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Leung ML, Woodhull W, Uggenti C, Schord S, Mato RP, Rodriguez DP, Ream M, Crow YJ, Mori M. Molecular characterization of an intronic RNASEH2B variant in a patient with Aicardi-Goutières syndrome. Eur J Med Genet 2023; 66:104731. [PMID: 36775013 DOI: 10.1016/j.ejmg.2023.104731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/12/2023] [Accepted: 02/10/2023] [Indexed: 02/12/2023]
Abstract
Aicardi-Goutières syndrome (AGS) is a progressive multisystem disorder including encephalopathy with significant impacts on intellectual and physical abilities. An early diagnosis is becoming ever more crucial, as targeted therapies are emerging. A deep understanding of the molecular heterogeneity of AGS can help guide the early diagnosis and clinical management of patients, and inform recurrence risks. Here, we detail the diagnostic odyssey of a patient with an early presentation of AGS. Exome and genome sequencing detected an intronic RNASEH2B variant missed in a conventional leukodystrophy NGS gene panel. RNA studies demonstrated that a c.322-17 A > G variant affected splicing and caused 16-nucleotide intronic retention in the RNASEH2B transcript, introducing an out-of-frame early termination codon. RNASEH2B expression in the patient's blood was reduced when compared to controls. Our study highlights the pathogenicity of this intronic variant and the importance of its inclusion in variant assessment.
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Affiliation(s)
- Marco L Leung
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Departments of Pathology, Departments of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
| | - Whitney Woodhull
- Division of Pediatric Neurology, Renown Children's Hospital, Reno, NV, USA; University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Carolina Uggenti
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Shauna Schord
- Division of Hospital Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Raul Perez Mato
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Diana P Rodriguez
- Department of Radiology, Nationwide Children's Hospital, Columbus, OH, USA; The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Margie Ream
- The Ohio State University College of Medicine, Columbus, OH, 43210, USA; Division of Pediatric Neurology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Yanick J Crow
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK; Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine, Université de Paris, Paris, France
| | - Mari Mori
- The Ohio State University College of Medicine, Columbus, OH, 43210, USA; Division of Genetic and Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
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2
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Li J, Khan S, Gu J, Filipe CDM, Didar TF, Li Y. A Simple Colorimetric Au-on-Au Tip Sensor with a New Functional Nucleic Acid Probe for Food-borne Pathogen Salmonella typhimurium. Angew Chem Int Ed Engl 2023; 62:e202300828. [PMID: 36932982 DOI: 10.1002/anie.202300828] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
An Au-on-Au tip sensor is developed for the detection of Salmonella typhimurium (Salmonella), using a new synthetic nucleic acid probe (NAP) as a linker for the immobilization of a DNA-conjugated Au nanoparticle (AuNP) onto a DNA-attached thin Au layer inside a pipette tip. In the presence of Salmonella, RNase H2 from Salmonella (STH2) cleaves the NAP and the freed DNA-conjugated AuNP can be visually detected by a paper strip. This portable biosensor does not require any electronic, electrochemical or optical equipment. It delivers a detection limit of 3.2 × 103 CFU/mL for Salmonella in 1 h without cell-culturing or signal amplification and does not show cross-reactivity with several control bacteria. Further, the sensor reliably detects Salmonella spiked in food samples, such as ground beef and chicken, milk, and eggs. The sensor can be reused and is stable at ambient temperature, showing its potential as a point-of-need device for the prevention of food poisoning by Salmonella.
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Affiliation(s)
- Jiuxing Li
- McMaster University, Biochemistry and Biomedical Sciences, CANADA
| | - Shadman Khan
- McMaster University, School of Biomedical Engineering, CANADA
| | - Jimmy Gu
- McMaster University, Biochemistry and Biomedical Sciences, CANADA
| | | | - Tohid F Didar
- McMaster University, School of Biomedical Engineering, CANADA
| | - Yingfu Li
- McMaster University, Biochemistry and Biomedical Sciences, 1280 Main Street West, L8S4K1, Hamilton, CANADA
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3
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Schulz MS, Sartorius von Bach CB, Marinkovic E, Günther C, Behrendt R, Roers A. Development of an RNase H2 Activity Assay for Clinical Screening. J Clin Med 2023; 12. [PMID: 36836134 DOI: 10.3390/jcm12041598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
As the key enzyme mediating ribonucleotide excision repair, RNase H2 is essential for the removal of single ribonucleotides from DNA in order to prevent genome damage. Loss of RNase H2 activity directly contributes to the pathogenesis of autoinflammatory and autoimmune diseases and might further play a role in ageing and neurodegeneration. Moreover, RNase H2 activity is a potential diagnostic and prognostic marker in several types of cancer. Until today, no method for quantification of RNase H2 activity has been validated for the clinical setting. Herein, validation and benchmarks of a FRET-based whole-cell lysate RNase H2 activity assay are presented, including standard conditions and procedures to calculate standardized RNase H2 activity. Spanning a wide working range, the assay is applicable to various human cell or tissue samples with overall methodological assay variability from 8.6% to 16%. Using our assay, we found RNase H2 activity was reduced in lymphocytes of two patients with systemic lupus erythematosus and one with systemic sclerosis carrying heterozygous mutations in one of the RNASEH2 genes. Implementation of larger control groups will help to assess the diagnostic and prognostic value of clinical screening for RNase H2 activity in the future.
