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Kopczyńska M, Saha U, Romanenko A, Nojima T, Gdula M, Kamieniarz-Gdula K. Defining gene ends: RNA polymerase II CTD threonine 4 phosphorylation marks transcription termination regions genome-wide. Nucleic Acids Res 2025; 53:gkae1240. [PMID: 39718990 PMCID: PMC11754735 DOI: 10.1093/nar/gkae1240] [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: 07/23/2024] [Revised: 11/06/2024] [Accepted: 12/03/2024] [Indexed: 12/26/2024] Open
Abstract
Defining the beginning of a eukaryotic protein-coding gene is relatively simple. It corresponds to the first ribonucleotide incorporated by RNA polymerase II (Pol II) into the nascent RNA molecule. This nucleotide is protected by capping and maintained in the mature messenger RNA (mRNA). However, in higher eukaryotes, the end of mRNA is separated from the sites of transcription termination by hundreds to thousands of base pairs. Currently used genomic annotations only take account of the end of the mature transcript - the sites where pre-mRNA cleavage occurs, while the regions in which transcription terminates are unannotated. Here, we describe the evidence for a marker of transcription termination, which could be widely applicable in genomic studies. Pol II termination regions can be determined genome-wide by detecting Pol II phosphorylated on threonine 4 of its C-terminal domain (Pol II CTD-T4ph). Pol II in this state pauses before leaving the DNA template. Up to date this potent mark has been underused because the evidence for its place and role in termination is scattered across multiple publications. We summarize the observations regarding Pol II CTD-T4ph in termination regions and present bioinformatic analyses that further support Pol II CTD-T4ph as a global termination mark in animals.
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Affiliation(s)
- Magda Kopczyńska
- Center for Advanced Technologies, Adam Mickiewicz University, Uniwersytetu Poznanskiego 10, 61-614 Poznan, Poland
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Upasana Saha
- Center for Advanced Technologies, Adam Mickiewicz University, Uniwersytetu Poznanskiego 10, 61-614 Poznan, Poland
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Anastasiia Romanenko
- Center for Advanced Technologies, Adam Mickiewicz University, Uniwersytetu Poznanskiego 10, 61-614 Poznan, Poland
| | - Takayuki Nojima
- Medical institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Michał R Gdula
- Center for Advanced Technologies, Adam Mickiewicz University, Uniwersytetu Poznanskiego 10, 61-614 Poznan, Poland
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
| | - Kinga Kamieniarz-Gdula
- Center for Advanced Technologies, Adam Mickiewicz University, Uniwersytetu Poznanskiego 10, 61-614 Poznan, Poland
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
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Aiello U, Porrua O, Libri D. Sen1: The Varied Virtues of a Multifaceted Helicase. J Mol Biol 2025; 437:168808. [PMID: 39357815 DOI: 10.1016/j.jmb.2024.168808] [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: 07/24/2024] [Revised: 09/26/2024] [Accepted: 09/26/2024] [Indexed: 10/04/2024]
Abstract
Several machineries concurrently work on the DNA, but among them RNA Polymerases (RNAPs) are the most widespread and active users. The homeostasis of such a busy genomic environment relies on the existence of mechanisms that allow limiting transcription to a functional level, both in terms of extent and rate. Sen1 is a central player in this sense: using its translocase activity this protein has evolved the specific function of dislodging RNAPs from the DNA template, thus ending the transcription cycle. Over the years, studies have shown that Sen1 uses this same mechanism in a multitude of situations, allowing termination of all three eukaryotic RNAPs in different contexts. In virtue of its helicase activity, Sen1 has also been proposed to have a prominent function in the resolution of co-transcriptional genotoxic R-loops, which can cause the stalling of replication forks. In this review, we provide a synopsis of past and recent findings on the functions of Sen1 in yeast and of its human homologue Senataxin (SETX).
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Affiliation(s)
- Umberto Aiello
- Stanford University School of Medicine, Department of Genetics, Stanford, CA, USA.
| | - Odil Porrua
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France
| | - Domenico Libri
- Institut de Génétique Moléculaire de Montpellier, Univ Montpellier, CNRS, Montpellier, France.
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3
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Appel CD, Bermek O, Williams RS. Expression, purification, and biochemical analysis of the RNA-DNA hybrid helicase Sen1/SETX from Chaetomium thermophilum. Methods Enzymol 2024; 705:223-250. [PMID: 39389664 DOI: 10.1016/bs.mie.2024.07.012] [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] [Indexed: 10/12/2024]
Abstract
Yeast Sen1 and its vertebrate ortholog Senataxin (also known as SETX) are RNA-DNA resolving helicases. Sen1 and SETX are implicated in multiple critical nuclear functions not limited to but including DNA replication and repair, RNA processing, and transcription. These> 200 kDa helicases have a two-domain architecture with an N-terminal regulatory helical repeat array linked to an SF1b helicase motor core via a variable sized central linker of low complexity sequence. Given the size of these proteins, production of milligram quantities of protein that is suitable for biochemical, biophysical, and protein structural analysis has been challenging. To overcome these limitations, we developed a robust selectable high-yield YFP-fusion protein expression method for Sen1 production in mammalian cells, followed by purification on a high-affinity YFP-binding camelid nanobody support. Herein, we detail methods and protocols for the expression and purification of recombinant Sen1 from the thermophilic fungus Chaetomium thermophilum, and the quantitative characterization of its RNA-DNA duplex resolution activity.
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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, United States
| | - 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, United States
| | - 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, United States.
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4
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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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5
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Yague-Sanz C. Shaping the chromatin landscape at rRNA and tRNA genes, an emerging new role for RNA polymerase II transcription? Yeast 2024; 41:135-147. [PMID: 38126234 DOI: 10.1002/yea.3921] [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: 10/18/2023] [Revised: 11/17/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Eukaryotic genes must be condensed into chromatin while remaining accessible to the transcriptional machinery to support gene expression. Among the three eukaryotic RNA polymerases (RNAP), RNAPII is unique, partly because of the C-terminal domain (CTD) of its largest subunit, Rpb1. Rpb1 CTD can be extensively modified during the transcription cycle, allowing for the co-transcriptional recruitment of specific interacting proteins. These include chromatin remodeling factors that control the opening or closing of chromatin. How the CTD-less RNAPI and RNAPIII deal with chromatin at rRNA and tRNA genes is less understood. Here, we review recent advances in our understanding of how the chromatin at tRNA genes and rRNA genes can be remodeled in response to environmental cues in yeast, with a particular focus on the role of local RNAPII transcription in recruiting chromatin remodelers at these loci. In fission yeast, RNAPII transcription at tRNA genes is important to re-establish a chromatin environment permissive to tRNA transcription, which supports growth from stationary phase. In contrast, local RNAPII transcription at rRNA genes correlates with the closing of the chromatin in starvation in budding and fission yeast, suggesting a role in establishing silent chromatin. These opposite roles might support a general model where RNAPII transcription recruits chromatin remodelers to tRNA and rRNA genes to promote the closing and reopening of chromatin in response to the environment.
