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Yellamaty R, Sharma S. Critical Cellular Functions and Mechanisms of Action of the RNA Helicase UAP56. J Mol Biol 2024; 436:168604. [PMID: 38729260 PMCID: PMC11168752 DOI: 10.1016/j.jmb.2024.168604] [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: 03/06/2024] [Revised: 04/24/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024]
Abstract
Posttranscriptional maturation and export from the nucleus to the cytoplasm are essential steps in the normal processing of many cellular RNAs. The RNA helicase UAP56 (U2AF associated protein 56; also known as DDX39B) has emerged as a critical player in facilitating and co-transcriptionally linking these steps. Originally identified as a helicase involved in pre-mRNA splicing, UAP56 has been shown to facilitate formation of the A complex during spliceosome assembly. Additionally, it has been found to be critical for interactions between components of the exon junction and transcription and export complexes to promote the loading of export receptors. Although it appears to be structurally similar to other helicase superfamily 2 members, UAP56's ability to interact with multiple different protein partners allows it to perform its various cellular functions. Herein, we describe the structure-activity relationship studies that identified protein interactions of UAP56 and its human paralog URH49 (UAP56-related helicase 49; also known as DDX39A) and are beginning to reveal molecular mechanisms by which interacting proteins and substrate RNAs may regulate these helicases. We also provide an overview of reports that have demonstrated less well-characterized roles for UAP56, including R-loop resolution and telomere maintenance. Finally, we discuss studies that indicate a potential pathogenic effect of UAP56 in the development of autoimmune diseases and cancer, and identify the association of somatic and genetic mutations in UAP56 with neurodevelopmental disorders.
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Affiliation(s)
- Ryan Yellamaty
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA.
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2
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Xu Y, Jiao Y, Liu C, Miao R, Liu C, Wang Y, Ma C, Liu J. R-loop and diseases: the cell cycle matters. Mol Cancer 2024; 23:84. [PMID: 38678239 PMCID: PMC11055327 DOI: 10.1186/s12943-024-02000-3] [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: 02/11/2024] [Accepted: 04/13/2024] [Indexed: 04/29/2024] Open
Abstract
The cell cycle is a crucial biological process that is involved in cell growth, development, and reproduction. It can be divided into G1, S, G2, and M phases, and each period is closely regulated to ensure the production of two similar daughter cells with the same genetic material. However, many obstacles influence the cell cycle, including the R-loop that is formed throughout this process. R-loop is a triple-stranded structure, composed of an RNA: DNA hybrid and a single DNA strand, which is ubiquitous in organisms from bacteria to mammals. The existence of the R-loop has important significance for the regulation of various physiological processes. However, aberrant accumulation of R-loop due to its limited resolving ability will be detrimental for cells. For example, DNA damage and genomic instability, caused by the R-loop, can activate checkpoints in the cell cycle, which in turn induce cell cycle arrest and cell death. At present, a growing number of factors have been proven to prevent or eliminate the accumulation of R-loop thereby avoiding DNA damage and mutations. Therefore, we need to gain detailed insight into the R-loop resolution factors at different stages of the cell cycle. In this review, we review the current knowledge of factors that play a role in resolving the R-loop at different stages of the cell cycle, as well as how mutations of these factors lead to the onset and progression of diseases.
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Affiliation(s)
- Yuqin Xu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yue Jiao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chengbin Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Rui Miao
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunyan Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Yilong Wang
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Chunming Ma
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China
| | - Jiao Liu
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China.
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Mérida-Cerro JA, Maraver-Cárdenas P, Rondón AG, Aguilera A. Rat1 promotes premature transcription termination at R-loops. Nucleic Acids Res 2024; 52:3623-3635. [PMID: 38281203 DOI: 10.1093/nar/gkae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/30/2024] Open
Abstract
Certain DNA sequences can adopt a non-B form in the genome that interfere with DNA-templated processes, including transcription. Among the sequences that are intrinsically difficult to transcribe are those that tend to form R-loops, three-stranded nucleic acid structures formed by a DNA-RNA hybrid and the displaced ssDNA. Here we compared the transcription of an endogenous gene with and without an R-loop-forming sequence inserted. We show that, in agreement with previous in vivo and in vitro analyses, transcription elongation is delayed by R-loops in yeast. Importantly, we demonstrate that the Rat1 transcription terminator factor facilitates transcription throughout such structures by inducing premature termination of arrested RNAPIIs. We propose that RNase H degrades the RNA moiety of the hybrid, providing an entry site for Rat1. Thus, we have uncovered an unanticipated function of Rat1 as a transcription restoring factor opening up the possibility that it may also promote transcription through other genomic DNA structures intrinsically difficult to transcribe. If R-loop-mediated transcriptional stress is not relieved by Rat1, it will cause genomic instability, probably through the increase of transcription-replication conflicts, a deleterious situation that could lead to cancer.
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Affiliation(s)
- José Antonio Mérida-Cerro
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Pablo Maraver-Cárdenas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Ana G Rondón
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
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4
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Boddu PC, Gupta AK, Roy R, De La Peña Avalos B, Olazabal-Herrero A, Neuenkirchen N, Zimmer JT, Chandhok NS, King D, Nannya Y, Ogawa S, Lin H, Simon MD, Dray E, Kupfer GM, Verma A, Neugebauer KM, Pillai MM. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape. Mol Cell 2024; 84:1475-1495.e18. [PMID: 38521065 PMCID: PMC11061666 DOI: 10.1016/j.molcel.2024.02.032] [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: 03/28/2023] [Revised: 11/26/2023] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy.
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Affiliation(s)
- Prajwal C Boddu
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Abhishek K Gupta
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Rahul Roy
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Bárbara De La Peña Avalos
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Anne Olazabal-Herrero
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA
| | - Nils Neuenkirchen
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Joshua T Zimmer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Namrata S Chandhok
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Darren King
- Section of Hematology and Medical Oncology, Department of Internal Medicine and Rogel Cancer Center, University of Michigan Health, Ann Arbor, MI, USA
| | - Yasuhito Nannya
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Haifan Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center (UTHSC) at San Antonio, San Antonio, TX, USA
| | - Gary M Kupfer
- Department of Oncology and Pediatrics, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Amit Verma
- Division of Hemato-Oncology, Department of Medicine and Department of Developmental and Molecular Biology, Albert Einstein-Montefiore Cancer Center, New York, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA
| | - Manoj M Pillai
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, 300 George Street, Suite 786, New Haven, CT 06511, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA; Yale Center for RNA Science and Medicine, Yale University, New Haven, CT, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
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5
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Shorey-Kendrick LE, McEvoy CT, Milner K, Harris J, Brownsberger J, Tepper RS, Park B, Gao L, Vu A, Morris CD, Spindel ER. Improvements in lung function following vitamin C supplementation to pregnant smokers are associated with buccal DNA methylation at 5 years of age. Clin Epigenetics 2024; 16:35. [PMID: 38413986 PMCID: PMC10900729 DOI: 10.1186/s13148-024-01644-8] [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: 10/17/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND We previously reported in the "Vitamin C to Decrease the Effects of Smoking in Pregnancy on Infant Lung Function" randomized clinical trial (RCT) that vitamin C (500 mg/day) supplementation to pregnant smokers is associated with improved respiratory outcomes that persist through 5 years of age. The objective of this study was to assess whether buccal cell DNA methylation (DNAm), as a surrogate for airway epithelium, is associated with vitamin C supplementation, improved lung function, and decreased occurrence of wheeze. METHODS We conducted epigenome-wide association studies (EWAS) using Infinium MethylationEPIC arrays and buccal DNAm from 158 subjects (80 placebo; 78 vitamin C) with pulmonary function testing (PFT) performed at the 5-year visit. EWAS were performed on (1) vitamin C treatment, (2) forced expiratory flow between 25 and 75% of expired volume (FEF25-75), and (3) offspring wheeze. Models were adjusted for sex, race, study site, gestational age at randomization (≤ OR > 18 weeks), proportion of epithelial cells, and latent covariates in addition to child length at PFT in EWAS for FEF25-75. We considered FDR p < 0.05 as genome-wide significant and nominal p < 0.001 as candidates for downstream analyses. Buccal DNAm measured in a subset of subjects at birth and near 1 year of age was used to determine whether DNAm signatures originated in utero, or emerged with age. RESULTS Vitamin C treatment was associated with 457 FDR significant (q < 0.05) differentially methylated CpGs (DMCs; 236 hypermethylated; 221 hypomethylated) and 53 differentially methylated regions (DMRs; 26 hyper; 27 hypo) at 5 years of age. FEF25-75 was associated with one FDR significant DMC (cg05814800), 1,468 candidate DMCs (p < 0.001), and 44 DMRs. Current wheeze was associated with 0 FDR-DMCs, 782 candidate DMCs, and 19 DMRs (p < 0.001). In 365/457 vitamin C FDR significant DMCs at 5 years of age, there was no significant interaction between time and treatment. CONCLUSIONS Vitamin C supplementation to pregnant smokers is associated with buccal DNA methylation in offspring at 5 years of age, and most methylation signatures appear to be persistent from the prenatal period. Buccal methylation at 5 years was also associated with current lung function and occurrence of wheeze, and these functionally associated loci are enriched for vitamin C associated loci. Clinical trial registration ClinicalTrials.gov, NCT01723696 and NCT03203603.
