 DOI: 10.1016/j.dnarep.2020.102994] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022]
Abstract
DNA helicases, known for their fundamentally important roles in genomic stability, are high profile players in cancer. Not only are there monogenic helicase disorders with a strong disposition to cancer, it is well appreciated that helicase variants are associated with specific cancers (e.g., breast cancer). Flipping the coin, DNA helicases are frequently overexpressed in cancerous tissues and reduction in helicase gene expression results in reduced proliferation and growth capacity, as well as DNA damage induction and apoptosis of cancer cells. The seminal roles of helicases in the DNA damage and replication stress responses, as well as DNA repair pathways, validate their vital importance in cancer biology and suggest their potential values as targets in anti-cancer therapy. In recent years, many laboratories have characterized the specialized roles of helicase to resolve transcription-replication conflicts, maintain telomeres, mediate cell cycle checkpoints, remodel stalled replication forks, and regulate transcription. In vivo models, particularly mice, have been used to interrogate helicase function and serve as a bridge for preclinical studies that may lead to novel therapeutic approaches. In this review, we will summarize our current knowledge of DNA helicases and their roles in cancer, emphasizing the latest developments.
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Affiliation(s)
- Srijita Dhar
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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17
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Kazadi D, Lim J, Rothschild G, Grinstein V, Laffleur B, Becherel O, Lavin MJ, Basu U. Effects of senataxin and RNA exosome on B-cell chromosomal integrity. Heliyon 2020; 6:e03442. [PMID: 32195383 PMCID: PMC7075999 DOI: 10.1016/j.heliyon.2020.e03442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 01/07/2020] [Accepted: 02/13/2020] [Indexed: 11/10/2022] Open
Abstract
Loss of function of senataxin (SETX), a bona-fide RNA/DNA helicase, is associated with neuronal degeneration leading to Ataxia and Ocular Apraxia (AOA) in human patients. SETX is proposed to promote transcription termination, DNA replication, DNA repair, and to unwind deleterious RNA:DNA hybrids in the genome. In all the above-mentioned mechanisms, SETX unwinds transcription complex-associated nascent RNA which is then degraded by the RNA exosome complex. Here we have used B cells isolated from a SETX mutant mouse model and compared genomic instability and immunoglobulin heavy chain locus (IgH) class switch recombination (CSR) to evaluate aberrant and programmed genomic rearrangements, respectively. Similar to RNA exosome mutant primary B cells, SETX mutant primary B cells display genomic instability but a modest decrease in efficiency of CSR. Furthermore, knockdown of Setx mRNAs from CH12–F3 B-cell lines leads to a defect in IgA CSR and accumulation of aberrant patterns of mutations in IgH switch sequences. Given that SETX mutant mice do not recapitulate the AOA neurodegenerative phenotype, it is possible that some aspects of SETX biology are rescued by redundant helicases in mice. Overall, our study provides new insights into the role of the SETX/RNA exosome axis in suppressing genomic instability so that programmed DNA breaks are properly orchestrated.
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Affiliation(s)
- David Kazadi
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Veronika Grinstein
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Brice Laffleur
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Olivier Becherel
- Centre for Clinical Research, University of Queensland, Brisbane, Qld, Australia
| | - Martin J Lavin
- Centre for Clinical Research, University of Queensland, Brisbane, Qld, Australia
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
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18
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Bader AS, Hawley BR, Wilczynska A, Bushell M. The roles of RNA in DNA double-strand break repair. Br J Cancer 2020; 122:613-623. [PMID: 31894141 PMCID: PMC7054366 DOI: 10.1038/s41416-019-0624-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 09/12/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022] Open
Abstract
Effective DNA repair is essential for cell survival: a failure to correctly repair damage leads to the accumulation of mutations and is the driving force for carcinogenesis. Multiple pathways have evolved to protect against both intrinsic and extrinsic genotoxic events, and recent developments have highlighted an unforeseen critical role for RNA in ensuring genome stability. It is currently unclear exactly how RNA molecules participate in the repair pathways, although many models have been proposed and it is possible that RNA acts in diverse ways to facilitate DNA repair. A number of well-documented DNA repair factors have been described to have RNA-binding capacities and, moreover, screens investigating DNA-damage repair mechanisms have identified RNA-binding proteins as a major group of novel factors involved in DNA repair. In this review, we integrate some of these datasets to identify commonalities that might highlight novel and interesting factors for future investigations. This emerging role for RNA opens up a new dimension in the field of DNA repair; we discuss its impact on our current understanding of DNA repair processes and consider how it might influence cancer progression.