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Affiliation(s)
- Carlo Yague-Sanz
- Damien Hermand's Laboratory, URPhyM-GEMO, The University of Namur, Namur, Belgium
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6
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Ayano T, Yokosawa T, Oki M. GTP-dependent regulation of heterochromatin fluctuations at subtelomeric regions in Saccharomyces cerevisiae. Genes Cells 2024; 29:217-230. [PMID: 38229233 PMCID: PMC11447825 DOI: 10.1111/gtc.13094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 01/18/2024]
Abstract
In eukaryotes, single cells in a population display different transcriptional profiles. One of the factors regulating this heterogeneity is the chromatin state in each cell. However, the mechanisms of epigenetic chromatin regulation of specific chromosomal regions remain unclear. Therefore, we used single-cell tracking system to analyze IMD2. IMD2 is located at the subtelomeric region of budding yeast, and its expression is epigenetically regulated by heterochromatin fluctuations. Treatment with mycophenolic acid, an inhibitor of de novo GTP biosynthesis, triggered a decrease in GTP, which caused heterochromatin fluctuations at the IMD2 locus. Interestingly, within individually tracked cells, IMD2 expression state underwent repeated switches even though IMD2 is positioned within the heterochromatin region. We also found that 30% of the cells in a population always expressed IMD2. Furthermore, the addition of nicotinamide, a histone deacetylase inhibitor, or guanine, the GTP biosynthesis factor in salvage pathway of GTP biosynthesis, regulated heterogeneity, resulting in IMD2 expression being uniformly induced or suppressed in the population. These results suggest that gene expression heterogeneity in the IMD2 region is regulated by changes in chromatin structure triggered by slight decreases in GTP.
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Affiliation(s)
- Takahito Ayano
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
- Research Fellowships of Japan Society for the Promotion of Science for Young Scientists (JSPS), Tokyo, Japan
| | - Takuma Yokosawa
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
| | - Masaya Oki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
- Life Science Innovation Center, University of Fukui, Fukui, Japan
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7
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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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8
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Zhu Y, Vvedenskaya IO, Sze SH, Nickels BE, Kaplan CD. Quantitative analysis of transcription start site selection reveals control by DNA sequence, RNA polymerase II activity and NTP levels. Nat Struct Mol Biol 2024; 31:190-202. [PMID: 38177677 PMCID: PMC10928753 DOI: 10.1038/s41594-023-01171-9] [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: 12/14/2021] [Accepted: 11/03/2023] [Indexed: 01/06/2024]
Abstract
Transcription start site (TSS) selection is a key step in gene expression and occurs at many promoter positions over a wide range of efficiencies. Here we develop a massively parallel reporter assay to quantitatively dissect contributions of promoter sequence, nucleoside triphosphate substrate levels and RNA polymerase II (Pol II) activity to TSS selection by 'promoter scanning' in Saccharomyces cerevisiae (Pol II MAssively Systematic Transcript End Readout, 'Pol II MASTER'). Using Pol II MASTER, we measure the efficiency of Pol II initiation at 1,000,000 individual TSS sequences in a defined promoter context. Pol II MASTER confirms proposed critical qualities of S. cerevisiae TSS -8, -1 and +1 positions, quantitatively, in a controlled promoter context. Pol II MASTER extends quantitative analysis to surrounding sequences and determines that they tune initiation over a wide range of efficiencies. These results enabled the development of a predictive model for initiation efficiency based on sequence. We show that genetic perturbation of Pol II catalytic activity alters initiation efficiency mostly independently of TSS sequence, but selectively modulates preference for the initiating nucleotide. Intriguingly, we find that Pol II initiation efficiency is directly sensitive to guanosine-5'-triphosphate levels at the first five transcript positions and to cytosine-5'-triphosphate and uridine-5'-triphosphate levels at the second position genome wide. These results suggest individual nucleoside triphosphate levels can have transcript-specific effects on initiation, representing a cryptic layer of potential regulation at the level of Pol II biochemical properties. The results establish Pol II MASTER as a method for quantitative dissection of transcription initiation in eukaryotes.
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Affiliation(s)
- Yunye Zhu
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Irina O Vvedenskaya
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Sing-Hoi Sze
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Bryce E Nickels
- Department of Genetics and Waksman Institute, Rutgers University, Piscataway, NJ, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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9
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Tsui A, Kouznetsova VL, Kesari S, Fiala M, Tsigelny IF. Role of Senataxin in Amyotrophic Lateral Sclerosis. J Mol Neurosci 2023; 73:996-1009. [PMID: 37982993 DOI: 10.1007/s12031-023-02169-0] [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: 09/05/2023] [Accepted: 10/23/2023] [Indexed: 11/21/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive, uncurable neurodegenerative disorder characterized by the degradation of motor neurons leading to muscle impairment, failure, and death. Senataxin, encoded by the SETX gene, is a human helicase protein whose mutations have been linked with ALS onset, particularly in its juvenile ALS4 form. Using senataxin's yeast homolog Sen1 as a model for study, it is suggested that senataxin's N-terminus interacts with RNA polymerase II, whilst its C-terminus engages in helicase activity. Senataxin is heavily involved in transcription regulation, termination, and R-loop resolution, enabled by recruitment and interactions with enzymes such as ubiquitin protein ligase SAN1 and ribonuclease H (RNase H). Senataxin also engages in DNA damage response (DDR), primarily interacting with the exosome subunit Rrp45. The Sen1 mutation E1597K, alongside the L389S and R2136H gain-of-function mutations to senataxin, is shown to cause negative structural and thus functional effects to the protein, thus contributing to a disruption in WT functions, motor neuron (MN) degeneration, and the manifestation of ALS clinical symptoms. This review corroborates and summarizes published papers concerning the structure and function of senataxin as well as the effects of their mutations in ALS pathology in order to compile current knowledge and provide a reference for future research. The findings compiled in this review are indicative of the experimental and therapeutic potential of senataxin and its mutations as a target in future ALS treatment/cure discovery, with some potential therapeutic routes also being discussed in the review.
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Affiliation(s)
- Andrew Tsui
- REHS Program, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
| | - Valentina L Kouznetsova
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA
- CureScience Institute, San Diego, CA, USA
- BiAna, San Diego, La Jolla, CA, USA
| | | | - Milan Fiala
- Department of Integrative Biology and Physiology, School of Medicine, UCLA, Los Angeles, CA, USA
| | - Igor F Tsigelny
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA, USA.
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
- CureScience Institute, San Diego, CA, USA.
- BiAna, San Diego, La Jolla, CA, USA.
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10
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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: 0.5] [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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11
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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: 0.5] [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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12
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Choudhary R, Niska-Blakie J, Adhil M, Liberi G, Achar YJ, Giannattasio M, Foiani M. Sen1 and Rrm3 ensure permissive topological conditions for replication termination. Cell Rep 2023; 42:112747. [PMID: 37405920 DOI: 10.1016/j.celrep.2023.112747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 04/17/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023] Open
Abstract
Replication forks terminate at TERs and telomeres. Forks that converge or encounter transcription generate topological stress. Combining genetics, genomics, and transmission electron microscopy, we find that Rrm3hPif1 and Sen1hSenataxin helicases assist termination at TERs; Sen1 specifically acts at telomeres. rrm3 and sen1 genetically interact and fail to terminate replication, exhibiting fragility at termination zones (TERs) and telomeres. sen1rrm3 accumulates RNA-DNA hybrids and X-shaped gapped or reversed converging forks at TERs; sen1, but not rrm3, builds up RNA polymerase II (RNPII) at TERs and telomeres. Rrm3 and Sen1 restrain Top1 and Top2 activities, preventing toxic accumulation of positive supercoil at TERs and telomeres. We suggest that Rrm3 and Sen1 coordinate the activities of Top1 and Top2 when forks encounter transcription head on or codirectionally, respectively, thus preventing the slowing down of DNA and RNA polymerases. Hence Rrm3 and Sen1 are indispensable to generate permissive topological conditions for replication termination.