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
| | - Cindy T McEvoy
- Department of Pediatrics, Pape Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA
| | - Kristin Milner
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Julia Harris
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Julie Brownsberger
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Robert S Tepper
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Byung Park
- Biostatistics Shared Resources, Knight Cancer Institute, Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland State University School of Public Health, Portland, OR, USA
| | - Lina Gao
- Biostatistics Shared Resources, Knight Cancer Institute, Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland State University School of Public Health, Portland, OR, USA
| | - Annette Vu
- Oregon Clinical & Translational Research Institute, Oregon Health and Science; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Cynthia D Morris
- Oregon Clinical & Translational Research Institute, Oregon Health and Science; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
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Werren EA, LaForce GR, Srivastava A, Perillo DR, Li S, Johnson K, Baris S, Berger B, Regan SL, Pfennig CD, de Munnik S, Pfundt R, Hebbar M, Jimenez-Heredia R, Karakoc-Aydiner E, Ozen A, Dmytrus J, Krolo A, Corning K, Prijoles EJ, Louie RJ, Lebel RR, Le TL, Amiel J, Gordon CT, Boztug K, Girisha KM, Shukla A, Bielas SL, Schaffer AE. TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome. Nat Commun 2024; 15:1640. [PMID: 38388531 PMCID: PMC10884030 DOI: 10.1038/s41467-024-45948-y] [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: 10/02/2022] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
THOC6 variants are the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 is critical for mammalian Transcription Export complex (TREX) tetramer formation, which is composed of four six-subunit THO monomers. The TREX tetramer facilitates mammalian RNA processing, in addition to the nuclear mRNA export functions of the TREX dimer conserved through yeast. Human and mouse TIDS model systems revealed novel THOC6-dependent, species-specific TREX tetramer functions. Germline biallelic Thoc6 loss-of-function (LOF) variants result in mouse embryonic lethality. Biallelic THOC6 LOF variants reduce the binding affinity of ALYREF to THOC5 without affecting the protein expression of TREX members, implicating impaired TREX tetramer formation. Defects in RNA nuclear export functions were not detected in biallelic THOC6 LOF human neural cells. Instead, mis-splicing was detected in human and mouse neural tissue, revealing novel THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for key signaling pathways known to regulate the transition from proliferative to neurogenic divisions during human corticogenesis. Together, these findings implicate altered RNA processing in the developmental biology of TIDS neuropathology.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Anshika Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Delia R Perillo
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Shaokun Li
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Katherine Johnson
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Safa Baris
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Brandon Berger
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Samantha L Regan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Christian D Pfennig
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sonja de Munnik
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 98195, Seattle, WA, USA
| | - Raúl Jimenez-Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Elif Karakoc-Aydiner
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Ahmet Ozen
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Jasmin Dmytrus
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Ana Krolo
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Ken Corning
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - E J Prijoles
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | | | - Robert Roger Lebel
- Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Thuy-Linh Le
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
| | - Jeanne Amiel
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, 75015, France
| | | | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, 1090, Austria
- St. Anna Children's Hospital and Children's Cancer Research Institute, Department of Pediatrics, Medical University of Vienna, Vienna, 1090, Austria
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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7
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Milano L, Gautam A, Caldecott KW. DNA damage and transcription stress. Mol Cell 2024; 84:70-79. [PMID: 38103560 DOI: 10.1016/j.molcel.2023.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023]
Abstract
Genome damage and transcription are intimately linked. Tens to hundreds of thousands of DNA lesions arise in each cell each day, many of which can directly or indirectly impede transcription. Conversely, the process of gene expression is itself a source of endogenous DNA lesions as a result of the susceptibility of single-stranded DNA to damage, conflicts with the DNA replication machinery, and engagement by cells of topoisomerases and base excision repair enzymes to regulate the initiation and progression of gene transcription. Although such processes are tightly regulated and normally accurate, on occasion, they can become abortive and leave behind DNA breaks that can drive genome rearrangements, instability, or cell death.
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Affiliation(s)
- Larissa Milano
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Amit Gautam
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Keith W Caldecott
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
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8
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Laspata N, Muoio D, Fouquerel E. Multifaceted Role of PARP1 in Maintaining Genome Stability Through Its Binding to Alternative DNA Structures. J Mol Biol 2024; 436:168207. [PMID: 37481154 DOI: 10.1016/j.jmb.2023.168207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/28/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
Alternative DNA structures that differ from the canonical B-form of DNA can arise from repetitive sequences and play beneficial roles in many cellular processes such as gene regulation and chromatin organization. However, they also threaten genomic stability in several ways including mutagenesis and collisions with replication and/or transcription machinery, which lead to genomic instability that is associated with human disease. Thus, the careful regulation of non-B-DNA structure formation and resolution is crucial for the maintenance of genome integrity. Several protein factors have been demonstrated to associate with alternative DNA structures to facilitate their removal, one of which is the ADP-ribose transferase (ART) PARP1 (also called ADP-ribosyltransferase diphtheria toxin-like 1 or ARTD1), a multifaceted DNA repair enzyme that recognizes single- and double-stranded DNA breaks and synthesizes chains of poly (ADP-ribose) (PAR) to recruit DNA repair proteins. It is now well appreciated that PARP1 recognizes several nucleic acid structures beyond DNA lesions, including stalled replication forks, DNA hairpins and cruciforms, R-loops, and DNA G-quadruplexes (G4 DNA). In this review, we summarize the current evidence of a direct association of PARP1 with each of these aforementioned alternative DNA structures, as well as discuss the role of PARP1 in the prevention of non-B-DNA structure-induced genetic instability. We will focus on the mechanisms of the recognition and binding by PARP1 to each alternative structure and the structure-based stimulation of PARP1 catalytic activity upon binding. Finally, we will discuss some of the outstanding gaps in the literature and offer speculative insight for questions that remain to be experimentally addressed.
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Affiliation(s)
- Natalie Laspata
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15232, USA; Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Daniela Muoio
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15232, USA
| | - Elise Fouquerel
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15232, USA.
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9
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Haji-Seyed-Javadi R, Koyen AE, Rath SK, Madden MZ, Hou Y, Song BS, Kenney AM, Lan L, Yao B, Yu DS. HELZ promotes R loop resolution to facilitate DNA double-strand break repair by homologous recombination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571747. [PMID: 38168208 PMCID: PMC10760136 DOI: 10.1101/2023.12.14.571747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
R loops are RNA-DNA hybrid containing structures involved in diverse cellular processes, including DNA double-strand break (DSB) repair. R loop homeostasis involving the formation and resolution of R loops is critical for DSB repair, and its dysregulation leads to genome instability. Here we show that the HELZ helicase promotes R loop resolution to facilitate DSB repair by homologous recombination (HR). HELZ depletion causes hypersensitivity to DSB-inducing agents, and HELZ localizes and binds to DSBs. HELZ depletion further leads to genomic instability in a R loop dependent manner and the accumulation of R loops globally and at DSBs. HELZ binds to R loops in response to DSBs and promotes their resolution, thereby facilitating HR to promote genome integrity. Our findings thus define a role for HELZ in promoting the resolution of R loops critical for DSB repair by HR.
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10
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Kern C, Radon C, Wende W, Leitner A, Sträßer K. Cross-linking mass spectrometric analysis of the endogenous TREX complex from Saccharomyces cerevisiae. RNA (NEW YORK, N.Y.) 2023; 29:1870-1880. [PMID: 37699651 PMCID: PMC10653388 DOI: 10.1261/rna.079758.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/22/2023] [Indexed: 09/14/2023]
Abstract
The conserved TREX complex has multiple functions in gene expression such as transcription elongation, 3' end processing, mRNP assembly and nuclear mRNA export as well as the maintenance of genomic stability. In Saccharomyces cerevisiae, TREX is composed of the pentameric THO complex, the DEAD-box RNA helicase Sub2, the nuclear mRNA export adaptor Yra1, and the SR-like proteins Gbp2 and Hrb1. Here, we present the structural analysis of the endogenous TREX complex of S. cerevisiae purified from its native environment. To this end, we used cross-linking mass spectrometry to gain structural information on regions of the complex that are not accessible to classical structural biology techniques. We also used negative-stain electron microscopy to investigate the organization of the cross-linked complex used for XL-MS by comparing our endogenous TREX complex with recently published structural models of recombinant THO-Sub2 complexes. According to our analysis, the endogenous yeast TREX complex preferentially assembles into a dimer.
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Affiliation(s)
- Carina Kern
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
| | - Christin Radon
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Wolfgang Wende
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Katja Sträßer
- Institute of Biochemistry, FB08, Justus Liebig University, 35392 Giessen, Germany
- Cardio-Pulmonary Institute (CPI), EXC 2026, 35392 Giessen, Germany
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11
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Sharma M, Mason AC, Dawson TR, Wente SR. Phosphorylation impacts GLE1 nuclear localization and association with DDX1. Adv Biol Regul 2023; 90:100990. [PMID: 37801910 DOI: 10.1016/j.jbior.2023.100990] [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: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/08/2023]
Abstract
Gle1 regulates gene expression at multiple steps from transcription to mRNA export to translation under stressed and non-stressed conditions. To better understand Gle1 function in stressed human cells, specific antibodies were generated that recognized the phosphorylation of threonine residue 102 (T102) in Gle1. A series of in vitro kinase assays indicated that T102 phosphorylation serves as a priming event for further phosphorylation in Gle1's N-terminal low complexity cluster. Indirect immunofluorescence microscopy with the anti-Gle1-pT102 antibodies revealed that basally phosphorylated Gle1 was pre-dominantly nuclear with punctate distribution; however, under sodium arsenite-induced stress, more cytoplasmic localization was detected. Immunoprecipitation with the anti-Gle1-pT102 antibody resulted in co-isolation of Gle1-pT102 with the DEAD-box protein DDX1 in a phosphatase sensitive manner. This suggested Gle1 phosphorylation might be linked to its role in regulating DDX1 during transcription termination. Notably, whereas the total Gle1-DDX1 association was decreased when Gle1 nucleocytoplasmic shuttling was disrupted, co-isolation of Gle1-pT102 and DDX1 increased under the same conditions. Taken together, these studies demonstrated that Gle1 phosphorylation impacts its cellular distribution and potentially drives nuclear Gle1 functions in transcription termination. We propose a model wherein phosphorylation of Gle1 either reduces its nucleocytoplasmic shuttling capacity or increases its binding affinity with nuclear interaction partners.
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Affiliation(s)
- Manisha Sharma
- Department of Cell and Development Biology, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Aaron C Mason
- Department of Cell and Development Biology, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - T Renee Dawson
- Department of Cell and Development Biology, School of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Susan R Wente
- Department of Biology, and Biochemistry, Wake Forest University, Winston-Salem, NC, USA
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12
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Kulski JK, Pfaff AL, Marney LD, Fröhlich A, Bubb VJ, Quinn JP, Koks S. Regulation of expression quantitative trait loci by SVA retrotransposons within the major histocompatibility complex. Exp Biol Med (Maywood) 2023; 248:2304-2318. [PMID: 38031415 PMCID: PMC10903234 DOI: 10.1177/15353702231209411] [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: 07/07/2023] [Accepted: 10/04/2023] [Indexed: 12/01/2023] Open
Abstract
Genomic and transcriptomic studies of expression quantitative trait loci (eQTL) revealed that SINE-VNTR-Alu (SVA) retrotransposon insertion polymorphisms (RIPs) within human genomes markedly affect the co-expression of many coding and noncoding genes by coordinated regulatory processes. This study examined the polymorphic SVA modulation of gene co-expression within the major histocompatibility complex (MHC) genomic region where more than 160 coding genes are involved in innate and adaptive immunity. We characterized the modulation of SVA RIPs utilizing the genomic and transcriptomic sequencing data obtained from whole blood of 1266 individuals in the Parkinson's Progression Markers Initiative (PPMI) cohort that included an analysis of human leukocyte antigen (HLA)-A regulation in a subpopulation of the cohort. The regulatory properties of eight SVAs located within the class I and class II MHC regions were associated with differential co-expression of 71 different genes within and 75 genes outside the MHC region. Some of the same genes were affected by two or more different SVA. Five SVA are annotated in the human genomic reference sequence GRCh38.p14/hg38, whereas the other three were novel insertions within individuals. We also examined and found distinct structural effects (long and short variants and the CT internal variants) for one of the SVA (R_SVA_24) insertions on the differential expression of the HLA-A gene within a subpopulation (550 individuals) of the PPMI cohort. This is the first time that many HLA and non-HLA genes (multilocus expression units) and splicing mechanisms have been shown to be regulated by eight structurally polymorphic SVA within the MHC genomic region by applying precise statistical analysis of RNA data derived from the blood samples of a human cohort population. This study shows that SVA within the MHC region are important regulators or rheostats of gene co-expression that might have potential roles in diversity, health, and disease.