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Affiliation(s)
- Aldo S Bader
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Ben R Hawley
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | | | - Martin Bushell
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
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19
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Brambati A, Zardoni L, Nardini E, Pellicioli A, Liberi G. The dark side of RNA:DNA hybrids. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 784:108300. [PMID: 32430097 DOI: 10.1016/j.mrrev.2020.108300] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/07/2020] [Accepted: 02/23/2020] [Indexed: 12/15/2022]
Abstract
RNA:DNA hybrids form when nascent transcripts anneal to the DNA template strand or any homologous DNA region. Co-transcriptional RNA:DNA hybrids, organized in R-loop structures together with the displaced non-transcribed strand, assist gene expression, DNA repair and other physiological cellular functions. A dark side of the matter is that RNA:DNA hybrids are also a cause of DNA damage and human diseases. In this review, we summarize recent advances in the understanding of the mechanisms by which the impairment of hybrid turnover promotes DNA damage and genome instability via the interference with DNA replication and DNA double-strand break repair. We also discuss how hybrids could contribute to cancer, neurodegeneration and susceptibility to viral infections, focusing on dysfunctions associated with the anti-R-loop helicase Senataxin.
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Affiliation(s)
- Alessandra Brambati
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy.
| | - Luca Zardoni
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy; Scuola Universitaria Superiore, IUSS, 27100, Pavia, Italy
| | - Eleonora Nardini
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy
| | - Achille Pellicioli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Giordano Liberi
- Istituto di Genetica Molecolare Luigi Luca Cavalli-Sforza, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy; IFOM Foundation, Via Adamello 16, 20139, Milan, Italy.
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20
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Han Z, Jasnovidova O, Haidara N, Tudek A, Kubicek K, Libri D, Stefl R, Porrua O. Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1. EMBO J 2020; 39:e101548. [PMID: 32107786 PMCID: PMC7110113 DOI: 10.15252/embj.2019101548] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 01/23/2020] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
Pervasive transcription is a widespread phenomenon leading to the production of a plethora of non‐coding RNAs (ncRNAs) without apparent function. Pervasive transcription poses a threat to proper gene expression that needs to be controlled. In yeast, the highly conserved helicase Sen1 restricts pervasive transcription by inducing termination of non‐coding transcription. However, the mechanisms underlying the specific function of Sen1 at ncRNAs are poorly understood. Here, we identify a motif in an intrinsically disordered region of Sen1 that mimics the phosphorylated carboxy‐terminal domain (CTD) of RNA polymerase II, and structurally characterize its recognition by the CTD‐interacting domain of Nrd1, an RNA‐binding protein that binds specific sequences in ncRNAs. In addition, we show that Sen1‐dependent termination strictly requires CTD recognition by the N‐terminal domain of Sen1. We provide evidence that the Sen1‐CTD interaction does not promote initial Sen1 recruitment, but rather enhances Sen1 capacity to induce the release of paused RNAPII from the DNA. Our results shed light on the network of protein–protein interactions that control termination of non‐coding transcription by Sen1.
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Affiliation(s)
- Zhong Han
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France.,Université Paris-Saclay, Yvette, France
| | - Olga Jasnovidova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Nouhou Haidara
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France.,Université Paris-Saclay, Yvette, France
| | - Agnieszka Tudek
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Karel Kubicek
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Domenico Libri
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Richard Stefl
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Odil Porrua
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
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21
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Appanah R, Lones EC, Aiello U, Libri D, De Piccoli G. Sen1 Is Recruited to Replication Forks via Ctf4 and Mrc1 and Promotes Genome Stability. Cell Rep 2020; 30:2094-2105.e9. [PMID: 32075754 PMCID: PMC7034062 DOI: 10.1016/j.celrep.2020.01.087] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 09/06/2019] [Accepted: 01/24/2020] [Indexed: 01/21/2023] Open
Abstract
DNA replication and RNA transcription compete for the same substrate during S phase. Cells have evolved several mechanisms to minimize such conflicts. Here, we identify the mechanism by which the transcription termination helicase Sen1 associates with replisomes. We show that the N terminus of Sen1 is both sufficient and necessary for replisome association and that it binds to the replisome via the components Ctf4 and Mrc1. We generated a separation of function mutant, sen1-3, which abolishes replisome binding without affecting transcription termination. We observe that the sen1-3 mutants show increased genome instability and recombination levels. Moreover, sen1-3 is synthetically defective with mutations in genes involved in RNA metabolism and the S phase checkpoint. RNH1 overexpression suppresses defects in the former, but not the latter. These findings illustrate how Sen1 plays a key function at replication forks during DNA replication to promote fork progression and chromosome stability.