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Affiliation(s)
- Ramveer Choudhary
- IFOM ETS - The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Joanna Niska-Blakie
- IFOM ETS - The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Mohamood Adhil
- IFOM ETS - The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Giordano Liberi
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza," CNR, Pavia, Italy
| | | | - Michele Giannattasio
- IFOM ETS - The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, Via Festa del Perdono, 7, 20122 Milan, Italy
| | - Marco Foiani
- IFOM ETS - The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milan, Italy; Università degli Studi di Milano, Via Festa del Perdono, 7, 20122 Milan, Italy.
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13
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Lipinski KA, Chi J, Chen X, Hoskins AA, Brow DA. Yeast U6 snRNA made by RNA polymerase II is less stable but functional. RNA (NEW YORK, N.Y.) 2022; 28:1606-1620. [PMID: 36195346 PMCID: PMC9670810 DOI: 10.1261/rna.079328.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
U6 small nuclear (sn)RNA is the shortest and most conserved snRNA in the spliceosome and forms a substantial portion of its active site. Unlike the other four spliceosomal snRNAs, which are synthesized by RNA polymerase (RNAP) II, U6 is made by RNAP III. To determine if some aspect of U6 function is incompatible with synthesis by RNAP II, we created a U6 snRNA gene with RNAP II promoter and terminator sequences. This "U6-II" gene is functional as the sole source of U6 snRNA in yeast, but its transcript is much less stable than U6 snRNA made by RNAP III. Addition of the U4 snRNA Sm protein binding site to U6-II increased its stability and led to formation of U6-II•Sm complexes. We conclude that synthesis of U6 snRNA by RNAP III is not required for its function and that U6 snRNPs containing the Sm complex can form in vivo. The ability to synthesize U6 snRNA with RNAP II relaxes sequence restraints imposed by intragenic RNAP III promoter and terminator elements and allows facile control of U6 levels via regulators of RNAP II transcription.
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Affiliation(s)
- Karli A Lipinski
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Jing Chi
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - Xin Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Aaron A Hoskins
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
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14
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Amodeo ME, Mitchell SPC, Pavan V, Kuehner JN. RNA polymerase II transcription attenuation at the yeast DNA repair gene DEF1 is biologically significant and dependent on the Hrp1 RNA-recognition motif. G3 (BETHESDA, MD.) 2022; 13:6782960. [PMID: 36315099 PMCID: PMC9836349 DOI: 10.1093/g3journal/jkac292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
Premature transcription termination (i.e. attenuation) is a potent gene regulatory mechanism that represses mRNA synthesis. Attenuation of RNA polymerase II is more prevalent than once appreciated, targeting 10-15% of mRNA genes in yeast through higher eukaryotes, but its significance and mechanism remain obscure. In the yeast Saccharomyces cerevisiae, polymerase II attenuation was initially shown to rely on Nrd1-Nab3-Sen1 termination, but more recently our laboratory characterized a hybrid termination pathway involving Hrp1, an RNA-binding protein in the 3'-end cleavage factor. One of the hybrid attenuation gene targets is DEF1, which encodes a repair protein that promotes degradation of polymerase II stalled at DNA lesions. In this study, we characterized the chromosomal DEF1 attenuator and the functional role of Hrp1. DEF1 attenuator mutants overexpressed Def1 mRNA and protein, exacerbated polymerase II degradation, and hindered cell growth, supporting a biologically significant DEF1 attenuator function. Using an auxin-induced Hrp1 depletion system, we identified new Hrp1-dependent attenuators in MNR2, SNG1, and RAD3 genes. An hrp1-5 mutant (L205S) known to impair binding to cleavage factor protein Rna14 also disrupted attenuation, but surprisingly no widespread defect was observed for an hrp1-1 mutant (K160E) located in the RNA-recognition motif. We designed a new RNA recognition motif mutant (hrp1-F162W) that altered a highly conserved residue and was lethal in single copy. In a heterozygous strain, hrp1-F162W exhibited dominant-negative readthrough defects at several gene attenuators. Overall, our results expand the hybrid RNA polymerase II termination pathway, confirming that Hrp1-dependent attenuation controls multiple yeast genes and may function through binding cleavage factor proteins and/or RNA.
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Affiliation(s)
- Maria E Amodeo
- Department of Cancer Immunology & Virology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Shane P C Mitchell
- Alzheimer Research Unit, MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, USA
| | - Vincent Pavan
- Department of Biology, Emmanuel College, Boston, MA 02115, USA
| | - Jason N Kuehner
- Corresponding author: Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA.
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15
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Xie J, Aiello U, Clement Y, Haidara N, Girbig M, Schmitzova J, Pena V, Müller CW, Libri D, Porrua O. An integrated model for termination of RNA polymerase III transcription. SCIENCE ADVANCES 2022; 8:eabm9875. [PMID: 35857496 PMCID: PMC9278858 DOI: 10.1126/sciadv.abm9875] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
RNA polymerase III (RNAPIII) synthesizes essential and abundant noncoding RNAs such as transfer RNAs. Controlling RNAPIII span of activity by accurate and efficient termination is a challenging necessity to ensure robust gene expression and to prevent conflicts with other DNA-associated machineries. The mechanism of RNAPIII termination is believed to be simpler than that of other eukaryotic RNA polymerases, solely relying on the recognition of a T-tract in the nontemplate strand. Here, we combine high-resolution genome-wide analyses and in vitro transcription termination assays to revisit the mechanism of RNAPIII transcription termination in budding yeast. We show that T-tracts are necessary but not always sufficient for termination and that secondary structures of the nascent RNAs are important auxiliary cis-acting elements. Moreover, we show that the helicase Sen1 plays a key role in a fail-safe termination pathway. Our results provide a comprehensive model illustrating how multiple mechanisms cooperate to ensure efficient RNAPIII transcription termination.
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Affiliation(s)
- Juanjuan Xie
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Umberto Aiello
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Yves Clement
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Nouhou Haidara
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Mathias Girbig
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, 69117 Heidelberg, Germany
- Joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Jana Schmitzova
- Max Planck Institute for Biophysical Chemistry, Macromolecular Crystallography, Am Fassberg 11, 37077 Goettingen, Germany
| | - Vladimir Pena
- Max Planck Institute for Biophysical Chemistry, Macromolecular Crystallography, Am Fassberg 11, 37077 Goettingen, Germany
| | - Christoph W. Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Domenico Libri
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- Corresponding author. (D.L.); (O.P.)
| | - Odil Porrua
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
- Corresponding author. (D.L.); (O.P.)
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16
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Aiello U, Challal D, Wentzinger G, Lengronne A, Appanah R, Pasero P, Palancade B, Libri D. Sen1 is a key regulator of transcription-driven conflicts. Mol Cell 2022; 82:2952-2966.e6. [PMID: 35839782 DOI: 10.1016/j.molcel.2022.06.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/04/2022] [Accepted: 06/13/2022] [Indexed: 10/17/2022]
Abstract
Cellular homeostasis requires the coordination of several machineries concurrently engaged in the DNA. Wide-spread transcription can interfere with other processes, and transcription-replication conflicts (TRCs) threaten genome stability. The conserved Sen1 helicase not only terminates non-coding transcription but also interacts with the replisome and reportedly resolves genotoxic R-loops. Sen1 prevents genomic instability, but how this relates to its molecular functions remains unclear. We generated high-resolution, genome-wide maps of transcription-dependent conflicts and R-loops using a Sen1 mutant that has lost interaction with the replisome but is termination proficient. We show that, under physiological conditions, Sen1 removes RNA polymerase II at TRCs within genes and the rDNA and at sites of transcription-transcription conflicts, thus qualifying as a "key regulator of conflicts." We demonstrate that genomic stability is affected by Sen1 mutation only when in addition to its role at the replisome, the termination of non-coding transcription or R-loop removal are additionally compromised.