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Affiliation(s)
- Jerzy K Kulski
- Department of Molecular Life Sciences, School of Medicine, Tokai University, Isehara, Kanagawa 259–1193, Japan
- Health and Medical Science. Division of Immunology and Microbiology, School of Biomedical Sciences, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Luke D Marney
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
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13
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Girasol MJ, Briggs EM, Marques CA, Batista JM, Beraldi D, Burchmore R, Lemgruber L, McCulloch R. Immunoprecipitation of RNA-DNA hybrid interacting proteins in Trypanosoma brucei reveals conserved and novel activities, including in the control of surface antigen expression needed for immune evasion by antigenic variation. Nucleic Acids Res 2023; 51:11123-11141. [PMID: 37843098 PMCID: PMC10639054 DOI: 10.1093/nar/gkad836] [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: 05/26/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
RNA-DNA hybrids are epigenetic features of genomes that provide a diverse and growing range of activities. Understanding of these functions has been informed by characterising the proteins that interact with the hybrids, but all such analyses have so far focused on mammals, meaning it is unclear if a similar spectrum of RNA-DNA hybrid interactors is found in other eukaryotes. The African trypanosome is a single-cell eukaryotic parasite of the Discoba grouping and displays substantial divergence in several aspects of core biology from its mammalian host. Here, we show that DNA-RNA hybrid immunoprecipitation coupled with mass spectrometry recovers 602 putative interactors in T. brucei mammal- and insect-infective cells, some providing activities also found in mammals and some lineage-specific. We demonstrate that loss of three factors, two putative helicases and a RAD51 paralogue, alters T. brucei nuclear RNA-DNA hybrid and DNA damage levels. Moreover, loss of each factor affects the operation of the parasite immune survival mechanism of antigenic variation. Thus, our work reveals the broad range of activities contributed by RNA-DNA hybrids to T. brucei biology, including new functions in host immune evasion as well as activities likely fundamental to eukaryotic genome function.
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Affiliation(s)
- Mark J Girasol
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
- University of the Philippines Manila, College of Medicine, Manila, Philippines
| | - Emma M Briggs
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
- University of Edinburgh, Institute for Immunology and Infection Research, School of Biological Sciences, Edinburgh, UK
| | - Catarina A Marques
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - José M Batista
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Dario Beraldi
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Richard Burchmore
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Leandro Lemgruber
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
| | - Richard McCulloch
- University of Glasgow, College of Medical, Veterinary and Life Sciences, School of Infection and Immunity, Wellcome Centre for Integrative Parasitology, Glasgow, UK
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14
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Yang S, Winstone L, Mondal S, Wu Y. Helicases in R-loop Formation and Resolution. J Biol Chem 2023; 299:105307. [PMID: 37778731 PMCID: PMC10641170 DOI: 10.1016/j.jbc.2023.105307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/03/2023] Open
Abstract
With the development and wide usage of CRISPR technology, the presence of R-loop structures, which consist of an RNA-DNA hybrid and a displaced single-strand (ss) DNA, has become well accepted. R-loop structures have been implicated in a variety of circumstances and play critical roles in the metabolism of nucleic acid and relevant biological processes, including transcription, DNA repair, and telomere maintenance. Helicases are enzymes that use an ATP-driven motor force to unwind double-strand (ds) DNA, dsRNA, or RNA-DNA hybrids. Additionally, certain helicases have strand-annealing activity. Thus, helicases possess unique positions for R-loop biogenesis: they utilize their strand-annealing activity to promote the hybridization of RNA to DNA, leading to the formation of R-loops; conversely, they utilize their unwinding activity to separate RNA-DNA hybrids and resolve R-loops. Indeed, numerous helicases such as senataxin (SETX), Aquarius (AQR), WRN, BLM, RTEL1, PIF1, FANCM, ATRX (alpha-thalassemia/mental retardation, X-linked), CasDinG, and several DEAD/H-box proteins are reported to resolve R-loops; while other helicases, such as Cas3 and UPF1, are reported to stimulate R-loop formation. Moreover, helicases like DDX1, DDX17, and DHX9 have been identified in both R-loop formation and resolution. In this review, we will summarize the latest understandings regarding the roles of helicases in R-loop metabolism. Additionally, we will highlight challenges associated with drug discovery in the context of targeting these R-loop helicases.
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Affiliation(s)
- Shizhuo Yang
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lacey Winstone
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sohaumn Mondal
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuliang Wu
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.
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15
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Bayona-Feliu A, Herrera-Moyano E, Badra-Fajardo N, Galván-Femenía I, Soler-Oliva ME, Aguilera A. The chromatin network helps prevent cancer-associated mutagenesis at transcription-replication conflicts. Nat Commun 2023; 14:6890. [PMID: 37898641 PMCID: PMC10613258 DOI: 10.1038/s41467-023-42653-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 10/09/2023] [Indexed: 10/30/2023] Open
Abstract
Genome instability is a feature of cancer cells, transcription being an important source of DNA damage. This is in large part associated with R-loops, which hamper replication, especially at head-on transcription-replication conflicts (TRCs). Here we show that TRCs trigger a DNA Damage Response (DDR) involving the chromatin network to prevent genome instability. Depletion of the key chromatin factors INO80, SMARCA5 and MTA2 results in TRCs, fork stalling and R-loop-mediated DNA damage which mostly accumulates at S/G2, while histone H3 Ser10 phosphorylation, a mark of chromatin compaction, is enriched at TRCs. Strikingly, TRC regions show increased mutagenesis in cancer cells with signatures of homologous recombination deficiency, transcription-coupled nucleotide excision repair (TC-NER) and of the AID/APOBEC cytidine deaminases, being predominant at head-on collisions. Thus, our results support that the chromatin network prevents R-loops and TRCs from genomic instability and mutagenic signatures frequently associated with cancer.
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Affiliation(s)
- Aleix Bayona-Feliu
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain.
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain.
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Emilia Herrera-Moyano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain
| | - Nibal Badra-Fajardo
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
| | - Iván Galván-Femenía
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - María Eugenia Soler-Oliva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092, Seville, Spain.
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012, Seville, Spain.
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16
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de Vivo A, Song H, Lee Y, Tirado-Class N, Sanchez A, Westerheide S, Dungrawala H, Kee Y. OTUD5 limits replication fork instability by organizing chromatin remodelers. Nucleic Acids Res 2023; 51:10467-10483. [PMID: 37713620 PMCID: PMC10602872 DOI: 10.1093/nar/gkad732] [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: 05/16/2023] [Revised: 08/01/2023] [Accepted: 08/25/2023] [Indexed: 09/17/2023] Open
Abstract
Proper regulation of replication fork progression is important for genomic maintenance. Subverting the transcription-induced conflicts is crucial in preserving the integrity of replication forks. Various chromatin remodelers, such as histone chaperone and histone deacetylases are known to modulate replication stress, but how these factors are organized or collaborate are not well understood. Here we found a new role of the OTUD5 deubiquitinase in limiting replication stress. We found that OTUD5 is recruited to replication forks, and its depletion causes replication fork stress. Through its C-terminal disordered tail, OTUD5 assembles a complex containing FACT, HDAC1 and HDAC2 at replication forks. A cell line engineered to specifically uncouple FACT interaction with OTUD5 exhibits increases in FACT loading onto chromatin, R-loop formation, and replication fork stress. OTUD5 mediates these processes by recruiting and stabilizing HDAC1 and HDAC2, which decreases H4K16 acetylation and FACT recruitment. Finally, proteomic analysis revealed that the cells with deficient OTUD5-FACT interaction activates the Fanconi Anemia pathway for survival. Altogether, this study identified a new interaction network among OTUD5-FACT-HDAC1/2 that limits transcription-induced replication stress.
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Affiliation(s)
- Angelo de Vivo
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
| | - Hongseon Song
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 333 Techno-Joongang-daero, Dalseong-gun, Daegu 42988, Republic of Korea
| | - Yujin Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 333 Techno-Joongang-daero, Dalseong-gun, Daegu 42988, Republic of Korea
| | - Neysha Tirado-Class
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
| | - Anthony Sanchez
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
| | - Sandy Westerheide
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
| | - Huzefa Dungrawala
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
| | - Younghoon Kee
- Department of Molecular Biosciences, College of Arts and Sciences, University of South Florida, Tampa, FL 33647, USA
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 333 Techno-Joongang-daero, Dalseong-gun, Daegu 42988, Republic of Korea
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17
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Camino LP, Dutta A, Barroso S, Pérez-Calero C, Katz JN, García-Rubio M, Sung P, Gómez-González B, Aguilera A. DICER ribonuclease removes harmful R-loops. Mol Cell 2023; 83:3707-3719.e5. [PMID: 37827159 PMCID: PMC11034902 DOI: 10.1016/j.molcel.2023.09.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 07/08/2023] [Accepted: 09/19/2023] [Indexed: 10/14/2023]
Abstract
R-loops, which consist of a DNA-RNA hybrid and a displaced DNA strand, are known to threaten genome integrity. To counteract this, different mechanisms suppress R-loop accumulation by either preventing the hybridization of RNA with the DNA template (RNA biogenesis factors), unwinding the hybrid (DNA-RNA helicases), or degrading the RNA moiety of the R-loop (type H ribonucleases [RNases H]). Thus far, RNases H are the only nucleases known to cleave DNA-RNA hybrids. Now, we show that the RNase DICER also resolves R-loops. Biochemical analysis reveals that DICER acts by specifically cleaving the RNA within R-loops. Importantly, a DICER RNase mutant impaired in R-loop processing causes a strong accumulation of R-loops in cells. Our results thus not only reveal a function of DICER as an R-loop resolvase independent of DROSHA but also provide evidence for the role of multi-functional RNA processing factors in the maintenance of genome integrity in higher eukaryotes.
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Affiliation(s)
- Lola P Camino
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Arijit Dutta
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Sonia Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Carmen Pérez-Calero
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Jeffrey N Katz
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - María García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Patrick Sung
- Greehey Children's Cancer Research Institute, Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla, CSIC, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
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18
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Li F, Zafar A, Luo L, Denning AM, Gu J, Bennett A, Yuan F, Zhang Y. R-Loops in Genome Instability and Cancer. Cancers (Basel) 2023; 15:4986. [PMID: 37894353 PMCID: PMC10605827 DOI: 10.3390/cancers15204986] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
R-loops are unique, three-stranded nucleic acid structures that primarily form when an RNA molecule displaces one DNA strand and anneals to the complementary DNA strand in a double-stranded DNA molecule. R-loop formation can occur during natural processes, such as transcription, in which the nascent RNA molecule remains hybridized with the template DNA strand, while the non-template DNA strand is displaced. However, R-loops can also arise due to many non-natural processes, including DNA damage, dysregulation of RNA degradation pathways, and defects in RNA processing. Despite their prevalence throughout the whole genome, R-loops are predominantly found in actively transcribed gene regions, enabling R-loops to serve seemingly controversial roles. On one hand, the pathological accumulation of R-loops contributes to genome instability, a hallmark of cancer development that plays a role in tumorigenesis, cancer progression, and therapeutic resistance. On the other hand, R-loops play critical roles in regulating essential processes, such as gene expression, chromatin organization, class-switch recombination, mitochondrial DNA replication, and DNA repair. In this review, we summarize discoveries related to the formation, suppression, and removal of R-loops and their influence on genome instability, DNA repair, and oncogenic events. We have also discussed therapeutical opportunities by targeting pathological R-loops.