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Affiliation(s)
- Rowin Appanah
- Warwick Medical School, University of Warwick, CV4 7AL Coventry, UK
| | | | - Umberto Aiello
- Institut Jacques Monod, CNRS, UMR7592, Université Paris Diderot, Paris Sorbonne Cité, Paris, France
| | - Domenico Libri
- Institut Jacques Monod, CNRS, UMR7592, Université Paris Diderot, Paris Sorbonne Cité, Paris, France
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22
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Abstract
The repair of DNA double-strand breaks occurs through a series of defined steps that are evolutionarily conserved and well-understood in most experimental organisms. However, it is becoming increasingly clear that repair does not occur in isolation from other DNA transactions. Transcription of DNA produces topological changes, RNA species, and RNA-dependent protein complexes that can dramatically influence the efficiency and outcomes of DNA double-strand break repair. The transcription-associated history of several double-strand break repair factors is reviewed here, with an emphasis on their roles in regulating R-loops and the emerging role of R-loops in coordination of repair events. Evidence for nucleolytic processing of R-loops is also discussed, as well as the molecular tools commonly used to measure RNA-DNA hybrids in cells.
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Affiliation(s)
- Tanya T Paull
- The Department of Molecular Biosciences and the Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
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23
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Sariki SK, Kumawat R, Singh V, Tomar RS. Flocculation ofSaccharomyces cerevisiaeis dependent on activation of Slt2 and Rlm1 regulated by the cell wall integrity pathway. Mol Microbiol 2019; 112:1350-1369. [DOI: 10.1111/mmi.14375] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Santhosh Kumar Sariki
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Ramesh Kumawat
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Vikash Singh
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
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24
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Rivosecchi J, Larochelle M, Teste C, Grenier F, Malapert A, Ricci EP, Bernard P, Bachand F, Vanoosthuyse V. Senataxin homologue Sen1 is required for efficient termination of RNA polymerase III transcription. EMBO J 2019; 38:e101955. [PMID: 31294478 DOI: 10.15252/embj.2019101955] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 01/13/2023] Open
Abstract
R-loop disassembly by the human helicase Senataxin contributes to genome integrity and to proper transcription termination at a subset of RNA polymerase II genes. Whether Senataxin also contributes to transcription termination at other classes of genes has remained unclear. Here, we show that Sen1, one of two fission yeast homologues of Senataxin, promotes efficient termination of RNA polymerase III (RNAP3) transcription in vivo. In the absence of Sen1, RNAP3 accumulates downstream of RNAP3-transcribed genes and produces long exosome-sensitive 3'-extended transcripts. Importantly, neither of these defects was affected by the removal of R-loops. The finding that Sen1 acts as an ancillary factor for RNAP3 transcription termination in vivo challenges the pre-existing view that RNAP3 terminates transcription autonomously. We propose that Sen1 is a cofactor for transcription termination that has been co-opted by different RNA polymerases in the course of evolution.
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Affiliation(s)
- Julieta Rivosecchi
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, CNRS, UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Marc Larochelle
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Camille Teste
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, CNRS, UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Frédéric Grenier
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Amélie Malapert
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, CNRS, UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, CNRS, UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Pascal Bernard
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, CNRS, UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - François Bachand
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, Canada.,Centre de Recherche du CHUS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Vincent Vanoosthuyse
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, CNRS, UMR 5239, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France
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25
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Makharashvili N, Arora S, Yin Y, Fu Q, Wen X, Lee JH, Kao CH, Leung JWC, Miller KM, Paull TT. Sae2/CtIP prevents R-loop accumulation in eukaryotic cells. eLife 2018; 7:e42733. [PMID: 30523780 PMCID: PMC6296784 DOI: 10.7554/elife.42733] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/30/2018] [Indexed: 02/06/2023] Open
Abstract
The Sae2/CtIP protein is required for efficient processing of DNA double-strand breaks that initiate homologous recombination in eukaryotic cells. Sae2/CtIP is also important for survival of single-stranded Top1-induced lesions and CtIP is known to associate directly with transcription-associated complexes in mammalian cells. Here we investigate the role of Sae2/CtIP at single-strand lesions in budding yeast and in human cells and find that depletion of Sae2/CtIP promotes the accumulation of stalled RNA polymerase and RNA-DNA hybrids at sites of highly expressed genes. Overexpression of the RNA-DNA helicase Senataxin suppresses DNA damage sensitivity and R-loop accumulation in Sae2/CtIP-deficient cells, and a catalytic mutant of CtIP fails to complement this sensitivity, indicating a role for CtIP nuclease activity in the repair process. Based on this evidence, we propose that R-loop processing by 5' flap endonucleases is a necessary step in the stabilization and removal of nascent R-loop initiating structures in eukaryotic cells.