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Affiliation(s)
- Umberto Aiello
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Drice Challal
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | | | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Rowin Appanah
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Benoit Palancade
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Domenico Libri
- Université Paris Cité, CNRS, Institut Jacques Monod, 75013 Paris, France.
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17
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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: 12] [Impact Index Per Article: 4.0] [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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18
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Couvillion M, Harlen KM, Lachance KC, Trotta KL, Smith E, Brion C, Smalec BM, Churchman LS. Transcription elongation is finely tuned by dozens of regulatory factors. eLife 2022; 11:e78944. [PMID: 35575476 PMCID: PMC9154744 DOI: 10.7554/elife.78944] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/15/2022] [Indexed: 11/30/2022] Open
Abstract
Understanding the complex network that regulates transcription elongation requires the quantitative analysis of RNA polymerase II (Pol II) activity in a wide variety of regulatory environments. We performed native elongating transcript sequencing (NET-seq) in 41 strains of Saccharomyces cerevisiae lacking known elongation regulators, including RNA processing factors, transcription elongation factors, chromatin modifiers, and remodelers. We found that the opposing effects of these factors balance transcription elongation and antisense transcription. Different sets of factors tightly regulate Pol II progression across gene bodies so that Pol II density peaks at key points of RNA processing. These regulators control where Pol II pauses with each obscuring large numbers of potential pause sites that are primarily determined by DNA sequence and shape. Antisense transcription varies highly across the regulatory landscapes analyzed, but antisense transcription in itself does not affect sense transcription at the same locus. Our findings collectively show that a diverse array of factors regulate transcription elongation by precisely balancing Pol II activity.
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Affiliation(s)
- Mary Couvillion
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Kevin M Harlen
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Kate C Lachance
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Kristine L Trotta
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Erin Smith
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Christian Brion
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Brendan M Smalec
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - L Stirling Churchman
- Blavatnik Institute, Department of Genetics, Harvard Medical SchoolBostonUnited States
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19
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Singh N, Asalam M, Ansari MO, Gerasimova NS, Studitsky VM, Akhtar MS. Transcription by RNA polymerase II and the CTD-chromatin crosstalk. Biochem Biophys Res Commun 2022; 599:81-86. [PMID: 35176629 DOI: 10.1016/j.bbrc.2022.02.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/10/2022] [Indexed: 12/24/2022]
Abstract
The epigenetic phenomenon is known to derive the phenotypic variation of an organism through an interconnected cellular network of histone modifications, DNA methylation and RNA regulatory network. Transcription for protein coding genes is a highly regulated process and carried out by a large multi-complex RNA Polymerase II. The carboxy terminal domain (CTD) of the largest subunit of RNA Polymerase II consists of a conserved and highly repetitive heptad sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. The epigenetically modified CTD is thought to selectively bind different protein complexes that participate in mRNA biogenesis and export. The CTD and chromatin appears to have a spatial relationship during the transcription cycle, where the epigenetic modifications of CTD not only influence the state of histone modification but also mediates CTD-chromatin crosstalk. In this mini review, we have surveyed and discussed current developments of RNA Polymerase II CTD and its new emerging crosstalk with chromatin, during the stage specific progression of RNA Polymerase II in transcription cycle. This review is mainly focussed on the insights in budding yeast.
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Affiliation(s)
- Neha Singh
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohd Asalam
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohd Owais Ansari
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Nadezhda S Gerasimova
- Department of Bioengineering, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vasily M Studitsky
- Department of Bioengineering, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Md Sohail Akhtar
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, India.
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20
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Kanagaraj R, Mitter R, Kantidakis T, Edwards MM, Benitez A, Chakravarty P, Fu B, Becherel O, Yang F, Lavin MF, Koren A, Stewart A, West SC. Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2. Proc Natl Acad Sci U S A 2022; 119:e2114314119. [PMID: 35042798 PMCID: PMC8795503 DOI: 10.1073/pnas.2114314119] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/14/2021] [Indexed: 12/21/2022] Open
Abstract
Mutations in the SETX gene, which encodes Senataxin, are associated with the progressive neurodegenerative diseases ataxia with oculomotor apraxia 2 (AOA2) and amyotrophic lateral sclerosis 4 (ALS4). To identify the causal defect in AOA2, patient-derived cells and SETX knockouts (human and mouse) were analyzed using integrated genomic and transcriptomic approaches. A genome-wide increase in chromosome instability (gains and losses) within genes and at chromosome fragile sites was observed, resulting in changes to gene-expression profiles. Transcription stress near promoters correlated with high GCskew and the accumulation of R-loops at promoter-proximal regions, which localized with chromosomal regions where gains and losses were observed. In the absence of Senataxin, the Cockayne syndrome protein CSB was required for the recruitment of the transcription-coupled repair endonucleases (XPG and XPF) and RAD52 recombination protein to target and resolve transcription bubbles containing R-loops, leading to genomic instability. These results show that transcription stress is an important contributor to SETX mutation-associated chromosome fragility and AOA2.