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Wang S, Shen H, Lin Q, Huang J, Zhang C, Liu Z, Sun M, Zhang J, Liao M, Li Y, Zhang J. Development of a Cleaved Probe-Based Loop-Mediated Isothermal Amplification Assay for Rapid Detection of African Swine Fever Virus. Front Cell Infect Microbiol 2022; 12:884430. [PMID: 35719327 PMCID: PMC9204333 DOI: 10.3389/fcimb.2022.884430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/25/2022] [Indexed: 11/21/2022] Open
Abstract
African Swine Fever (ASF), caused by African swine fever virus (ASFV), is a highly contagious and lethal viral disease of pigs. However, commercial vaccines are not yet available, and neither are drugs to prevent or control ASF. Therefore, rapid, accurate on-site diagnosis is urgently needed for detection during the early stages of ASFV infection. Herein, a cleaved probe-based loop-mediated isothermal amplification (CP-LAMP) detection method was established. Based on the original primer sets, we targeted the ASFV 9GL gene sequence to design a probe harboring a ribonucleotide insertion. Ribonuclease H2 (RNase H2) enzyme activity can only be activated when the probe is perfectly complementary, resulting in hydrolytic release of a quencher moiety, and consequent signal amplification. The method displayed robust sensitivity, with copy number detection as low as 13 copies/µL within 40 min at constant temperature (62°C). Visualization of the fluorescence product was employed using a self-designed 3D-printed visualization function cassette, and the CP-LAMP method achieved specific identification and visual detection of ASFV. Moreover, coupling the dual function cassette and smartphone quantitation makes the CP-LAMP assay first user-friendly, cost-effective, portable, rapid, and accurate point-of-care testing (POCT) platform for ASFV.
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Affiliation(s)
- Songqi Wang
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; The Research Center for African Swine Fever Prevention and Control; College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Haiyan Shen
- Maoming Branch Center of Guangdong Laboratory for LingNan Modern Agricultural Science and Technology; Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Foshan, China
| | - Qijie Lin
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; The Research Center for African Swine Fever Prevention and Control; College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jun Huang
- College of Life Science and Engineering, Foshan University, Guangzhou, China
| | - Chunhong Zhang
- Maoming Branch Center of Guangdong Laboratory for LingNan Modern Agricultural Science and Technology; Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Foshan, China
| | - Zhicheng Liu
- Maoming Branch Center of Guangdong Laboratory for LingNan Modern Agricultural Science and Technology; Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Foshan, China
| | - Minhua Sun
- Maoming Branch Center of Guangdong Laboratory for LingNan Modern Agricultural Science and Technology; Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Foshan, China
| | - Jianfeng Zhang
- Maoming Branch Center of Guangdong Laboratory for LingNan Modern Agricultural Science and Technology; Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Foshan, China
| | - Ming Liao
- Maoming Branch Center of Guangdong Laboratory for LingNan Modern Agricultural Science and Technology; Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Foshan, China
| | - Yugu Li
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; The Research Center for African Swine Fever Prevention and Control; College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jianmin Zhang
- Key Laboratory of Zoonoses Prevention and Control of Guangdong Province; The Research Center for African Swine Fever Prevention and Control; College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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Li J, Gu J, Zhang H, Liu R, Zhang W, Mohammed-Elsabagh M, Xia J, Morrison D, Zakaria S, Chang D, Arrabi A, Li Y. A Highly Specific DNA Aptamer for RNase H2 from Clostridium difficile. ACS Appl Mater Interfaces 2021; 13:9464-9471. [PMID: 33410654 DOI: 10.1021/acsami.0c20277] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Molecular recognition elements with high specificity are of great importance for the study of molecular interactions, accurate diagnostics, drug design, and personalized medicine. Herein, a highly specific DNA aptamer for RNase H2 from Clostridium difficile (C. difficile) was generated by SELEX and minimized to 40 nucleotides. The aptamer exhibits a dissociation constant (Kd) of 1.8 ± 0.5 nM and an inhibition constant (IC50) of 7.1 ± 0.6 nM for C. difficile RNase H2, both of which are 2 orders of magnitude better for the same enzyme from other control bacteria. The fluorescent version of the aptamer can distinguish C. difficile from several other control bacteria in a cell lysate assay. This work demonstrates that a ubiquitous protein like RNase H2 can still be used as the target for the development of highly specific aptamers and the combination of the protein and the aptamer can achieve the recognition specificity needed for a diagnostic test and drug development.