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Affiliation(s)
- Nodar Makharashvili
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Sucheta Arora
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Yizhi Yin
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Qiong Fu
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Oncology Branch, Center for Cancer ResearchNational Cancer Institute, National Institutes of HealthBethesdaUnited States
| | - Xuemei Wen
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Ji-Hoon Lee
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Chung-Hsuan Kao
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Justin WC Leung
- Department of Radiation OncologyUniversity of Arkansas for Medical SciencesLittle RockUnited States
| | - Kyle M Miller
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
| | - Tanya T Paull
- Howard Hughes Medical Institute, The University of Texas at AustinAustinUnited states
- Department of Molecular BiosciencesThe University of Texas at AustinAustinUnited States
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26
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Tedeschi FA, Cloutier SC, Tran EJ, Jankowsky E. The DEAD-box protein Dbp2p is linked to noncoding RNAs, the helicase Sen1p, and R-loops. RNA (NEW YORK, N.Y.) 2018; 24:1693-1705. [PMID: 30262458 PMCID: PMC6239179 DOI: 10.1261/rna.067249.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/20/2018] [Indexed: 06/08/2023]
Abstract
The DEAD-box RNA helicase Dbp2p is highly conserved in eukaryotes and has been implicated in transcription, ribosome biogenesis, mRNP assembly, nuclear export, and long noncoding RNA (lncRNA) function. It is not understood how Dbp2p performs these seemingly unrelated biological roles. An important step toward addressing this question is the determination of cellular RNA binding sites of Dbp2p. Here, we identify transcriptome-wide RNA binding sites of Dbp2p from Saccharomyces cerevisiae using UV-crosslinking, denaturing tandem affinity purification, and next generation sequencing. We find that Dbp2p crosslinks to mRNAs and ribosomal RNAs, and markedly to noncoding RNAs, including snoRNA, snRNAs, and tRNAs. In snoRNAs, Dbp2p preferentially crosslinks at sites near the 3' ends. These sites coincide with regions where RNA-DNA hybrids (R-loops) form and with binding sites of Sen1p, another RNA helicase that functions in transcription termination and 3' processing of noncoding RNAs. We show that Dbp2p interacts in an RNA-independent manner with Sen1p in vivo. Dbp2p crosslinks to tRNAs and other RNAs also at sites where R-loops form. Collectively, our data link Dbp2p to noncoding RNAs, Sen1p, and R-loops. The transcriptome-wide connection to R-loops provides a unifying theme for diverse cellular roles of Dbp2p.
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Affiliation(s)
- Frank A Tedeschi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Sara C Cloutier
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
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27
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Lawson MR, Ma W, Bellecourt MJ, Artsimovitch I, Martin A, Landick R, Schulten K, Berger JM. Mechanism for the Regulated Control of Bacterial Transcription Termination by a Universal Adaptor Protein. Mol Cell 2018; 71:911-922.e4. [PMID: 30122535 DOI: 10.1016/j.molcel.2018.07.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/21/2018] [Accepted: 07/13/2018] [Indexed: 12/14/2022]
Abstract
NusG/Spt5 proteins are the only transcription factors utilized by all cellular organisms. In enterobacteria, NusG antagonizes the transcription termination activity of Rho, a hexameric helicase, during the synthesis of ribosomal and actively translated mRNAs. Paradoxically, NusG helps Rho act on untranslated transcripts, including non-canonical antisense RNAs and those arising from translational stress; how NusG fulfills these disparate functions is unknown. Here, we demonstrate that NusG activates Rho by assisting helicase isomerization from an open-ring, RNA-loading state to a closed-ring, catalytically active translocase. A crystal structure of closed-ring Rho in complex with NusG reveals the physical basis for this activation and further explains how Rho is excluded from translationally competent RNAs. This study demonstrates how a universally conserved transcription factor acts to modulate the activity of a ring-shaped ATPase motor and establishes how the innate sequence bias of a termination factor can be modulated to silence pervasive, aberrant transcription.
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Affiliation(s)
- Michael R Lawson
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Wen Ma
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science Technology, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Michael J Bellecourt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Klaus Schulten
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science Technology, Urbana, IL 61801, USA; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - James M Berger
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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28
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RNA Polymerase II Transcription Attenuation at the Yeast DNA Repair Gene, DEF1, Involves Sen1-Dependent and Polyadenylation Site-Dependent Termination. G3-GENES GENOMES GENETICS 2018; 8:2043-2058. [PMID: 29686108 PMCID: PMC5982831 DOI: 10.1534/g3.118.200072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Termination of RNA Polymerase II (Pol II) activity serves a vital cellular role by separating ubiquitous transcription units and influencing RNA fate and function. In the yeast Saccharomyces cerevisiae, Pol II termination is carried out by cleavage and polyadenylation factor (CPF-CF) and Nrd1-Nab3-Sen1 (NNS) complexes, which operate primarily at mRNA and non-coding RNA genes, respectively. Premature Pol II termination (attenuation) contributes to gene regulation, but there is limited knowledge of its prevalence and biological significance. In particular, it is unclear how much crosstalk occurs between CPF-CF and NNS complexes and how Pol II attenuation is modulated during stress adaptation. In this study, we have identified an attenuator in the DEF1 DNA repair gene, which includes a portion of the 5′-untranslated region (UTR) and upstream open reading frame (ORF). Using a plasmid-based reporter gene system, we conducted a genetic screen of 14 termination mutants and their ability to confer Pol II read-through defects. The DEF1 attenuator behaved as a hybrid terminator, relying heavily on CPF-CF and Sen1 but without Nrd1 and Nab3 involvement. Our genetic selection identified 22 cis-acting point mutations that clustered into four regions, including a polyadenylation site efficiency element that genetically interacts with its cognate binding-protein Hrp1. Outside of the reporter gene context, a DEF1 attenuator mutant increased mRNA and protein expression, exacerbating the toxicity of a constitutively active Def1 protein. Overall, our data support a biologically significant role for transcription attenuation in regulating DEF1 expression, which can be modulated during the DNA damage response.