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Affiliation(s)
- Fang Li
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Alyan Zafar
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ariana Maria Denning
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Jun Gu
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Ansley Bennett
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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19
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Werren E, LaForce G, Srivastava A, Perillo D, Johnson K, Berger B, Regan S, Pfennig C, Baris S, de Munnik S, Pfundt R, Hebbar M, Jimenez Heredia R, Karakoc-Aydiner E, Ozen A, Dmytrus J, Krolo A, Corning K, Prijoles E, Louie R, Lebel R, Le TL, Amiel J, Gordon C, Boztug K, Girisha K, Shukla A, Bielas S, Schaffer A. Mechanisms of mRNA processing defects in inherited THOC6 intellectual disability syndrome. RESEARCH SQUARE 2023:rs.3.rs-2126145. [PMID: 37720017 PMCID: PMC10503840 DOI: 10.21203/rs.3.rs-2126145/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
THOC6 is the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 facilitates the formation of the Transcription Export complex (TREX) tetramer, composed of four THO monomers. The TREX tetramer supports mammalian mRNA processing that is distinct from yeast TREX dimer functions. Human and mouse TIDS model systems allow novel THOC6-dependent TREX tetramer functions to be investigated. Biallelic loss-of-functon(LOF) THOC6 variants do not influence the expression and localization of TREX members in human cells, but our data suggests reduced binding affinity of ALYREF. Impairment of TREX nuclear export functions were not detected in cells with biallelic THOC6 LOF. Instead, mRNA mis-splicing was observed in human and mouse neural tissue, revealing novel insights into THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for regulation of key signaling pathways in human corticogenesis that dictate the transition from proliferative to neurogenic divisions that may inform TIDS neuropathology.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jasmin Dmytrus
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of Sciences
| | - Ana Krolo
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases
| | | | | | | | | | - Thuy-Linh Le
- Imagine Institute, INSERM U1163, Paris Descartes University
| | | | - Christopher Gordon
- Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine
| | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases
| | - Katta Girisha
- Kasturba Medical College, Manipal, Manipal Academy of Higher Education
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20
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Xie Y, Gao S, Zhang K, Bhat P, Clarke BP, Batten K, Mei M, Gazzara M, Shay JW, Lynch KW, Angelos AE, Hill PS, Ivey AL, Fontoura BMA, Ren Y. Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly. Cell Rep 2023; 42:112988. [PMID: 37578863 PMCID: PMC10508174 DOI: 10.1016/j.celrep.2023.112988] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/10/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023] Open
Abstract
mRNA in eukaryotic cells is packaged into highly compacted ribonucleoprotein particles (mRNPs) in the nucleus and exported to the cytoplasm for translation. mRNP packaging and export require the evolutionarily conserved transcription-export (TREX) complex. TREX facilitates loading of various RNA-binding proteins on mRNA through the action of its DDX39B subunit. SARNP (Tho1 [transcriptional defect of Hpr1 by overexpression 1] in yeast) is shown to interact with DDX39B and affect mRNA export. The molecular mechanism of how SARNP recognizes DDX39B and functions in mRNP assembly is unclear. Here, we determine the crystal structure of a Tho1/DDX39B/RNA complex, revealing a multivalent interaction mediated by tandem DDX39B interacting motifs in SARNP/Tho1. The high-order complex of SARNP and DDX39B is evolutionarily conserved, and human SARNP can engage with five DDX39B molecules. RNA sequencing (RNA-seq) from SARNP knockdown cells shows the most affected RNAs in export are GC rich. Our work suggests the role of the high-order SARNP/DDX39B/RNA complex in mRNP assembly and export.
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Affiliation(s)
- Yihu Xie
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Shengyan Gao
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Ke Zhang
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Prasanna Bhat
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Bradley P Clarke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Kimberly Batten
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Menghan Mei
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Matthew Gazzara
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jerry W Shay
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Kristen W Lynch
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexia E Angelos
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Pate S Hill
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Austin L Ivey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA
| | - Beatriz M A Fontoura
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039, USA.
| | - Yi Ren
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA; Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.
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21
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Fernandes RV, Lingner J. The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase+ cells and telomeric recombination in ALT+ cells. Nucleic Acids Res 2023; 51:6702-6722. [PMID: 37246640 PMCID: PMC10359610 DOI: 10.1093/nar/gkad448] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/26/2023] [Accepted: 05/14/2023] [Indexed: 05/30/2023] Open
Abstract
Telomeres are the nucleoprotein structures at the ends of linear chromosomes. Telomeres are transcribed into long non-coding Telomeric Repeat-Containing RNA (TERRA), whose functions rely on its ability to associate with telomeric chromatin. The conserved THO complex (THOC) was previously identified at human telomeres. It links transcription with RNA processing, decreasing the accumulation of co-transcriptional DNA:RNA hybrids throughout the genome. Here, we explore the role of THOC at human telomeres, as a regulator of TERRA localization to chromosome ends. We show that THOC counteracts TERRA association with telomeres via R-loops formed co-transcriptionally and also post-transcriptionally, in trans. We demonstrate that THOC binds nucleoplasmic TERRA, and that RNaseH1 loss, which increases telomeric R-loops, promotes THOC occupancy at telomeres. Additionally, we show that THOC counteracts lagging and mainly leading strand telomere fragility, suggesting that TERRA R-loops can interfere with replication fork progression. Finally, we observed that THOC suppresses telomeric sister-chromatid exchange and C-circle accumulation in ALT cancer cells, which maintain telomeres by recombination. Altogether, our findings reveal crucial roles of THOC in telomeric homeostasis through the co- and post-transcriptional regulation of TERRA R-loops.
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Affiliation(s)
- Rita Valador Fernandes
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Joachim Lingner
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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22
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Zhang X, Duan J, Li Y, Jin X, Wu C, Yang X, Lu W, Ge W. NKAP acts with HDAC3 to prevent R-loop associated genome instability. Cell Death Differ 2023; 30:1811-1828. [PMID: 37322264 PMCID: PMC10307950 DOI: 10.1038/s41418-023-01182-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 05/09/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023] Open
Abstract
Persistent R-loop accumulation can cause DNA damage and lead to genome instability, which contributes to various human diseases. Identification of molecules and signaling pathways in controlling R-loop homeostasis provide important clues about their physiological and pathological roles in cells. Here, we show that NKAP (NF-κB activating protein) is essential for preventing R-loop accumulation and maintaining genome integrity through forming a protein complex with HDAC3. NKAP depletion causes DNA damage and genome instability. Aberrant accumulation of R-loops is present in NKAP-deficient cells and leads to DNA damage and DNA replication fork progression defects. Moreover, NKAP depletion induced R-loops and DNA damage are dependent on transcription. Consistently, the NKAP interacting protein HDAC3 exhibits a similar role in suppressing R-loop associated DNA damage and replication stress. Further analysis uncovers that HDAC3 functions to stabilize NKAP protein, independent of its deacetylase activity. In addition, NKAP prevents R-loop formation by maintaining RNA polymerase II pausing. Importantly, R-loops induced by NKAP or HDAC3 depletion are processed into DNA double-strand breaks by XPF and XPG endonucleases. These findings indicate that both NKAP and HDAC3 are novel key regulators of R-loop homeostasis, and their dysregulation might drive tumorigenesis by causing R-loop associated genome instability.
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Affiliation(s)
- Xing Zhang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Jingwei Duan
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Yang Li
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Xiaoye Jin
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Cheng Wu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Xiaohang Yang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China
| | - Weiguo Lu
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
- Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
| | - Wanzhong Ge
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310058, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, 310058, Zhejiang, China.
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23
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Holland CL, Weis MF, England CJ, Berry AM, Hall PD, Lewis LK. Deficiency in homologous recombination is associated with changes in cell cycling and morphology in Saccharomyces cerevisiae. Exp Cell Res 2023:113701. [PMID: 37393982 DOI: 10.1016/j.yexcr.2023.113701] [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: 05/04/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/04/2023]
Abstract
Exposure of eukaryotic cells to ionizing radiation or clastogenic chemicals leads to formation of DNA double-strand breaks (DSBs). These lesions are also generated internally by chemicals and enzymes, in the absence of exogenous agents, though the sources and consequences of such endogenously generated DSBs remain poorly understood. In the current study, we have investigated the impact of reduced recombinational repair of endogenous DSBs on stress responses, cell morphology and other physical properties of S. cerevisiae (budding yeast) cells. Use of phase contrast and DAPI-based fluorescence microscopy combined with FACS analysis confirmed that recombination-deficient rad52 cell cultures exhibit chronically high levels of G2 phase cells. Cell cycle phase transit times during G1, S and M were similar in WT and rad52 cells, but the length of G2 phase was increased by three-fold in the mutants. rad52 cells were larger than WT in all phases of the cycle and displayed other quantifiable changes in physical characteristics. The high G2 cell phenotype was abolished when DNA damage checkpoint genes, but not spindle assembly checkpoint genes, were co-inactivated with RAD52. Several other RAD52 group mutants (rad51, rad54, rad55, rad57 and rad59) also exhibited the high G2 cell phenotype. The results indicate that recombination deficiency leads to accumulation of unrepaired DSBs during normal mitotic growth that activate a major stress response and produce distinct changes in cellular physiology and morphology.
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Affiliation(s)
- Cory L Holland
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Monica F Weis
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Corbin J England
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Armand M Berry
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - Paige D Hall
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA
| | - L Kevin Lewis
- Chemistry and Biochemistry, Texas State University, 601 University Drive, San Marcos, TX, 78666, USA.
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24
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Zhang Y, Luo J, Yang W, Ye WC. CircRNAs in colorectal cancer: potential biomarkers and therapeutic targets. Cell Death Dis 2023; 14:353. [PMID: 37296107 PMCID: PMC10250185 DOI: 10.1038/s41419-023-05881-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/09/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Globally, colorectal cancer (CRC) is the third most prevalent cancer and the second leading cause of cancer-related deaths. Circular RNAs (circRNAs) are single-stranded RNA with covalently closed-loop structures and are highly stable, conserved, and abundantly expressed in various organs and tissues. Recent research found abnormal circRNA expression in CRC patients' blood/serum, cells, CRC tissues, and exosomes. Furthermore, mounting data demonstrated that circRNAs are crucial to the development of CRC. CircRNAs have been shown to exert biological functions by acting as microRNA sponges, RNA-binding protein sponges, regulators of gene splicing and transcription, and protein/peptide translators. These characteristics make circRNAs potential markers for CRC diagnosis and prognosis, potential therapeutic targets, and circRNA-based therapies. However, further studies are still necessary to improve the understanding of the roles and biological mechanisms of circRNAs in the development of CRC. In this review, up-to-date research on the role of circRNAs in CRC was examined, focusing on their potential application in CRC diagnosis and targeted therapy, which would advance the knowledge of the functions of circRNAs in the development and progression of CRC.
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Affiliation(s)
- Yuying Zhang
- Central Laboratory, Shenzhen Longhua Maternity and Child Healthcare Hospital, Shenzhen, 518109, China
| | - Jingyan Luo
- Forevergen Biosciences Centre, Guangzhou International Biotech Island, Guangzhou, 510300, China
| | - Weikang Yang
- Department of Prevention and Healthcare, Shenzhen Longhua Maternity and Child Healthcare Hospital, Shenzhen, 518109, China
| | - Wen-Chu Ye
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.