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Affiliation(s)
- Radhakrishnan Kanagaraj
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom;
| | - Richard Mitter
- Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | | | - Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Anaid Benitez
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Probir Chakravarty
- Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Beiyuan Fu
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Olivier Becherel
- Center for Clinical Research, University of Queensland, Herston, QLD 4029, Australia
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, United Kingdom
| | - Martin F Lavin
- Center for Clinical Research, University of Queensland, Herston, QLD 4029, Australia
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Aengus Stewart
- Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Stephen C West
- DNA Recombination and Repair Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom;
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21
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Aoi Y, Takahashi YH, Shah AP, Iwanaszko M, Rendleman EJ, Khan NH, Cho BK, Goo YA, Ganesan S, Kelleher NL, Shilatifard A. SPT5 stabilization of promoter-proximal RNA polymerase II. Mol Cell 2021; 81:4413-4424.e5. [PMID: 34480849 PMCID: PMC8687145 DOI: 10.1016/j.molcel.2021.08.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/28/2021] [Accepted: 08/03/2021] [Indexed: 01/02/2023]
Abstract
Based on in vitro studies, it has been demonstrated that the DSIF complex, composed of SPT4 and SPT5, regulates the elongation stage of transcription catalyzed by RNA polymerase II (RNA Pol II). The precise cellular function of SPT5 is not clear, because conventional gene depletion strategies for SPT5 result in loss of cellular viability. Using an acute inducible protein depletion strategy to circumvent this issue, we report that SPT5 loss triggers the ubiquitination and proteasomal degradation of the core RNA Pol II subunit RPB1, a process that we show to be evolutionarily conserved from yeast to human cells. RPB1 degradation requires the E3 ligase Cullin 3, the unfoldase VCP/p97, and a novel form of CDK9 kinase complex. Our study demonstrates that SPT5 stabilizes RNA Pol II specifically at promoter-proximal regions, permitting RNA Pol II release from promoters into gene bodies and providing mechanistic insight into the cellular function of SPT5 in safeguarding accurate gene expression.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yoh-Hei Takahashi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Avani P Shah
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Marta Iwanaszko
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Emily J Rendleman
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nabiha H Khan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Byoung-Kyu Cho
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60611, USA
| | - Young Ah Goo
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60611, USA
| | - Sheetal Ganesan
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Neil L Kelleher
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Proteomics Center of Excellence, Northwestern University, Evanston, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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22
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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: 31] [Impact Index Per Article: 7.8] [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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23
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Turner RE, Harrison PF, Swaminathan A, Kraupner-Taylor CA, Goldie BJ, See M, Peterson AL, Schittenhelm RB, Powell DR, Creek DJ, Dichtl B, Beilharz TH. Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast. eLife 2021; 10:65331. [PMID: 34232857 PMCID: PMC8263057 DOI: 10.7554/elife.65331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 06/22/2021] [Indexed: 01/23/2023] Open
Abstract
Most eukaryotic mRNAs accommodate alternative sites of poly(A) addition in the 3’ untranslated region in order to regulate mRNA function. Here, we present a systematic analysis of 3’ end formation factors, which revealed 3’UTR lengthening in response to a loss of the core machinery, whereas a loss of the Sen1 helicase resulted in shorter 3’UTRs. We show that the anti-cancer drug cordycepin, 3’ deoxyadenosine, caused nucleotide accumulation and the usage of distal poly(A) sites. Mycophenolic acid, a drug which reduces GTP levels and impairs RNA polymerase II (RNAP II) transcription elongation, promoted the usage of proximal sites and reversed the effects of cordycepin on alternative polyadenylation. Moreover, cordycepin-mediated usage of distal sites was associated with a permissive chromatin template and was suppressed in the presence of an rpb1 mutation, which slows RNAP II elongation rate. We propose that alternative polyadenylation is governed by temporal coordination of RNAP II transcription and 3’ end processing and controlled by the availability of 3’ end factors, nucleotide levels and chromatin landscape.
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Affiliation(s)
- Rachael Emily Turner
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Paul F Harrison
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Angavai Swaminathan
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Calvin A Kraupner-Taylor
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Belinda J Goldie
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Michael See
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Amanda L Peterson
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - David R Powell
- Monash Bioinformatics Platform, Monash University, Melbourne, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Bernhard Dichtl
- School of Life and Environmental Sciences, Deakin University, Geelong, Australia
| | - Traude H Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
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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: 2] [Impact Index Per Article: 0.5] [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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25
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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: 26] [Impact Index Per Article: 6.5] [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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26
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Palancade B, Rothstein R. The Ultimate (Mis)match: When DNA Meets RNA. Cells 2021; 10:cells10061433. [PMID: 34201169 PMCID: PMC8227541 DOI: 10.3390/cells10061433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 12/20/2022] Open
Abstract
RNA-containing structures, including ribonucleotide insertions, DNA:RNA hybrids and R-loops, have recently emerged as critical players in the maintenance of genome integrity. Strikingly, different enzymatic activities classically involved in genome maintenance contribute to their generation, their processing into genotoxic or repair intermediates, or their removal. Here we review how this substrate promiscuity can account for the detrimental and beneficial impacts of RNA insertions during genome metabolism. We summarize how in vivo and in vitro experiments support the contribution of DNA polymerases and homologous recombination proteins in the formation of RNA-containing structures, and we discuss the role of DNA repair enzymes in their removal. The diversity of pathways that are thus affected by RNA insertions likely reflects the ancestral function of RNA molecules in genome maintenance and transmission.
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Affiliation(s)
- Benoit Palancade
- Institut Jacques Monod, Université de Paris, CNRS, F-75006 Paris, France
- Correspondence: (B.P.); (R.R.)
| | - Rodney Rothstein
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
- Correspondence: (B.P.); (R.R.)
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27
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Villa T, Barucco M, Martin-Niclos MJ, Jacquier A, Libri D. Degradation of Non-coding RNAs Promotes Recycling of Termination Factors at Sites of Transcription. Cell Rep 2021; 32:107942. [PMID: 32698007 DOI: 10.1016/j.celrep.2020.107942] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 05/08/2020] [Accepted: 06/30/2020] [Indexed: 12/27/2022] Open
Abstract
A large share of the non-coding transcriptome in yeast is controlled by the Nrd1-Nab3-Sen1 (NNS) complex, which promotes transcription termination of non-coding RNA (ncRNA) genes, and by the nuclear exosome, which limits the steady-state levels of the transcripts produced. How unconstrained ncRNA levels affect RNA metabolism and gene expression are long-standing and important questions. Here, we show that degradation of ncRNAs by the exosome is required for freeing Nrd1 and Nab3 from the released transcript after termination. In exosome mutants, these factors are sequestered by ncRNAs and cannot be efficiently recycled to sites of transcription, inducing termination defects at NNS targets. ncRNA-dependent, genome-wide termination defects can be recapitulated by the expression of a degradation-resistant, circular RNA containing a natural NNS target in exosome-proficient cells. Our results have important implications for the mechanism of termination, the general impact of ncRNAs abundance, and the importance of nuclear ncRNA degradation.
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Affiliation(s)
- Tommaso Villa
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France.
| | - Mara Barucco
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France
| | | | - Alain Jacquier
- Institut Pasteur, Centre National de la Recherche Scientifique, UMR3525 Paris, France
| | - Domenico Libri
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France.
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28
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Abraham KJ, Khosraviani N, Chan JNY, Gorthi A, Samman A, Zhao DY, Wang M, Bokros M, Vidya E, Ostrowski LA, Oshidari R, Pietrobon V, Patel PS, Algouneh A, Singhania R, Liu Y, Yerlici VT, De Carvalho DD, Ohh M, Dickson BC, Hakem R, Greenblatt JF, Lee S, Bishop AJR, Mekhail K. Nucleolar RNA polymerase II drives ribosome biogenesis. Nature 2020; 585:298-302. [PMID: 32669707 PMCID: PMC7486236 DOI: 10.1038/s41586-020-2497-0] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/21/2020] [Indexed: 12/16/2022]
Abstract
Proteins are manufactured by ribosomes-macromolecular complexes of protein and RNA molecules that are assembled within major nuclear compartments called nucleoli1,2. Existing models suggest that RNA polymerases I and III (Pol I and Pol III) are the only enzymes that directly mediate the expression of the ribosomal RNA (rRNA) components of ribosomes. Here we show, however, that RNA polymerase II (Pol II) inside human nucleoli operates near genes encoding rRNAs to drive their expression. Pol II, assisted by the neurodegeneration-associated enzyme senataxin, generates a shield comprising triplex nucleic acid structures known as R-loops at intergenic spacers flanking nucleolar rRNA genes. The shield prevents Pol I from producing sense intergenic noncoding RNAs (sincRNAs) that can disrupt nucleolar organization and rRNA expression. These disruptive sincRNAs can be unleashed by Pol II inhibition, senataxin loss, Ewing sarcoma or locus-associated R-loop repression through an experimental system involving the proteins RNaseH1, eGFP and dCas9 (which we refer to as 'red laser'). We reveal a nucleolar Pol-II-dependent mechanism that drives ribosome biogenesis, identify disease-associated disruption of nucleoli by noncoding RNAs, and establish locus-targeted R-loop modulation. Our findings revise theories of labour division between the major RNA polymerases, and identify nucleolar Pol II as a major factor in protein synthesis and nuclear organization, with potential implications for health and disease.