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29
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Mischo HE, Chun Y, Harlen KM, Smalec BM, Dhir S, Churchman LS, Buratowski S. Cell-Cycle Modulation of Transcription Termination Factor Sen1. Mol Cell 2018; 70:312-326.e7. [PMID: 29656924 PMCID: PMC5919780 DOI: 10.1016/j.molcel.2018.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 06/26/2017] [Accepted: 03/08/2018] [Indexed: 01/14/2023]
Abstract
Many non-coding transcripts (ncRNA) generated by RNA polymerase II in S. cerevisiae are terminated by the Nrd1-Nab3-Sen1 complex. However, Sen1 helicase levels are surprisingly low compared with Nrd1 and Nab3, raising questions regarding how ncRNA can be terminated in an efficient and timely manner. We show that Sen1 levels increase during the S and G2 phases of the cell cycle, leading to increased termination activity of NNS. Overexpression of Sen1 or failure to modulate its abundance by ubiquitin-proteasome-mediated degradation greatly decreases cell fitness. Sen1 toxicity is suppressed by mutations in other termination factors, and NET-seq analysis shows that its overexpression leads to a decrease in ncRNA production and altered mRNA termination. We conclude that Sen1 levels are carefully regulated to prevent aberrant termination. We suggest that ncRNA levels and coding gene transcription termination are modulated by Sen1 to fulfill critical cell cycle-specific functions. Transcription termination factor Sen1 levels fluctuate throughout the cell cycle APC targets Sen1 for degradation during G1 Reduced Sen1 levels lower efficiency of Sen1-mediated termination Sen1 overexpression reduces cell viability because of excessive termination
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Affiliation(s)
- Hannah E Mischo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK; Mechanisms of Transcription Laboratory, Clare Hall Laboratories, Cancer Research UK London Research Institute, South Mimms EN6 3LD, UK.
| | - Yujin Chun
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin M Harlen
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan M Smalec
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Somdutta Dhir
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK
| | | | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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30
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Senataxin resolves RNA:DNA hybrids forming at DNA double-strand breaks to prevent translocations. Nat Commun 2018; 9:533. [PMID: 29416069 PMCID: PMC5803260 DOI: 10.1038/s41467-018-02894-w] [Citation(s) in RCA: 221] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/05/2018] [Indexed: 12/21/2022] Open
Abstract
Ataxia with oculomotor apraxia 2 (AOA-2) and amyotrophic lateral sclerosis (ALS4) are neurological disorders caused by mutations in the gene encoding for senataxin (SETX), a putative RNA:DNA helicase involved in transcription and in the maintenance of genome integrity. Here, using ChIP followed by high throughput sequencing (ChIP-seq), we report that senataxin is recruited at DNA double-strand breaks (DSBs) when they occur in transcriptionally active loci. Genome-wide mapping unveiled that RNA:DNA hybrids accumulate on DSB-flanking chromatin but display a narrow, DSB-induced, depletion near DNA ends coinciding with senataxin binding. Although neither required for resection nor for timely repair of DSBs, senataxin was found to promote Rad51 recruitment, to minimize illegitimate rejoining of distant DNA ends and to sustain cell viability following DSB production in active genes. Our data suggest that senataxin functions at DSBs in order to limit translocations and ensure cell viability, providing new insights on AOA2/ALS4 neuropathies.
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31
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Grunseich C, Wang IX, Watts JA, Burdick JT, Guber RD, Zhu Z, Bruzel A, Lanman T, Chen K, Schindler AB, Edwards N, Ray-Chaudhury A, Yao J, Lehky T, Piszczek G, Crain B, Fischbeck KH, Cheung VG. Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters. Mol Cell 2018; 69:426-437.e7. [PMID: 29395064 PMCID: PMC5815878 DOI: 10.1016/j.molcel.2017.12.030] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 12/11/2017] [Accepted: 12/28/2017] [Indexed: 12/15/2022]
Abstract
R-loops are three-stranded nucleic acid structures found abundantly and yet often viewed as by-products of transcription. Studying cells from patients with a motor neuron disease (amyotrophic lateral sclerosis 4 [ALS4]) caused by a mutation in senataxin, we uncovered how R-loops promote transcription. In ALS4 patients, the senataxin mutation depletes R-loops with a consequent effect on gene expression. With fewer R-loops in ALS4 cells, the expression of BAMBI, a negative regulator of transforming growth factor β (TGF-β), is reduced; that then leads to the activation of the TGF-β pathway. We uncovered that genome-wide R-loops influence promoter methylation of over 1,200 human genes. DNA methyl-transferase 1 favors binding to double-stranded DNA over R-loops. Thus, in forming R-loops, nascent RNA blocks DNA methylation and promotes further transcription. Hence, our results show that nucleic acid structures, in addition to sequences, influence the binding and activity of regulatory proteins.