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25
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Marchena-Cruz E, Camino LP, Bhandari J, Silva S, Marqueta-Gracia JJ, Amdeen SA, Guillén-Mendoza C, García-Rubio ML, Calderón-Montaño JM, Xue X, Luna R, Aguilera A. DDX47, MeCP2, and other functionally heterogeneous factors protect cells from harmful R loops. Cell Rep 2023; 42:112148. [PMID: 36827184 PMCID: PMC10066596 DOI: 10.1016/j.celrep.2023.112148] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 12/20/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Unscheduled R loops can be a source of genome instability, a hallmark of cancer cells. Although targeted proteomic approaches and cellular analysis of specific mutants have uncovered factors potentially involved in R-loop homeostasis, we report a more open screening of factors whose depletion causes R loops based on the ability of activation-induced cytidine deaminase (AID) to target R loops. Immunofluorescence analysis of γH2AX caused by small interfering RNAs (siRNAs) covering 3,205 protein-coding genes identifies 59 potential candidates, from which 13 are analyzed further and show a significant increase of R loops. Such candidates are enriched in factors involved in chromatin, transcription, and RNA biogenesis and other processes. A more focused study shows that the DDX47 helicase is an R-loop resolvase, whereas the MeCP2 methyl-CpG-binding protein uncovers a link between DNA methylation and R loops. Thus, our results suggest that a plethora of gene dysfunctions can alter cell physiology via affecting R-loop homeostasis by different mechanisms.
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Affiliation(s)
- Esther Marchena-Cruz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Lola P Camino
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Jay Bhandari
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Sónia Silva
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - José Javier Marqueta-Gracia
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Shahad A Amdeen
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Cristina Guillén-Mendoza
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - José M Calderón-Montaño
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain
| | - Xiaoyu Xue
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Rosa Luna
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departmento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
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26
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Laspata N, Kaur P, Mersaoui S, Muoio D, Liu Z, Bannister MH, Nguyen H, Curry C, Pascal J, Poirier G, Wang H, Masson JY, Fouquerel E. PARP1 associates with R-loops to promote their resolution and genome stability. Nucleic Acids Res 2023; 51:2215-2237. [PMID: 36794853 PMCID: PMC10018367 DOI: 10.1093/nar/gkad066] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/19/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
PARP1 is a DNA-dependent ADP-Ribose transferase with ADP-ribosylation activity that is triggered by DNA breaks and non-B DNA structures to mediate their resolution. PARP1 was also recently identified as a component of the R-loop-associated protein-protein interaction network, suggesting a potential role for PARP1 in resolving this structure. R-loops are three-stranded nucleic acid structures that consist of a RNA-DNA hybrid and a displaced non-template DNA strand. R-loops are involved in crucial physiological processes but can also be a source of genome instability if persistently unresolved. In this study, we demonstrate that PARP1 binds R-loops in vitro and associates with R-loop formation sites in cells which activates its ADP-ribosylation activity. Conversely, PARP1 inhibition or genetic depletion causes an accumulation of unresolved R-loops which promotes genomic instability. Our study reveals that PARP1 is a novel sensor for R-loops and highlights that PARP1 is a suppressor of R-loop-associated genomic instability.
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Affiliation(s)
- Natalie Laspata
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15213, USA
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Parminder Kaur
- Physics Department, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, Raleigh, NC 27695, USA
| | - Sofiane Yacine Mersaoui
- CHU de Québec Research Centre, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, McMahon, Québec City, Québec G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, Canada
| | - Daniela Muoio
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15213, USA
| | - Zhiyan Silvia Liu
- Department of Pharmacology, The Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Maxwell Henry Bannister
- Department of Pharmacology, The Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hai Dang Nguyen
- Department of Pharmacology, The Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Caroline Curry
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Guy G Poirier
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, Canada
- CHU de Québec Research Centre, CHUL Pavilion, Oncology Division, Quebec, Canada
| | - Hong Wang
- Physics Department, Raleigh, NC 27695, USA
- Center for Human Health and the Environment, Raleigh, NC 27695, USA
- Toxicology Program, North Carolina State University, Raleigh, NC, USA
| | - Jean-Yves Masson
- CHU de Québec Research Centre, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, McMahon, Québec City, Québec G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Université Laval, Quebec, Canada
| | - Elise Fouquerel
- UPMC Hillman Cancer Center, University of Pittsburgh Cancer Institute, Department of Pharmacology and Chemical Biology, Pittsburgh, PA 15213, USA
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27
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Yu Z, Richard S. DDX47 untangles R-loops with only certain other helicases. Trends Cell Biol 2023; 33:359-360. [PMID: 36914533 DOI: 10.1016/j.tcb.2023.03.001] [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: 03/01/2023] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/13/2023]
Abstract
R-loops, formed transiently during gene transcription, are tightly controlled to avoid conflict with ongoing processes. Marchena-Cruz et al. identified DExD/H box RNA helicase DDX47 using a new R-loop resolving screen and defined a unique role for this helicase in nucleolar R-loops and its interplay with senataxin (SETX) and DDX39B.
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Affiliation(s)
- Zhenbao Yu
- Segal Cancer Center, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec H3T 1E2, Canada; Gerald Bronfman Department of Oncology McGill University, Montréal, Québec H3T 1E2, Canada; Department of Biochemistry, McGill University, Montréal, Québec H3T 1E2, Canada; Department of Human Genetics McGill University, Montréal, Québec H3T 1E2, Canada; Department of Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec H3T 1E2, Canada; Gerald Bronfman Department of Oncology McGill University, Montréal, Québec H3T 1E2, Canada; Department of Biochemistry, McGill University, Montréal, Québec H3T 1E2, Canada; Department of Human Genetics McGill University, Montréal, Québec H3T 1E2, Canada; Department of Medicine, McGill University, Montréal, Québec H3T 1E2, Canada.
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28
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DEAD-box ATPases as regulators of biomolecular condensates and membrane-less organelles. Trends Biochem Sci 2023; 48:244-258. [PMID: 36344372 DOI: 10.1016/j.tibs.2022.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Abstract
RNA-dependent DEAD-box ATPases (DDXs) are emerging as major regulators of RNA-containing membrane-less organelles (MLOs). On the one hand, oligomerizing DDXs can promote condensate formation 'in cis', often using RNA as a scaffold. On the other hand, DDXs can disrupt RNA-RNA and RNA-protein interactions and thereby 'in trans' remodel the multivalent interactions underlying MLO formation. In this review, we discuss the best studied examples of DDXs modulating MLOs in cis and in trans. Further, we illustrate how this contributes to the dynamic assembly and turnover of MLOs which might help cells to modulate RNA sequestration and processing in a temporal and spatial manner.
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29
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Boddu PC, Gupta A, Roy R, De La Pena Avalos B, Herrero AO, Neuenkirchen N, Zimmer J, Chandhok N, King D, Nannya Y, Ogawa S, Lin H, Simon M, Dray E, Kupfer G, Verma AK, Neugebauer KM, Pillai MM. Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530019. [PMID: 36891287 PMCID: PMC9994134 DOI: 10.1101/2023.02.25.530019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human disease remains unexplored. Here, we investigated the impact of non-synonymous mutations in SF3B1 and U2AF1, two commonly mutated splicing factors in cancer, on transcription. We find that the mutations impair RNA Polymerase II (RNAPII) transcription elongation along gene bodies leading to transcription-replication conflicts, replication stress and altered chromatin organization. This elongation defect is linked to disrupted pre-spliceosome assembly due to impaired association of HTATSF1 with mutant SF3B1. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC complex, which, when modulated, normalize transcription defects and their downstream effects. Our findings shed light on the mechanisms by which oncogenic mutant spliceosomes impact chromatin organization through their effects on RNAPII transcription elongation and present a rationale for targeting the Sin3/HDAC complex as a potential therapeutic strategy. GRAPHICAL ABSTRACT HIGHLIGHTS Oncogenic mutations of SF3B1 and U2AF1 cause a gene-body RNAPII elongation defectRNAPII transcription elongation defect leads to transcription replication conflicts, DNA damage response, and changes to chromatin organization and H3K4me3 marksThe transcription elongation defect is linked to disruption of the early spliceosome formation through impaired interaction of HTATSF1 with mutant SF3B1.Changes to chromatin organization reveal potential therapeutic strategies by targeting the Sin3/HDAC pathway.
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Polenkowski M, Allister AB, Burbano de Lara S, Pierce A, Geary B, El Bounkari O, Wiehlmann L, Hoffmann A, Whetton AD, Tamura T, Tran DDH. THOC5 complexes with DDX5, DDX17, and CDK12 to regulate R loop structures and transcription elongation rate. iScience 2022; 26:105784. [PMID: 36590164 PMCID: PMC9800341 DOI: 10.1016/j.isci.2022.105784] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/10/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
THOC5, a member of the THO complex, is essential for the 3'processing of some inducible genes, the export of a subset of mRNAs and stem cell survival. Here we show that THOC5 depletion results in altered 3'cleavage of >50% of mRNAs and changes in RNA polymerase II binding across genes. THOC5 is recruited close to high-density polymerase II sites, suggesting that THOC5 is involved in transcriptional elongation. Indeed, measurement of elongation rates in vivo demonstrated decreased rates in THOC5-depleted cells. Furthermore, THOC5 is preferentially recruited to its target genes in slow polymerase II cells compared with fast polymerase II cells. Importantly chromatin-associated THOC5 interacts with CDK12 (a modulator of transcription elongation) and RNA helicases DDX5, DDX17, and THOC6 only in slow polymerase II cells. The CDK12/THOC5 interaction promotes CDK12 recruitment to R-loops in a THOC6-dependent manner. These data demonstrate a novel function of THOC5 in transcription elongation.