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Affiliation(s)
- Karan J Abraham
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Negin Khosraviani
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Janet N Y Chan
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aparna Gorthi
- Greehey Children's Cancer Research Institute, Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, TX, USA
| | - Anas Samman
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Dorothy Y Zhao
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Miling Wang
- Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Michael Bokros
- Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Elva Vidya
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lauren A Ostrowski
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Roxanne Oshidari
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Violena Pietrobon
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Parasvi S Patel
- Princess Margaret Cancer Research Centre, University Health Network, and Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Arash Algouneh
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Research Centre, University Health Network, and Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Rajat Singhania
- Princess Margaret Cancer Research Centre, University Health Network, and Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Yupeng Liu
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - V Talya Yerlici
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Daniel D De Carvalho
- Princess Margaret Cancer Research Centre, University Health Network, and Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Michael Ohh
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Brendan C Dickson
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Razq Hakem
- Princess Margaret Cancer Research Centre, University Health Network, and Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jack F Greenblatt
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Stephen Lee
- Sylvester Comprehensive Cancer Center, Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Alexander J R Bishop
- Greehey Children's Cancer Research Institute, Department of Cell Systems and Anatomy, University of Texas Health at San Antonio, San Antonio, TX, USA
- Mays Cancer Center, University of Texas Health at San Antonio, San Antonio, TX, USA
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
- Canada Research Chairs Program, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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29
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Quintero-Cadena P, Lenstra TL, Sternberg PW. RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting. Mol Cell 2020; 79:207-220.e8. [DOI: 10.1016/j.molcel.2020.05.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/09/2020] [Accepted: 05/19/2020] [Indexed: 12/15/2022]
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30
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A Systematic Review of Genotype-Phenotype Correlation across Cohorts Having Causal Mutations of Different Genes in ALS. J Pers Med 2020; 10:jpm10030058. [PMID: 32610599 PMCID: PMC7564886 DOI: 10.3390/jpm10030058] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis is a rare and fatal neurodegenerative disease characterised by progressive deterioration of upper and lower motor neurons that eventually culminates in severe muscle atrophy, respiratory failure and death. There is a concerning lack of understanding regarding the mechanisms that lead to the onset of ALS and as a result there are no reliable biomarkers that aid in the early detection of the disease nor is there an effective treatment. This review first considers the clinical phenotypes associated with ALS, and discusses the broad categorisation of ALS and ALS-mimic diseases into upper and lower motor neuron diseases, before focusing on the genetic aetiology of ALS and considering the potential relationship of mutations of different genes to variations in phenotype. For this purpose, a systematic review is conducted collating data from 107 original published clinical studies on monogenic forms of the disease, surveying the age and site of onset, disease duration and motor neuron involvement. The collected data highlight the complexity of the disease's genotype-phenotype relationship, and thus the need for a nuanced approach to the development of clinical assays and therapeutics.
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31
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Victorino JF, Fox MJ, Smith-Kinnaman WR, Peck Justice SA, Burriss KH, Boyd AK, Zimmerly MA, Chan RR, Hunter GO, Liu Y, Mosley AL. RNA Polymerase II CTD phosphatase Rtr1 fine-tunes transcription termination. PLoS Genet 2020; 16:e1008317. [PMID: 32187185 PMCID: PMC7105142 DOI: 10.1371/journal.pgen.1008317] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 03/30/2020] [Accepted: 01/31/2020] [Indexed: 12/15/2022] Open
Abstract
RNA Polymerase II (RNAPII) transcription termination is regulated by the phosphorylation status of the C-terminal domain (CTD). The phosphatase Rtr1 has been shown to regulate serine 5 phosphorylation on the CTD; however, its role in the regulation of RNAPII termination has not been explored. As a consequence of RTR1 deletion, interactions within the termination machinery and between the termination machinery and RNAPII were altered as quantified by Disruption-Compensation (DisCo) network analysis. Of note, interactions between RNAPII and the cleavage factor IA (CF1A) subunit Pcf11 were reduced in rtr1Δ, whereas interactions with the CTD and RNA-binding termination factor Nrd1 were increased. Globally, rtr1Δ leads to decreases in numerous noncoding RNAs that are linked to the Nrd1, Nab3 and Sen1 (NNS) -dependent RNAPII termination pathway. Genome-wide analysis of RNAPII and Nrd1 occupancy suggests that loss of RTR1 leads to increased termination at noncoding genes. Additionally, premature RNAPII termination increases globally at protein-coding genes with a decrease in RNAPII occupancy occurring just after the peak of Nrd1 recruitment during early elongation. The effects of rtr1Δ on RNA expression levels were lost following deletion of the exosome subunit Rrp6, which works with the NNS complex to rapidly degrade a number of noncoding RNAs following termination. Overall, these data suggest that Rtr1 restricts the NNS-dependent termination pathway in WT cells to prevent premature termination of mRNAs and ncRNAs. Rtr1 facilitates low-level elongation of noncoding transcripts that impact RNAPII interference thereby shaping the transcriptome. Many cellular RNAs including those that encode for proteins are produced by the enzyme RNA Polymerase II. In this work, we have defined a new role for the phosphatase Rtr1 in the regulation of RNA Polymerase II progression from the start of transcription to the 3’ end of the gene where the nascent RNA from protein-coding genes is typically cleaved and polyadenylated. Deletion of the gene that encodes RTR1 leads to changes in the interactions between RNA polymerase II and the termination machinery. Rtr1 loss also causes early termination of RNA Polymerase II at many of its target gene types, including protein coding genes and noncoding RNAs. Evidence suggests that the premature termination observed in RTR1 knockout cells occurs through the termination factor and RNA binding protein Nrd1 and its binding partner Nab3. Deletion of RRP6, a known component of the Nrd1-Nab3 termination coupled RNA degradation pathway, is epistatic to RTR1 suggesting that Rrp6 is required to terminate and/or degrade many of the noncoding RNAs that have increased turnover in RTR1 deletion cells. These findings suggest that Rtr1 normally promotes elongation of RNA Polymerase II transcripts through prevention of Nrd1-directed termination.
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Affiliation(s)
- Jose F. Victorino
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Melanie J. Fox
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Whitney R. Smith-Kinnaman
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Sarah A. Peck Justice
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Katlyn H. Burriss
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Asha K. Boyd
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Megan A. Zimmerly
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Rachel R. Chan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Gerald O. Hunter
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Amber L. Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
- * E-mail:
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32
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Hu A, Li J, Tang W, Liu G, Zhang H, Liu C, Chen X. Anthralin Suppresses the Proliferation of Influenza Virus by Inhibiting the Cap-Binding and Endonuclease Activity of Viral RNA Polymerase. Front Microbiol 2020; 11:178. [PMID: 32132985 PMCID: PMC7040080 DOI: 10.3389/fmicb.2020.00178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 01/24/2020] [Indexed: 11/23/2022] Open
Abstract
Influenza virus RNA-dependent RNA polymerase (vRdRp) does not have capping activity and relies on the capped RNAs produced by the host RNA polymerase II (RNAPII). The viral polymerases process the capped RNAs to produce short capped RNA fragments that are used as primers to initiate the transcription of viral mRNAs. This process, known as cap-snatching, can be targeted by antiviral therapeutics. Here, anthralin was identified as an inhibitor against influenza a virus (IAV) infection by targeting the cap-snatching activity of the viral polymerase. Anthralin, an FDA-approved drug used in the treatment of psoriasis, shows antiviral activity against IAV infection in vitro and in vivo. Importantly, anthralin significantly reduces weight loss, lung injury, and mortality caused by IAV infection in mice. The mechanism of action study revealed that anthralin inhibits the cap-binding function of PB2 subunit and endonuclease activity of PA. As a result, viral mRNA transcription is blocked, leading to the decreases in viral RNA replication and viral protein expression. In conclusion, anthralin has been demonstrated to have the potential of an alternative antiviral against influenza virus infection. Also, targeting the captive pocket structure that includes the N-terminus of PA endonuclease domain and the C-terminal of PB2 cap-binding domain of IAV RdRp may be an excellent strategy for developing anti-influenza drugs.