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Affiliation(s)
- Christopher Grunseich
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Isabel X Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Jason A Watts
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Joshua T Burdick
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Robert D Guber
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Zhengwei Zhu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Alan Bruzel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tyler Lanman
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Kelian Chen
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Alice B Schindler
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Nancy Edwards
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Abhik Ray-Chaudhury
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Jianhua Yao
- Department of Radiology and Imaging Sciences, Clinical Center, NIH, Bethesda, MD, USA
| | - Tanya Lehky
- Electromyography Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Grzegorz Piszczek
- Biophysics Core, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Barbara Crain
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth H Fischbeck
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
| | - Vivian G Cheung
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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32
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Han Z, Porrua O. Helicases as transcription termination factors: Different solutions for a common problem. Transcription 2017; 9:152-158. [PMID: 28886303 DOI: 10.1080/21541264.2017.1361503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Helicases are enzymes that remodel nucleic acids or protein-nucleic acid complexes in an ATP-dependent manner. They are ubiquitous and can play many diverse functions related to the metabolism of nucleic acids. A few helicases from both the prokaryotic and the eukaryotic worlds have the ability to induce transcription termination. Here we discuss how the same biological function is achieved by different helicases with quite divergent structures and mechanisms of action.
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Affiliation(s)
- Zhong Han
- a Institut Jacques Monod, Centre Nationale pour la Recherche Scientifique (CNRS), UMR 7592, Université Paris Diderot, Sorbonne Paris Cité , Paris , France.,b Université Paris-Saclay , Gif sur Yvette , France
| | - Odil Porrua
- a Institut Jacques Monod, Centre Nationale pour la Recherche Scientifique (CNRS), UMR 7592, Université Paris Diderot, Sorbonne Paris Cité , Paris , France
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33
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Han Z, Libri D, Porrua O. Biochemical characterization of the helicase Sen1 provides new insights into the mechanisms of non-coding transcription termination. Nucleic Acids Res 2017; 45:1355-1370. [PMID: 28180347 PMCID: PMC5388409 DOI: 10.1093/nar/gkw1230] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/10/2016] [Accepted: 11/28/2016] [Indexed: 01/02/2023] Open
Abstract
Pervasive transcription is widespread and needs to be controlled in order to avoid interference with gene expression. In Saccharomyces cerevisiae, the highly conserved helicase Sen1 plays a key role in restricting pervasive transcription by eliciting early termination of non-coding transcription. However, many aspects of the mechanism of termination remain unclear. In this study we characterize the biochemical activities of Sen1 and their role in termination. First, we demonstrate that the helicase domain (HD) is sufficient to dissociate the elongation complex (EC) in vitro. Both full-length Sen1 and its HD can translocate along single-stranded RNA and DNA in the 5΄ to 3΄ direction. Surprisingly, however, we show that Sen1 is a relatively poorly processive enzyme, implying that it must be recruited in close proximity to the RNA polymerase II (RNAPII) for efficient termination. We present evidence that Sen1 can promote forward translocation of stalled polymerases by acting on the nascent transcript. In addition, we find that dissociation of the EC by Sen1 is favoured by the reannealing of the DNA upstream of RNAPII. Taken together, our results provide new clues to understand the mechanism of Sen1-dependent transcription termination and a rationale for the kinetic competition between elongation and termination.