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Affiliation(s)
- Mareike Polenkowski
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | - Aldrige Bernardus Allister
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Humangenetik, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | | | - Andrew Pierce
- Stem Cell and Leukemia Protoemics Laboratory, University of Manchester, Manchester M20 3LJ, UK
| | - Bethany Geary
- Stem Cell and Leukemia Protoemics Laboratory, University of Manchester, Manchester M20 3LJ, UK
| | - Omar El Bounkari
- Institute for Stroke and Dementia Research, Ludwig-Maximilians-Universität, 81377 Munich, Germany
| | - Lutz Wiehlmann
- Pädiatrische Pneumologie Hannover Medical School, Hannover D-30623, Germany
| | - Andrea Hoffmann
- Department of Orthopedic Surgery, Hannover Medical School, Hannover D-30623, Germany
| | - Anthony D. Whetton
- Stoller Biomarker Discovery Centre, University of Manchester, Manchester M13 9PL, UK
| | - Teruko Tamura
- Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany
| | - Doan Duy Hai Tran
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover D-30623, Germany,Institut für Zellbiochemie, Medizinische Hochschule Hannover, Hannover D-30623, Germany,Corresponding author
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31
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Hodson C, van Twest S, Dylewska M, O'Rourke JJ, Tan W, Murphy VJ, Walia M, Abbouche L, Nieminuszczy J, Dunn E, Bythell-Douglas R, Heierhorst J, Niedzwiedz W, Deans AJ. Branchpoint translocation by fork remodelers as a general mechanism of R-loop removal. Cell Rep 2022; 41:111749. [PMID: 36476850 DOI: 10.1016/j.celrep.2022.111749] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/05/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022] Open
Abstract
Co-transcriptional R loops arise from stalling of RNA polymerase, leading to the formation of stable DNA:RNA hybrids. Unresolved R loops promote genome instability but are counteracted by helicases and nucleases. Here, we show that branchpoint translocases are a third class of R-loop-displacing enzyme in vitro. In cells, deficiency in the Fanconi-anemia-associated branchpoint translocase FANCM causes R-loop accumulation, particularly after treatment with DNA:RNA-hybrid-stabilizing agents. This correlates with FANCM localization at R-loop-prone regions of the genome. Moreover, other branchpoint translocases associated with human disease, such as SMARCAL1 and ZRANB3, and those from lower organisms can also remove R loops in vitro. Branchpoint translocases are more potent than helicases in resolving R loops, indicating their evolutionary important role in R-loop suppression. In human cells, FANCM, SMARCAL1, and ZRANB3 depletion causes additive effects on R-loop accumulation and DNA damage. Our work reveals a mechanistic basis for R-loop displacement that is linked to genome stability.
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Affiliation(s)
- Charlotte Hodson
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Sylvie van Twest
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Julienne J O'Rourke
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Winnie Tan
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Vincent J Murphy
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Mannu Walia
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Lara Abbouche
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Elyse Dunn
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Rohan Bythell-Douglas
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Jörg Heierhorst
- Department of Medicine (St Vincent's Health), University of Melbourne, Fitzroy, VIC 3065, Australia; Molecular Genetics Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | | | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia; Department of Medicine (St Vincent's Health), University of Melbourne, Fitzroy, VIC 3065, Australia.
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32
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Boleslavska B, Oravetzova A, Shukla K, Nascakova Z, Ibini O, Hasanova Z, Andrs M, Kanagaraj R, Dobrovolna J, Janscak P. DDX17 helicase promotes resolution of R-loop-mediated transcription-replication conflicts in human cells. Nucleic Acids Res 2022; 50:12274-12290. [PMID: 36453994 PMCID: PMC9757067 DOI: 10.1093/nar/gkac1116] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
R-loops are three-stranded nucleic acid structures composed of an RNA:DNA hybrid and displaced DNA strand. These structures can halt DNA replication when formed co-transcriptionally in the opposite orientation to replication fork progression. A recent study has shown that replication forks stalled by co-transcriptional R-loops can be restarted by a mechanism involving fork cleavage by MUS81 endonuclease, followed by ELL-dependent reactivation of transcription, and fork religation by the DNA ligase IV (LIG4)/XRCC4 complex. However, how R-loops are eliminated to allow the sequential restart of transcription and replication in this pathway remains elusive. Here, we identified the human DDX17 helicase as a factor that associates with R-loops and counteracts R-loop-mediated replication stress to preserve genome stability. We show that DDX17 unwinds R-loops in vitro and promotes MUS81-dependent restart of R-loop-stalled forks in human cells in a manner dependent on its helicase activity. Loss of DDX17 helicase induces accumulation of R-loops and the formation of R-loop-dependent anaphase bridges and micronuclei. These findings establish DDX17 as a component of the MUS81-LIG4-ELL pathway for resolution of R-loop-mediated transcription-replication conflicts, which may be involved in R-loop unwinding.
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Affiliation(s)
- Barbora Boleslavska
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic,Faculty of Science, Charles University in Prague, Albertov 6, 128 00 Prague 2, Czech Republic
| | - Anna Oravetzova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic,Faculty of Science, Charles University in Prague, Albertov 6, 128 00 Prague 2, Czech Republic
| | - Kaustubh Shukla
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Zuzana Nascakova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | | | - Zdenka Hasanova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Martin Andrs
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague 4, Czech Republic
| | - Radhakrishnan Kanagaraj
- School of Life Sciences, University of Bedfordshire, Park Square, Luton LU1 3JU, UK,School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK,Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai 600119, India
| | - Jana Dobrovolna
- Correspondence may also be addressed to Jana Dobrovolna. Tel: +420 241063127;
| | - Pavel Janscak
- To whom correspondence should be addressed. Tel: +41 44 6353470;
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Chen L, Wang Y, Lin J, Song Z, Wang Q, Zhao W, Wang Y, Xiu X, Deng Y, Li X, Li Q, Wang X, Li J, Liu X, Liu K, Zhou J, Li K, Liu Y, Liao S, Deng Q, Xu C, Sun Q, Wu S, Zhang K, Guan MX, Zhou T, Sun F, Cai X, Huang C, Shan G. Exportin 4 depletion leads to nuclear accumulation of a subset of circular RNAs. Nat Commun 2022; 13:5769. [PMID: 36182935 PMCID: PMC9526749 DOI: 10.1038/s41467-022-33356-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/09/2022] [Indexed: 12/19/2022] Open
Abstract
Numerous RNAs are exported from the nucleus, abnormalities of which lead to cellular complications and diseases. How thousands of circular RNAs (circRNAs) are exported from the nucleus remains elusive. Here, we provide lines of evidence to demonstrate a link between the conserved Exportin 4 (XPO4) and nuclear export of a subset of circRNAs in metazoans. Exonic circRNAs (ecircRNAs) with higher expression levels, larger length, and lower GC content are more sensitive to XPO4 deficiency. Cellular insufficiency of XPO4 leads to nuclear circRNA accumulation, circRNA:DNA (ciR-loop) formation, linear RNA:DNA (liR-loop) buildup, and DNA damage. DDX39 known to modulate circRNA export can resolve ciR-loop, and splicing factors involved in the biogenesis of circRNAs can also affect the levels of ciR-loop. Testis and brain are two organs with high abundance of circRNAs, and insufficient XPO4 levels are detrimental, as Xpo4 heterozygous mice display male infertility and neural phenotypes. Increased levels of ciR-loop, R-loop, and DNA damage along with decreased cell numbers are observed in testis and hippocampus of Xpo4 heterozygotes. This study sheds light on the understandings of mechanism of circRNA export and reveals the significance of efficient nuclear export of circRNAs in cellular physiology. This study identifies the evolutionarily conserved Exportin 4 as an essential regulator in the nuclear export of circRNAs. Defective circRNA export results in R-loop formation and DNA damage in cells, as well as testis and neurological defects in mice.
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Affiliation(s)
- Liang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Yucong Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 401331, China.,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Qinwei Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Wenfang Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Yan Wang
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325003, China.,State Key Laboratory of Optometry, Ophthalmology, and Visual Science, 270 Xueyuan Road, Wenzhou, Zhejiang, 325003, China
| | - Xiaoyu Xiu
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325003, China.,State Key Laboratory of Optometry, Ophthalmology, and Visual Science, 270 Xueyuan Road, Wenzhou, Zhejiang, 325003, China
| | - Yuqi Deng
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Xiuzhi Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Qiqi Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Xiaolin Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jingxin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Xu Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Kunpeng Liu
- Center for Plant Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jincong Zhou
- Center for Plant Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Kuan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuchan Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Shanhui Liao
- Division of Life Science and Medicine, CAS Key Laboratory of Structural Biology, University of Science and Technology of China, Hefei, 230027, China
| | - Qin Deng
- Analytical and Testing Center, Chongqing University, Chongqing, 400030, China
| | - Chao Xu
- Division of Life Science and Medicine, CAS Key Laboratory of Structural Biology, University of Science and Technology of China, Hefei, 230027, China
| | - Qianwen Sun
- Center for Plant Biology, School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shengzhou Wu
- School of Optometry and Ophthalmology and the Eye Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, 325003, China.,State Key Laboratory of Optometry, Ophthalmology, and Visual Science, 270 Xueyuan Road, Wenzhou, Zhejiang, 325003, China
| | - Kaiming Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Min-Xin Guan
- The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Zhejiang Provincial Key Lab of Genetic and Developmental Disorder, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Tianhua Zhou
- Department of Cell Biology and Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Cancer Center, Institute of Gastroenterology, Zhejiang University, Hangzhou, 310016, China
| | - Fei Sun
- Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Xiujun Cai
- Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China. .,Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
| | - Ge Shan
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China. .,Department of Pulmonary and Critical Care Medicine, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
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DDX39B drives colorectal cancer progression by promoting the stability and nuclear translocation of PKM2. Signal Transduct Target Ther 2022; 7:275. [PMID: 35973989 PMCID: PMC9381590 DOI: 10.1038/s41392-022-01096-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/07/2022] [Accepted: 06/28/2022] [Indexed: 12/04/2022] Open
Abstract
Metastasis is a major cause of colorectal cancer (CRC) mortality, but its molecular mechanisms are still not fully understood. Here, we show that upregulated DDX39B correlates with liver metastases and aggressive phenotypes in CRC. DDX39B is an independent prognostic factor associated with poor clinical outcome in CRC patients. We demonstrate that Sp1 potently activates DDX39B transcription by directly binding to the GC box of the DDX39B promoter in CRC cells. DDX39B overexpression augments the proliferation, migration, and invasion of CRC cells, while the opposite results are obtained in DDX39B-deficient CRC cells. Mechanistically, DDX39B interacts directly with and stabilizes PKM2 by competitively suppressing STUB1-mediated PKM2 ubiquitination and degradation. Importantly, DDX39B recruits importin α5 to accelerate the nuclear translocation of PKM2 independent of ERK1/2-mediated phosphorylation of PKM2, leading to the transactivation of oncogenes and glycolysis-related genes. Consequently, DDX39B enhances glucose uptake and lactate production to activate Warburg effect in CRC. We identify that Arg319 of DDX39B is required for PKM2 binding as well as PKM2 nuclear accumulation and for DDX39B to promote CRC growth and metastasis. In addition, blocking PKM2 nuclear translocation or treatment with glycolytic inhibitor 2-deoxy-D-glucose efficiently abolishes DDX39B-triggered malignant development in CRC. Taken together, our findings uncover a key role for DDX39B in modulating glycolytic reprogramming and aggressive progression, and implicate DDX39B as a potential therapeutic target in CRC.
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35
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Jia R, Lin J, You J, Li S, Shan G, Huang C. The DEAD-box helicase Hlc regulates basal transcription and chromatin opening of stress-responsive genes. Nucleic Acids Res 2022; 50:9175-9189. [PMID: 35950495 PMCID: PMC9458421 DOI: 10.1093/nar/gkac684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/17/2022] [Accepted: 07/28/2022] [Indexed: 12/24/2022] Open
Abstract
Stress-responsive genes are lowly transcribed under normal conditions and robustly induced in response to stress. The significant difference between basal and induced transcription indicates that the general transcriptional machinery requires a mechanism to distinguish each transcription state. However, what factors specifically function in basal transcription remains poorly understood. Using a classic model stress-responsive gene (Drosophila MtnA), we found that knockdown of the DEAD-box helicase Hlc resulted in a significant transcription attenuation of MtnA under normal, but not stressed, conditions. Mechanistically, Hlc directly binds to the MtnA locus to maintain the accessibility of chromatin near the transcriptional start site, which allows the recruitment of RNA polymerase II and subsequent MtnA transcription. Using RNA-seq, we then identified plenty of additional stress-responsive genes whose basal transcription was reduced upon knockdown of Hlc. Taken together, these data suggest that Hlc-mediated basal transcription regulation is an essential and widespread mechanism for precise control of stress-responsive genes.