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Affiliation(s)
- Ao Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Tang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Ge Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Haiwei Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Chunlan Liu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xulin Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China.,Guangdong Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou, China
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33
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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: 4.0] [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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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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35
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Chen FX, Smith ER, Shilatifard A. Born to run: control of transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol 2019; 19:464-478. [PMID: 29740129 DOI: 10.1038/s41580-018-0010-5] [Citation(s) in RCA: 285] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The dynamic regulation of transcription elongation by RNA polymerase II (Pol II) is an integral part of the implementation of gene expression programmes during development. In most metazoans, the majority of transcribed genes exhibit transient pausing of Pol II at promoter-proximal regions, and the release of Pol II into gene bodies is controlled by many regulatory factors that respond to environmental and developmental cues. Misregulation of the elongation stage of transcription is implicated in cancer and other human diseases, suggesting that mechanistic understanding of transcription elongation control is therapeutically relevant. In this Review, we discuss the features, establishment and maintenance of Pol II pausing, the transition into productive elongation, the control of transcription elongation by enhancers and by factors of other cellular processes, such as topoisomerases and poly(ADP-ribose) polymerases (PARPs), and the potential of therapeutic targeting of the elongation stage of transcription by Pol II.
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Affiliation(s)
- Fei Xavier Chen
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Edwin R Smith
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ali Shilatifard
- Simpson Querrey Center for Epigenetics and the Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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36
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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: 26] [Impact Index Per Article: 4.3] [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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37
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Hegedüs É, Kókai E, Nánási P, Imre L, Halász L, Jossé R, Antunovics Z, Webb MR, El Hage A, Pommier Y, Székvölgyi L, Dombrádi V, Szabó G. Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae. Nucleic Acids Res 2019; 46:10649-10668. [PMID: 30445637 PMCID: PMC6237785 DOI: 10.1093/nar/gky743] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/16/2018] [Indexed: 12/12/2022] Open
Abstract
Molecular combing and gel electrophoretic studies revealed endogenous nicks with free 3'OH ends at ∼100 kb intervals in the genomic DNA (gDNA) of unperturbed and G1-synchronized Saccharomyces cerevisiae cells. Analysis of the distribution of endogenous nicks by Nick ChIP-chip indicated that these breaks accumulated at active RNA polymerase II (RNAP II) promoters, reminiscent of the promoter-proximal transient DNA breaks of higher eukaryotes. Similar periodicity of endogenous nicks was found within the ribosomal rDNA cluster, involving every ∼10th of the tandemly repeated 9.1 kb units of identical sequence. Nicks were mapped by Southern blotting to a few narrow regions within the affected units. Three of them were overlapping the RNAP II promoters, while the ARS-containing IGS2 region was spared of nicks. By using a highly sensitive reverse-Southwestern blot method to map free DNA ends with 3'OH, nicks were shown to be distinct from other known rDNA breaks and linked to the regulation of rDNA silencing. Nicks in rDNA and the rest of the genome were typically found at the ends of combed DNA molecules, occasionally together with R-loops, comprising a major pool of vulnerable sites that are connected with transcriptional regulation.
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Affiliation(s)
- Éva Hegedüs
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Endre Kókai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Nánási
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Imre
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - László Halász
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Rozenn Jossé
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (CCR-NCI), NIH, Bethesda, MD, USA
| | - Zsuzsa Antunovics
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | | | - Aziz El Hage
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute (CCR-NCI), NIH, Bethesda, MD, USA
| | - Lóránt Székvölgyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.,MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Viktor Dombrádi
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Gábor Szabó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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A Novel G-Quadruplex Binding Protein in Yeast-Slx9. Molecules 2019; 24:molecules24091774. [PMID: 31067825 PMCID: PMC6539110 DOI: 10.3390/molecules24091774] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 01/01/2023] Open
Abstract
G-quadruplex (G4) structures are highly stable four-stranded DNA and RNA secondary structures held together by non-canonical guanine base pairs. G4 sequence motifs are enriched at specific sites in eukaryotic genomes, suggesting regulatory functions of G4 structures during different biological processes. Considering the high thermodynamic stability of G4 structures, various proteins are necessary for G4 structure formation and unwinding. In a yeast one-hybrid screen, we identified Slx9 as a novel G4-binding protein. We confirmed that Slx9 binds to G4 DNA structures in vitro. Despite these findings, Slx9 binds only insignificantly to G-rich/G4 regions in Saccharomyces cerevisiae as demonstrated by genome-wide ChIP-seq analysis. However, Slx9 binding to G4s is significantly increased in the absence of Sgs1, a RecQ helicase that regulates G4 structures. Different genetic and molecular analyses allowed us to propose a model in which Slx9 recognizes and protects stabilized G4 structures in vivo.
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Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination. Genetics 2019; 212:153-174. [PMID: 30902808 DOI: 10.1534/genetics.119.302058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/19/2019] [Indexed: 11/18/2022] Open
Abstract
RNA helicases are a class of enzymes that unwind RNA duplexes in vitro but whose cellular functions are largely enigmatic. Here, we provide evidence that the DEAD-box protein Dbp2 remodels RNA-protein complex (RNP) structure to facilitate efficient termination of transcription in Saccharomyces cerevisiae via the Nrd1-Nab3-Sen1 (NNS) complex. First, we find that loss of DBP2 results in RNA polymerase II accumulation at the 3' ends of small nucleolar RNAs and a subset of mRNAs. In addition, Dbp2 associates with RNA sequence motifs and regions bound by Nrd1 and can promote its recruitment to NNS-targeted regions. Using Structure-seq, we find altered RNA/RNP structures in dbp2∆ cells that correlate with inefficient termination. We also show a positive correlation between the stability of structures in the 3' ends and a requirement for Dbp2 in termination. Taken together, these studies provide a role for RNA remodeling by Dbp2 and further suggests a mechanism whereby RNA structure is exploited for gene regulation.
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40
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Schmid M, Jensen TH. The Nuclear RNA Exosome and Its Cofactors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:113-132. [PMID: 31811632 DOI: 10.1007/978-3-030-31434-7_4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The RNA exosome is a highly conserved ribonuclease endowed with 3'-5' exonuclease and endonuclease activities. The multisubunit complex resides in both the nucleus and the cytoplasm, with varying compositions and activities between the two compartments. While the cytoplasmic exosome functions mostly in mRNA quality control pathways, the nuclear RNA exosome partakes in the 3'-end processing and complete decay of a wide variety of substrates, including virtually all types of noncoding (nc) RNAs. To handle these diverse tasks, the nuclear exosome engages with dedicated cofactors, some of which serve as activators by stimulating decay through oligoA addition and/or RNA helicase activities or, as adaptors, by recruiting RNA substrates through their RNA-binding capacities. Most nuclear exosome cofactors contain the essential RNA helicase Mtr4 (MTR4 in humans). However, apart from Mtr4, nuclear exosome cofactors have undergone significant evolutionary divergence. Here, we summarize biochemical and functional knowledge about the nuclear exosome and exemplify its cofactor variety by discussing the best understood model organisms-the budding yeast Saccharomyces cerevisiae, the fission yeast Schizosaccharomyces pombe, and human cells.