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Affiliation(s)
- Zhong Han
- Institut Jacques Monod, UMR7592, Centre Nationale pour la Recherche Scientifique (CNRS), Université Paris-Diderot, Sorbonne Paris Cité, F-75205 Paris, France.,Université Paris-Saclay, 91190 Gif sur Yvette, France
| | - Domenico Libri
- Institut Jacques Monod, UMR7592, Centre Nationale pour la Recherche Scientifique (CNRS), Université Paris-Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Odil Porrua
- Institut Jacques Monod, UMR7592, Centre Nationale pour la Recherche Scientifique (CNRS), Université Paris-Diderot, Sorbonne Paris Cité, F-75205 Paris, France
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34
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Chen X, Poorey K, Carver MN, Müller U, Bekiranov S, Auble DT, Brow DA. Transcriptomes of six mutants in the Sen1 pathway reveal combinatorial control of transcription termination across the Saccharomyces cerevisiae genome. PLoS Genet 2017; 13:e1006863. [PMID: 28665995 PMCID: PMC5513554 DOI: 10.1371/journal.pgen.1006863] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 07/17/2017] [Accepted: 06/10/2017] [Indexed: 01/04/2023] Open
Abstract
Transcriptome studies on eukaryotic cells have revealed an unexpected abundance and diversity of noncoding RNAs synthesized by RNA polymerase II (Pol II), some of which influence the expression of protein-coding genes. Yet, much less is known about biogenesis of Pol II non-coding RNA than mRNAs. In the budding yeast Saccharomyces cerevisiae, initiation of non-coding transcripts by Pol II appears to be similar to that of mRNAs, but a distinct pathway is utilized for termination of most non-coding RNAs: the Sen1-dependent or “NNS” pathway. Here, we examine the effect on the S. cerevisiae transcriptome of conditional mutations in the genes encoding six different essential proteins that influence Sen1-dependent termination: Sen1, Nrd1, Nab3, Ssu72, Rpb11, and Hrp1. We observe surprisingly diverse effects on transcript abundance for the different proteins that cannot be explained simply by differing severity of the mutations. Rather, we infer from our results that termination of Pol II transcription of non-coding RNA genes is subject to complex combinatorial control that likely involves proteins beyond those studied here. Furthermore, we identify new targets and functions of Sen1-dependent termination, including a role in repression of meiotic genes in vegetative cells. In combination with other recent whole-genome studies on termination of non-coding RNAs, our results provide promising directions for further investigation. The information stored in the DNA of a cell’s chromosomes is transmitted to the rest of the cell by transcribing the DNA into RNA copies or “transcripts”. The fidelity of this process, and thus the health of the cell, depends critically on the proper function of proteins that direct transcription. Since hundreds of genes, each specifying a unique RNA transcript, are arranged in tandem along each chromosome, the beginning and end of each gene must be marked in the DNA sequence. Although encoded in DNA, the signal for terminating an RNA transcript is usually recognized in the transcript itself. We examined the genome-wide functional targets of six proteins implicated in transcription termination by identifying transcripts whose structure or abundance is altered by a mutation that compromises the activity of each protein. For a small minority of transcripts, a mutation in any of the six proteins disrupts termination. Much more commonly, a transcript is affected by a mutation in only one or a few of the six proteins, revealing the varying extent to which the proteins cooperate with one another. We discovered affected transcripts that were not known to be controlled by any of the six proteins, including a cohort of genes required for meiosis.
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Affiliation(s)
- Xin Chen
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Kunal Poorey
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - Melissa N. Carver
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - Ulrika Müller
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
| | - David T. Auble
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, United States of America
- * E-mail: (DAB); (DTA)
| | - David A. Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
- * E-mail: (DAB); (DTA)
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35
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Leonaitė B, Han Z, Basquin J, Bonneau F, Libri D, Porrua O, Conti E. Sen1 has unique structural features grafted on the architecture of the Upf1-like helicase family. EMBO J 2017; 36:1590-1604. [PMID: 28408439 PMCID: PMC5452015 DOI: 10.15252/embj.201696174] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 03/06/2017] [Accepted: 03/09/2017] [Indexed: 11/09/2022] Open
Abstract
The superfamily 1B (SF1B) helicase Sen1 is an essential protein that plays a key role in the termination of non‐coding transcription in yeast. Here, we identified the ~90 kDa helicase core of Saccharomyces cerevisiae Sen1 as sufficient for transcription termination in vitro and determined the corresponding structure at 1.8 Å resolution. In addition to the catalytic and auxiliary subdomains characteristic of the SF1B family, Sen1 has a distinct and evolutionarily conserved structural feature that “braces” the helicase core. Comparative structural analyses indicate that the “brace” is essential in shaping a favorable conformation for RNA binding and unwinding. We also show that subdomain 1C (the “prong”) is an essential element for 5′‐3′ unwinding and for Sen1‐mediated transcription termination in vitro. Finally, yeast Sen1 mutant proteins mimicking the disease forms of the human orthologue, senataxin, show lower capacity of RNA unwinding and impairment of transcription termination in vitro. The combined biochemical and structural data thus provide a molecular model for the specificity of Sen1 in transcription termination and more generally for the unwinding mechanism of 5′‐3′ helicases.