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Affiliation(s)
| | | | | | - Shi Li
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ge Shan
- School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chuan Huang
- To whom correspondence should be addressed. Tel: +86 19956025374;
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36
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Misic J, Milenkovic D, Al-Behadili A, Xie X, Jiang M, Jiang S, Filograna R, Koolmeister C, Siira S, Jenninger L, Filipovska A, Clausen A, Caporali L, Valentino M, La Morgia C, Carelli V, Nicholls T, Wredenberg A, Falkenberg M, Larsson NG. Mammalian RNase H1 directs RNA primer formation for mtDNA replication initiation and is also necessary for mtDNA replication completion. Nucleic Acids Res 2022; 50:8749-8766. [PMID: 35947649 PMCID: PMC9410905 DOI: 10.1093/nar/gkac661] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/08/2022] [Accepted: 08/04/2022] [Indexed: 12/24/2022] Open
Abstract
The in vivo role for RNase H1 in mammalian mitochondria has been much debated. Loss of RNase H1 is embryonic lethal and to further study its role in mtDNA expression we characterized a conditional knockout of Rnaseh1 in mouse heart. We report that RNase H1 is essential for processing of RNA primers to allow site-specific initiation of mtDNA replication. Without RNase H1, the RNA:DNA hybrids at the replication origins are not processed and mtDNA replication is initiated at non-canonical sites and becomes impaired. Importantly, RNase H1 is also needed for replication completion and in its absence linear deleted mtDNA molecules extending between the two origins of mtDNA replication are formed accompanied by mtDNA depletion. The steady-state levels of mitochondrial transcripts follow the levels of mtDNA, and RNA processing is not altered in the absence of RNase H1. Finally, we report the first patient with a homozygous pathogenic mutation in the hybrid-binding domain of RNase H1 causing impaired mtDNA replication. In contrast to catalytically inactive variants of RNase H1, this mutant version has enhanced enzyme activity but shows impaired primer formation. This finding shows that the RNase H1 activity must be strictly controlled to allow proper regulation of mtDNA replication.
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Affiliation(s)
- Jelena Misic
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | | | - Ali Al-Behadili
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Min Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Shan Jiang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Roberta Filograna
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, WA 6009, Australia
| | - Louise Jenninger
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, WA 6009, Australia,Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Anders R Clausen
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Maria Lucia Valentino
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy,Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Chiara La Morgia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy,Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
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37
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Petermann E, Lan L, Zou L. Sources, resolution and physiological relevance of R-loops and RNA-DNA hybrids. Nat Rev Mol Cell Biol 2022; 23:521-540. [PMID: 35459910 DOI: 10.1038/s41580-022-00474-x] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
RNA-DNA hybrids are generated during transcription, DNA replication and DNA repair and are crucial intermediates in these processes. When RNA-DNA hybrids are stably formed in double-stranded DNA, they displace one of the DNA strands and give rise to a three-stranded structure called an R-loop. R-loops are widespread in the genome and are enriched at active genes. R-loops have important roles in regulating gene expression and chromatin structure, but they also pose a threat to genomic stability, especially during DNA replication. To keep the genome stable, cells have evolved a slew of mechanisms to prevent aberrant R-loop accumulation. Although R-loops can cause DNA damage, they are also induced by DNA damage and act as key intermediates in DNA repair such as in transcription-coupled repair and RNA-templated DNA break repair. When the regulation of R-loops goes awry, pathological R-loops accumulate, which contributes to diseases such as neurodegeneration and cancer. In this Review, we discuss the current understanding of the sources of R-loops and RNA-DNA hybrids, mechanisms that suppress and resolve these structures, the impact of these structures on DNA repair and genome stability, and opportunities to therapeutically target pathological R-loops.
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Affiliation(s)
- Eva Petermann
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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38
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Cañas JC, García-Rubio ML, García A, Antequera F, Gómez-González B, Aguilera A. A role for the Saccharomyces cerevisiae Rtt109 histone acetyltransferase in R-loop homeostasis and associated genome instability. Genetics 2022; 222:6648348. [PMID: 35866610 PMCID: PMC9434296 DOI: 10.1093/genetics/iyac108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 07/08/2022] [Indexed: 12/02/2022] Open
Abstract
The stability of the genome is occasionally challenged by the formation of DNA–RNA hybrids and R-loops, which can be influenced by the chromatin context. This is mainly due to the fact that DNA–RNA hybrids hamper the progression of replication forks, leading to fork stalling and, ultimately, DNA breaks. Through a specific screening of chromatin modifiers performed in the yeast Saccharomyces cerevisiae, we have found that the Rtt109 histone acetyltransferase is involved in several steps of R-loop-metabolism and their associated genetic instability. On the one hand, Rtt109 prevents DNA–RNA hybridization by the acetylation of histone H3 lysines 14 and 23 and, on the other hand, it is involved in the repair of replication-born DNA breaks, such as those that can be caused by R-loops, by acetylating lysines 14 and 56. In addition, Rtt109 loss renders cells highly sensitive to replication stress in combination with R-loop-accumulating THO-complex mutants. Our data evidence that the chromatin context simultaneously influences the occurrence of DNA–RNA hybrid-associated DNA damage and its repair, adding complexity to the source of R-loop-associated genetic instability.
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Affiliation(s)
- Juan Carlos Cañas
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC, 41092 Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - María Luisa García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC, 41092 Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Alicia García
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, 37007, Salamanca, Spain
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica (IBFG), CSIC-Universidad de Salamanca, 37007, Salamanca, Spain
| | - Belén Gómez-González
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC, 41092 Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC, 41092 Seville, Spain.,Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
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39
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Lin WL, Chen JK, Wen X, He W, Zarceno GA, Chen Y, Chen S, Paull TT, Liu HW. DDX18 prevents R-loop-induced DNA damage and genome instability via PARP-1. Cell Rep 2022; 40:111089. [PMID: 35858569 DOI: 10.1016/j.celrep.2022.111089] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/02/2022] [Accepted: 06/22/2022] [Indexed: 01/05/2023] Open
Abstract
R loops occur frequently in genomes and contribute to fundamental biological processes at multiple levels. Consequently, understanding the molecular and cellular biology of R loops has become an emerging area of research. Here, it is shown that poly(ADP-ribose) polymerase-1 (PARP-1) can mediate the association of DDX18, a putative RNA helicase, with R loops thereby modulating R-loop homeostasis in endogenous R-loop-prone and DNA lesion regions. DDX18 depletion results in aberrant endogenous R-loop accumulation, which leads to DNA-replication defects. In addition, DDX18 depletion renders cells more sensitive to DNA-damaging agents and reduces RPA32 and RAD51 foci formation in response to irradiation. Notably, DDX18 depletion leads to γH2AX accumulation and genome instability, and RNase H1 overexpression rescues all the DNA-repair defects caused by DDX18 depletion. Taken together, these studies uncover a function of DDX18 in R-loop-mediated events and suggest a role for PARP-1 in mediating the binding of specific DDX-family proteins with R loops in cells.
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Affiliation(s)
- Wen-Ling Lin
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Jung-Kuei Chen
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Xuemei Wen
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Wei He
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA; School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Geovanny A Zarceno
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Yutian Chen
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Shi Chen
- School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; Shenzhen Institute of Translational Medicine, Health Science Center, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518055, China
| | - Tanya T Paull
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Hung-Wen Liu
- Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA; Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA; Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
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40
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Kamp JA, Lemmens BBLG, Romeijn RJ, González-Prieto R, Olsen J, Vertegaal ACO, van Schendel R, Tijsterman M. THO complex deficiency impairs DNA double-strand break repair via the RNA surveillance kinase SMG-1. Nucleic Acids Res 2022; 50:6235-6250. [PMID: 35670662 PMCID: PMC9226523 DOI: 10.1093/nar/gkac472] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 05/11/2022] [Accepted: 06/02/2022] [Indexed: 12/25/2022] Open
Abstract
The integrity and proper expression of genomes are safeguarded by DNA and RNA surveillance pathways. While many RNA surveillance factors have additional functions in the nucleus, little is known about the incidence and physiological impact of converging RNA and DNA signals. Here, using genetic screens and genome-wide analyses, we identified unforeseen SMG-1-dependent crosstalk between RNA surveillance and DNA repair in living animals. Defects in RNA processing, due to viable THO complex or PNN-1 mutations, induce a shift in DNA repair in dividing and non-dividing tissues. Loss of SMG-1, an ATM/ATR-like kinase central to RNA surveillance by nonsense-mediated decay (NMD), restores DNA repair and radio-resistance in THO-deficient animals. Mechanistically, we find SMG-1 and its downstream target SMG-2/UPF1, but not NMD per se, to suppress DNA repair by non-homologous end-joining in favour of single strand annealing. We postulate that moonlighting proteins create short-circuits in vivo, allowing aberrant RNA to redirect DNA repair.
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Affiliation(s)
| | | | - Ron J Romeijn
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Román González-Prieto
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Alfred C O Vertegaal
- Department of Cell & Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Robin van Schendel
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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41
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Cristini A, Tellier M, Constantinescu F, Accalai C, Albulescu LO, Heiringhoff R, Bery N, Sordet O, Murphy S, Gromak N. RNase H2, mutated in Aicardi-Goutières syndrome, resolves co-transcriptional R-loops to prevent DNA breaks and inflammation. Nat Commun 2022; 13:2961. [PMID: 35618715 PMCID: PMC9135716 DOI: 10.1038/s41467-022-30604-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 05/10/2022] [Indexed: 11/29/2022] Open
Abstract
RNase H2 is a specialized enzyme that degrades RNA in RNA/DNA hybrids and deficiency of this enzyme causes a severe neuroinflammatory disease, Aicardi Goutières syndrome (AGS). However, the molecular mechanism underlying AGS is still unclear. Here, we show that RNase H2 is associated with a subset of genes, in a transcription-dependent manner where it interacts with RNA Polymerase II. RNase H2 depletion impairs transcription leading to accumulation of R-loops, structures that comprise RNA/DNA hybrids and a displaced DNA strand, mainly associated with short and intronless genes. Importantly, accumulated R-loops are processed by XPG and XPF endonucleases which leads to DNA damage and activation of the immune response, features associated with AGS. Consequently, we uncover a key role for RNase H2 in the transcription of human genes by maintaining R-loop homeostasis. Our results provide insight into the mechanistic contribution of R-loops to AGS pathogenesis.