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Affiliation(s)
- Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.
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41
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Nab3's localization to a nuclear granule in response to nutrient deprivation is determined by its essential prion-like domain. PLoS One 2018; 13:e0209195. [PMID: 30557374 PMCID: PMC6296506 DOI: 10.1371/journal.pone.0209195] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 11/30/2018] [Indexed: 12/20/2022] Open
Abstract
Ribonucleoprotein (RNP) granules are higher order assemblies of RNA, RNA-binding proteins, and other proteins, that regulate the transcriptome and protect RNAs from environmental challenge. There is a diverse range of RNP granules, many cytoplasmic, which provide various levels of regulation of RNA metabolism. Here we present evidence that the yeast transcription termination factor, Nab3, is targeted to intranuclear granules in response to glucose starvation by Nab3’s proline/glutamine-rich, prion-like domain (PrLD) which can assemble into amyloid in vitro. Localization to the granule is reversible and sensitive to the chemical probe 1,6 hexanediol suggesting condensation is driven by phase separation. Nab3’s RNA recognition motif is also required for localization as seen for other PrLD-containing RNA-binding proteins that phase separate. Although the PrLD is necessary, it is not sufficient to localize to the granule. A heterologous PrLD that functionally replaces Nab3’s essential PrLD, directed localization to the nuclear granule, however a chimeric Nab3 molecule with a heterologous PrLD that cannot restore termination function or viability, does not form granules. The Nab3 nuclear granule shows properties similar to well characterized cytoplasmic compartments formed by phase separation, suggesting that, as seen for other elements of the transcription machinery, termination factor condensation is functionally important.
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42
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Kufel J, Grzechnik P. Small Nucleolar RNAs Tell a Different Tale. Trends Genet 2018; 35:104-117. [PMID: 30563726 DOI: 10.1016/j.tig.2018.11.005] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/16/2018] [Accepted: 11/21/2018] [Indexed: 12/21/2022]
Abstract
Transcribing RNA Polymerase II interacts with multiple factors that orchestrate maturation and stabilisation of messenger RNA. For the majority of noncoding RNAs, the polymerase complex employs entirely different strategies, which usually direct the nascent transcript to ribonucleolytic degradation. However, some noncoding RNA classes use endo- and exonucleases to achieve functionality. Here we review processing of small nucleolar RNAs that are transcribed by RNA Polymerase II as precursors, and whose 5' and 3' ends undergo processing to release mature, functional molecules. The maturation strategies of these noncoding RNAs in various organisms follow a similar pattern but employ different factors and are strictly correlated with genomic organisation of their genes.
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Affiliation(s)
- Joanna Kufel
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Pawel Grzechnik
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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43
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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: 53] [Impact Index Per Article: 7.6] [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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44
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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: 3.1] [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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45
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Abstract
R loops are transient three-stranded nucleic acid structures that form physiologically during transcription when a nascent RNA transcript hybridizes with the DNA template strand, leaving a single strand of displaced nontemplate DNA. However, aberrant persistence of R-loops can cause DNA damage by inducing genomic instability. Indeed, evidence has emerged that R-loops might represent a key element in the pathogenesis of human diseases, including cancer, neurodegeneration, and motor neuron disorders. Mutations in genes directly involved in R-loop biology, such as SETX (senataxin), or unstable DNA expansion eliciting R-loop generation, such as C9ORF72 HRE, can cause DNA damage and ultimately result in motor neuron cell death. In this review, we discuss current advancements in this field with a specific focus on motor neuron diseases associated with deregulation of R-loop structures. These mechanisms can represent novel therapeutic targets for these devastating, incurable diseases.
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46
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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: 0.6] [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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47
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Didychuk AL, Butcher SE, Brow DA. The life of U6 small nuclear RNA, from cradle to grave. RNA (NEW YORK, N.Y.) 2018; 24:437-460. [PMID: 29367453 PMCID: PMC5855946 DOI: 10.1261/rna.065136.117] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Removal of introns from precursor messenger RNA (pre-mRNA) and some noncoding transcripts is an essential step in eukaryotic gene expression. In the nucleus, this process of RNA splicing is carried out by the spliceosome, a multi-megaDalton macromolecular machine whose core components are conserved from yeast to humans. In addition to many proteins, the spliceosome contains five uridine-rich small nuclear RNAs (snRNAs) that undergo an elaborate series of conformational changes to correctly recognize the splice sites and catalyze intron removal. Decades of biochemical and genetic data, along with recent cryo-EM structures, unequivocally demonstrate that U6 snRNA forms much of the catalytic core of the spliceosome and is highly dynamic, interacting with three snRNAs, the pre-mRNA substrate, and >25 protein partners throughout the splicing cycle. This review summarizes the current state of knowledge on how U6 snRNA is synthesized, modified, incorporated into snRNPs and spliceosomes, recycled, and degraded.
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Affiliation(s)
- Allison L Didychuk
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53706, USA
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48
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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: 154] [Impact Index Per Article: 22.0] [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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Bennett CL, La Spada AR. Senataxin, A Novel Helicase at the Interface of RNA Transcriptome Regulation and Neurobiology: From Normal Function to Pathological Roles in Motor Neuron Disease and Cerebellar Degeneration. ADVANCES IN NEUROBIOLOGY 2018; 20:265-281. [DOI: 10.1007/978-3-319-89689-2_10] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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50
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Yurko N, Liu X, Yamazaki T, Hoque M, Tian B, Manley JL. MPK1/SLT2 Links Multiple Stress Responses with Gene Expression in Budding Yeast by Phosphorylating Tyr1 of the RNAP II CTD. Mol Cell 2017; 68:913-925.e3. [PMID: 29220656 DOI: 10.1016/j.molcel.2017.11.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/21/2017] [Accepted: 11/15/2017] [Indexed: 12/28/2022]
Abstract
The RNA polymerase II largest subunit C-terminal domain consists of repeated YSPTSPS heptapeptides. The role of tyrosine-1 (Tyr1) remains incompletely understood, as, for example, mutating all Tyr1 residues to Phe (Y1F) is lethal in vertebrates but a related mutant has only a mild phenotype in S. pombe. Here we show that Y1F substitution in budding yeast resulted in a strong slow-growth phenotype. The Y1F strain was also hypersensitive to several different cellular stresses that involve MAP kinase signaling. These phenotypes were all linked to transcriptional changes, and we also identified genetic and biochemical interactions between Tyr1 and both transcription initiation and termination factors. Further studies uncovered defects related to MAP kinase I (Slt2) pathways, and we provide evidence that Slt2 phosphorylates Tyr1 in vitro and in vivo. Our study has thus identified Slt2 as a Tyr1 kinase, and in doing so provided links between stress response activation and Tyr1 phosphorylation.
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Affiliation(s)
- Nathan Yurko
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Xiaochuan Liu
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Takashi Yamazaki
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Mainul Hoque
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - James L Manley
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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