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Affiliation(s)
- Bronislava Leonaitė
- Max Planck Institute of Biochemistry, Munich, Germany.,Graduate School of Quantitative Biosciences, Ludwig-Maximilians-University, Munich, Germany
| | - Zhong Han
- Institut Jacques Monod, Centre Nationale pour la Recherche Scientifique (CNRS), UMR 7592 Université Paris Diderot, Paris, France.,Université Paris-Saclay, Gif sur Yvette, France
| | | | | | - Domenico Libri
- Institut Jacques Monod, Centre Nationale pour la Recherche Scientifique (CNRS), UMR 7592 Université Paris Diderot, Paris, France
| | - Odil Porrua
- Institut Jacques Monod, Centre Nationale pour la Recherche Scientifique (CNRS), UMR 7592 Université Paris Diderot, Paris, France
| | - Elena Conti
- Max Planck Institute of Biochemistry, Munich, Germany
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36
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Li W, Li S. Facilitators and Repressors of Transcription-coupled DNA Repair in Saccharomyces cerevisiae. Photochem Photobiol 2016; 93:259-267. [PMID: 27796045 DOI: 10.1111/php.12655] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/12/2016] [Indexed: 12/11/2022]
Abstract
Nucleotide excision repair is a well-conserved DNA repair pathway that removes bulky and/or helix-distorting DNA lesions, such as UV-induced cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts. Transcription-coupled repair (TCR) is a subpathway of nucleotide excision repair that is dedicated to rapid removal of DNA lesions in the transcribed strand of actively transcribed genes. In eukaryotic cells, TCR is triggered by RNA polymerase II (RNAP II). Rad26, a DNA-dependent ATPase, Rpb9, a nonessential subunit of RNAP II, and Sen1, a 5' to 3' RNA/DNA and DNA helicase, have been shown to facilitate TCR in Saccharomyces cerevisiae. In contrast, a number of factors have also been found to repress TCR in the yeast. These TCR repressors include Rpb4, another nonessential subunit of RNAP II, Spt4/5, a transcription elongation factor complex, and the RNAP II-associated factor 1 complex (PAFc). It appears that the eukaryotic TCR process involves intricate interplays of RNAP II with TCR facilitators and repressors. In this minireview, we summarize recent advances in TCR in S. cerevisiae.
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Affiliation(s)
- Wentao Li
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA
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Sariki SK, Sahu PK, Golla U, Singh V, Azad GK, Tomar RS. Sen1, the homolog of human Senataxin, is critical for cell survival through regulation of redox homeostasis, mitochondrial function, and the TOR pathway inSaccharomyces cerevisiae. FEBS J 2016; 283:4056-4083. [DOI: 10.1111/febs.13917] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/30/2016] [Accepted: 10/05/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Santhosh Kumar Sariki
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
| | - Pushpendra Kumar Sahu
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
| | - Upendarrao Golla
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
| | - Vikash Singh
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
| | - Gajendra Kumar Azad
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
| | - Raghuvir S. Tomar
- Laboratory of Chromatin Biology; Department of Biological Sciences; Indian Institute of Science Education and Research; Bhopal India
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Groh M, Albulescu LO, Cristini A, Gromak N. Senataxin: Genome Guardian at the Interface of Transcription and Neurodegeneration. J Mol Biol 2016; 429:3181-3195. [PMID: 27771483 DOI: 10.1016/j.jmb.2016.10.021] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/14/2016] [Accepted: 10/15/2016] [Indexed: 12/12/2022]
Abstract
R-loops comprise an RNA/DNA hybrid and a displaced single-stranded DNA. They play crucial biological functions and are implicated in neurological diseases, including ataxias, amyotrophic lateral sclerosis, nucleotide expansion disorders (Friedreich ataxia and fragile X syndrome), and cancer. Currently, it is unclear which mechanisms cause R-loop structures to become pathogenic. The RNA/DNA helicase senataxin (SETX) is one of the best characterised R-loop-binding factors in vivo. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). SETX is known to play a role in transcription, neurogenesis, and antiviral response. Here, we review the causes of R-loop dysregulation in neurodegenerative diseases and how these structures contribute to pathomechanisms. We will discuss the importance of SETX as a genome guardian in suppressing aberrant R-loop formation and analyse how SETX mutations can lead to neurodegeneration in AOA2/ALS4. Finally, we will discuss the implications for other R-loop-associated neurodegenerative diseases and point to future therapeutic approaches to treat these disorders.
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Affiliation(s)
- Matthias Groh
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK
| | - Laura Oana Albulescu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK
| | - Agnese Cristini
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, UK.
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Porrua O, Boudvillain M, Libri D. Transcription Termination: Variations on Common Themes. Trends Genet 2016; 32:508-522. [DOI: 10.1016/j.tig.2016.05.007] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/28/2016] [Accepted: 05/31/2016] [Indexed: 11/29/2022]
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The expanding biology of the C9orf72 nucleotide repeat expansion in neurodegenerative disease. Nat Rev Neurosci 2016; 17:383-95. [PMID: 27150398 DOI: 10.1038/nrn.2016.38] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A nucleotide repeat expansion (NRE) within the chromosome 9 open reading frame 72 (C9orf72) gene was the first of this type of mutation to be linked to multiple neurological conditions, including amyotrophic lateral sclerosis and frontotemporal dementia. The pathogenic mechanisms through which the C9orf72 NRE contributes to these disorders include loss of C9orf72 function and gain-of-function mechanisms of C9orf72 driven by toxic RNA and protein species encoded by the NRE. These mechanisms have been linked to several cellular defects - including nucleocytoplasmic trafficking deficits and nuclear stress - that have been observed in both patients and animal models.
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