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Affiliation(s)
- Agnese Cristini
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Michael Tellier
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Flavia Constantinescu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Clelia Accalai
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Laura Oana Albulescu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Robin Heiringhoff
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Nicolas Bery
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Olivier Sordet
- Cancer Research Center of Toulouse, INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037, Toulouse, France
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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42
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Georgakopoulos-Soares I, Parada GE, Hemberg M. Secondary structures in RNA synthesis, splicing and translation. Comput Struct Biotechnol J 2022; 20:2871-2884. [PMID: 35765654 PMCID: PMC9198270 DOI: 10.1016/j.csbj.2022.05.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/19/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022] Open
Abstract
Even though the functional role of mRNA molecules is primarily decided by the nucleotide sequence, several properties are determined by secondary structure conformations. Examples of secondary structures include long range interactions, hairpins, R-loops and G-quadruplexes and they are formed through interactions of non-adjacent nucleotides. Here, we discuss advances in our understanding of how secondary structures can impact RNA synthesis, splicing, translation and mRNA half-life. During RNA synthesis, secondary structures determine RNA polymerase II (RNAPII) speed, thereby influencing splicing. Splicing is also determined by RNA binding proteins and their binding rates are modulated by secondary structures. For the initiation of translation, secondary structures can control the choice of translation start site. Here, we highlight the mechanisms by which secondary structures modulate these processes, discuss advances in technologies to detect and study them systematically, and consider the roles of RNA secondary structures in disease.
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43
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Brickner JR, Garzon JL, Cimprich KA. Walking a tightrope: The complex balancing act of R-loops in genome stability. Mol Cell 2022; 82:2267-2297. [PMID: 35508167 DOI: 10.1016/j.molcel.2022.04.014] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 12/14/2022]
Abstract
Although transcription is an essential cellular process, it is paradoxically also a well-recognized cause of genomic instability. R-loops, non-B DNA structures formed when nascent RNA hybridizes to DNA to displace the non-template strand as single-stranded DNA (ssDNA), are partially responsible for this instability. Yet, recent work has begun to elucidate regulatory roles for R-loops in maintaining the genome. In this review, we discuss the cellular contexts in which R-loops contribute to genomic instability, particularly during DNA replication and double-strand break (DSB) repair. We also summarize the evidence that R-loops participate as an intermediate during repair and may influence pathway choice to preserve genomic integrity. Finally, we discuss the immunogenic potential of R-loops and highlight their links to disease should they become pathogenic.
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Affiliation(s)
- Joshua R Brickner
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jada L Garzon
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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44
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Weis K, Hondele M. The Role of DEAD-Box ATPases in Gene Expression and the Regulation of RNA-Protein Condensates. Annu Rev Biochem 2022; 91:197-219. [PMID: 35303788 DOI: 10.1146/annurev-biochem-032620-105429] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DEAD-box ATPases constitute a very large protein family present in all cells, often in great abundance. From bacteria to humans, they play critical roles in many aspects of RNA metabolism, and due to their widespread importance in RNA biology, they have been characterized in great detail at both the structural and biochemical levels. DEAD-box proteins function as RNA-dependent ATPases that can unwind short duplexes of RNA, remodel ribonucleoprotein (RNP) complexes, or act as clamps to promote RNP assembly. Yet, it often remains enigmatic how individual DEAD-box proteins mechanistically contribute to specific RNA-processing steps. Here, we review the role of DEAD-box ATPases in the regulation of gene expression and propose that one common function of these enzymes is in the regulation of liquid-liquid phase separation of RNP condensates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Karsten Weis
- Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland;
| | - Maria Hondele
- Biozentrum, University of Basel, Basel, Switzerland;
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45
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Suthapot P, Xiao T, Felsenfeld G, Hongeng S, Wongtrakoongate P. The RNA helicases DDX5 and DDX17 facilitate neural differentiation of human pluripotent stem cells NTERA2. Life Sci 2022; 291:120298. [PMID: 35007564 DOI: 10.1016/j.lfs.2021.120298] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 12/31/2022]
Abstract
AIMS Understanding human neurogenesis is critical toward regenerative medicine for neurodegeneration. However, little is known how neural differentiation is regulated by DEAD box-containing RNA helicases, which comprise a diverse class of RNA remodeling enzymes. MATERIALS AND METHODS ChIP-seq was utilized to identify binding sites of DDX5 and DDX17 in both human pluripotent stem cell (hPSC) line NTERA2 and their retinoic acid-induced neural derivatives. RNA-seq was used to elucidate genes differentially expressed upon depletion of DDX5 and DDX17. Neurosphere assay, flow cytometry, and immunofluorescence staining were performed to test the effect of depletion of the two RNA helicases in neural differentiation. KEY FINDINGS We show here that expression of DDX5 and DDX17 is abundant throughout neural differentiation of NTERA2, and is mostly localized within the nucleus. The two RNA helicases occupy chromatin genome-wide at regions associated with neurogenesis-related genes in both hPSCs and their neural derivatives. Further, both DDX5 and DDX17 are mutually required for controlling transcriptional expression of these genes, but are not important for maintenance of stem cell state of hPSCs. In contrast, they facilitate early neural differentiation of hPSCs, generation of neurospheres from the stem cells, and transcriptional expression of key neurogenic transcription factors such as SOX1 and PAX6 during neural differentiation. Importantly, DDX5 and DDX17 are critical for differentiation of hPSCs toward NESTIN- and TUBB3-positive cells, which represent neural progenitors and mature neurons, respectively. SIGNIFICANCE Collectively, our findings suggest the role of DDX5 and DDX17 in transcriptional regulation of genes involved in neurogenesis, and hence in neural differentiation of hPSCs.
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Affiliation(s)
- Praewa Suthapot
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Tiaojiang Xiao
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0540, MD, USA
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda 20892-0540, MD, USA
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Patompon Wongtrakoongate
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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46
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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: 7] [Impact Index Per Article: 3.5] [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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47
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Proximity labeling identifies a repertoire of site-specific R-loop modulators. Nat Commun 2022; 13:53. [PMID: 35013239 PMCID: PMC8748879 DOI: 10.1038/s41467-021-27722-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/06/2021] [Indexed: 11/11/2022] Open
Abstract
R-loops are three-stranded nucleic acid structures that accumulate on chromatin in neurological diseases and cancers and contribute to genome instability. Using a proximity-dependent labeling system, we identified distinct classes of proteins that regulate R-loops in vivo through different mechanisms. We show that ATRX suppresses R-loops by interacting with RNAs and preventing R-loop formation. Our proteomics screen also discovered an unexpected enrichment for proteins containing zinc fingers and homeodomains. One of the most consistently enriched proteins was activity-dependent neuroprotective protein (ADNP), which is frequently mutated in ASD and causal in ADNP syndrome. We find that ADNP resolves R-loops in vitro and that it is necessary to suppress R-loops in vivo at its genomic targets. Furthermore, deletion of the ADNP homeodomain severely diminishes R-loop resolution activity in vitro, results in R-loop accumulation at ADNP targets, and compromises neuronal differentiation. Notably, patient-derived human induced pluripotent stem cells that contain an ADNP syndrome-causing mutation exhibit R-loop and CTCF accumulation at ADNP targets. Our findings point to a specific role for ADNP-mediated R-loop resolution in physiological and pathological neuronal function and, more broadly, to a role for zinc finger and homeodomain proteins in R-loop regulation, with important implications for developmental disorders and cancers. R-loops are three-stranded nucleic acid structures that contribute to genome instability and accumulate in neurological diseases. Here the authors identify R-loop proximal factors, which are enriched for zinc finger and homeodomain proteins, including activity-dependent neuroprotective protein (ADNP). ADNP plays a role in R-loop resolution and loss-of-function leads to R-loop accumulation.
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48
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Beghè C, Gromak N. R-Loop Immunoprecipitation: A Method to Detect R-Loop Interacting Factors. Methods Mol Biol 2022; 2528:215-237. [PMID: 35704194 DOI: 10.1007/978-1-0716-2477-7_14] [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] [Indexed: 06/15/2023]
Abstract
R-loops are non-B-DNA structures consisting of an RNA/DNA hybrid and a displaced single-stranded DNA. They arise during transcription and play important biological roles. However, perturbation of R-loop levels represents a source of DNA damage and genome instability resulting in human diseases, including cancer and neurodegeneration. In this chapter, we describe a protocol which allows detection of R-loop interactors using affinity purification with S9.6 antibody, specific for RNA/DNA hybrids, followed by Western blotting or mass spectrometry. Multiple specificity controls including addition of synthetic competitors and RNase H treatment are described to verify the specificity of identified R-loop-binding factors. The identification of new R-loop interacting factors and the characterization of their involvement in R-loop biology provides a powerful resource to study the role of these important structures in health and disease.
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Affiliation(s)
- Chiara Beghè
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Natalia Gromak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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49
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Wu W, He JN, Lan M, Zhang P, Chu WK. Transcription-Replication Collisions and Chromosome Fragility. Front Genet 2021; 12:804547. [PMID: 34956339 PMCID: PMC8703014 DOI: 10.3389/fgene.2021.804547] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Accurate replication of the entire genome is critical for cell division and propagation. Certain regions in the genome, such as fragile sites (common fragile sites, rare fragile sites, early replicating fragile sites), rDNA and telomeres, are intrinsically difficult to replicate, especially in the presence of replication stress caused by, for example, oncogene activation during tumor development. Therefore, these regions are particularly prone to deletions and chromosome rearrangements during tumorigenesis, rendering chromosome fragility. Although, the mechanism underlying their “difficult-to-replicate” nature and genomic instability is still not fully understood, accumulating evidence suggests transcription might be a major source of endogenous replication stress (RS) leading to chromosome fragility. Here, we provide an updated overview of how transcription affects chromosome fragility. Furthermore, we will use the well characterized common fragile sites (CFSs) as a model to discuss pathways involved in offsetting transcription-induced RS at these loci with a focus on the recently discovered atypical DNA synthesis repair pathway Mitotic DNA Synthesis (MiDAS).
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Affiliation(s)
- Wei Wu
- Zhejiang Provincial Key Laboratory of Pancreatic Diseases, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Jing Na He
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong, China
| | - Mengjiao Lan
- Zhejiang Provincial Key Laboratory of Pancreatic Diseases, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Pumin Zhang
- Zhejiang Provincial Key Laboratory of Pancreatic Diseases, The First Affiliated Hospital of Zhejiang University, Hangzhou, China
| | - Wai Kit Chu
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong, China
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R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability. Nat Commun 2021; 12:7314. [PMID: 34916496 PMCID: PMC8677849 DOI: 10.1038/s41467-021-27530-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription poses a threat to genomic stability through the formation of R-loops that can obstruct progression of replication forks. R-loops are three-stranded nucleic acid structures formed by an RNA-DNA hybrid with a displaced non-template DNA strand. We developed RNA-DNA Proximity Proteomics to map the R-loop proximal proteome of human cells using quantitative mass spectrometry. We implicate different cellular proteins in R-loop regulation and identify a role of the tumor suppressor DDX41 in opposing R-loop and double strand DNA break accumulation in promoters. DDX41 is enriched in promoter regions in vivo, and can unwind RNA-DNA hybrids in vitro. R-loop accumulation upon loss of DDX41 is accompanied with replication stress, an increase in the formation of double strand DNA breaks and transcriptome changes associated with the inflammatory response. Germline loss-of-function mutations in DDX41 lead to predisposition to acute myeloid leukemia in adulthood. We propose that R-loop accumulation and genomic instability-associated inflammatory response may contribute to the development of familial AML with mutated DDX41.
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