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Affiliation(s)
- Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jimmy Gu
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Hongfen Zhang
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
- School of Pharmaceutical Science, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Rudi Liu
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Wenqing Zhang
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Mostafa Mohammed-Elsabagh
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Jianrun Xia
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Devon Morrison
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Sandy Zakaria
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Dingran Chang
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Amjad Arrabi
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4K1, Canada
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Polaczek R, Schürmann P, Speith LM, Geffers R, Dürst M, Hillemanns P, Park-Simon TW, Liebrich C, Dörk T. Germline variation of Ribonuclease H2 genes in ovarian cancer patients. J Ovarian Res 2020; 13:146. [PMID: 33353557 PMCID: PMC7756920 DOI: 10.1186/s13048-020-00753-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/07/2020] [Indexed: 12/02/2022] Open
Abstract
Epithelial ovarian carcinoma (EOC) is a genetically heterogeneous disease that is partly driven by molecular defects in mismatch repair (MMR) or homology-directed DNA repair (HDR). Ribonuclease H2 serves to remove mis-incorporated ribonucleotides from DNA which alleviates HDR mechanisms and guides the MMR machinery. Although Ribonuclease H2 has been implicated in cancer, the role of germline variants for ovarian cancer is unknown. In the present case-control study, we sequenced the coding and flanking untranslated regions of the RNASEH2A, RNASEH2B and RNASEH2C genes, encoding all three subunits of Ribonuclease H2, in a total of 602 German patients with EOC and of 940 healthy females from the same population. We identified one patient with a truncating variant in RNASEH2B, p.C44X, resulting in a premature stop codon. This patient had high-grade serous EOC with an 8 years survival after platinum/taxane-based therapy. Subsequent analysis of TCGA data similarly showed a significantly longer progression-free survival in ovarian cancer patients with low RNASEH2B or RNASEH2C expression levels. In conclusion, loss-of-function variants in Ribonuclease H2 genes are not common predisposing factors in ovarian cancer but the possibility that they modulate therapeutic platinum response deserves further investigation.
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Affiliation(s)
- Rahel Polaczek
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Peter Schürmann
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Lisa-Marie Speith
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Robert Geffers
- Genome Analytics Unit, Helmholtz Institute for Infection Research, Braunschweig, Germany
| | - Matthias Dürst
- Department of Gynaecology and Obstetrics, University Clinics Jena, Jena, Germany
| | - Peter Hillemanns
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Tjoung-Won Park-Simon
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany
| | - Clemens Liebrich
- Department of Gynaecology and Obstetrics, Hospital Wolfsburg, Wolfsburg, Germany
| | - Thilo Dörk
- Department of Gynaecology and Obstetrics, Gynaecology Research Unit (OE 6411), Hannover Medical School, Carl-Neuberg-Str. 1, D-30625, Hannover, Germany.
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Kellner V, Luke B. Molecular and physiological consequences of faulty eukaryotic ribonucleotide excision repair. EMBO J 2020; 39:e102309. [PMID: 31833079 PMCID: PMC6996501 DOI: 10.15252/embj.2019102309] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 10/22/2019] [Accepted: 11/26/2019] [Indexed: 01/11/2023] Open
Abstract
The duplication of the eukaryotic genome is an intricate process that has to be tightly safe-guarded. One of the most frequently occurring errors during DNA synthesis is the mis-insertion of a ribonucleotide instead of a deoxyribonucleotide. Ribonucleotide excision repair (RER) is initiated by RNase H2 and results in error-free removal of such mis-incorporated ribonucleotides. If left unrepaired, DNA-embedded ribonucleotides result in a variety of alterations within chromosomal DNA, which ultimately lead to genome instability. Here, we review how genomic ribonucleotides lead to chromosomal aberrations and discuss how the tight regulation of RER timing may be important for preventing unwanted DNA damage. We describe the structural impact of unrepaired ribonucleotides on DNA and chromatin and comment on the potential consequences for cellular fitness. In the context of the molecular mechanisms associated with faulty RER, we have placed an emphasis on how and why increased levels of genomic ribonucleotides are associated with severe autoimmune syndromes, neuropathology, and cancer. In addition, we discuss therapeutic directions that could be followed for pathologies associated with defective removal of ribonucleotides from double-stranded DNA.
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Affiliation(s)
- Vanessa Kellner
- Institute of Molecular Biology (IMB)MainzGermany
- Present address:
Department of BiologyNew York UniversityNew YorkNYUSA
| | - Brian Luke
- Institute of Molecular Biology (IMB)MainzGermany
- Institute of Developmental Biology and Neurobiology (IDN)Johannes Gutenberg UniversitätMainzGermany
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8
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Uehara R, Cerritelli SM, Hasin N, Sakhuja K, London M, Iranzo J, Chon H, Grinberg A, Crouch RJ. Two RNase H2 Mutants with Differential rNMP Processing Activity Reveal a Threshold of Ribonucleotide Tolerance for Embryonic Development. Cell Rep 2019; 25:1135-1145.e5. [PMID: 30380406 PMCID: PMC6309994 DOI: 10.1016/j.celrep.2018.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/18/2018] [Accepted: 10/03/2018] [Indexed: 11/30/2022] Open
Abstract
RNase H2 has two distinct functions: initiation of the ribonucleotide excision repair (RER) pathway by cleaving ribonucleotides (rNMPs) incorporated during DNA replication and processing the RNA portion of an R-loop formed during transcription. An RNase H2 mutant lacking RER activity but supporting R-loop removal revealed that rNMPs in DNA initiate p53-dependent DNA damage response and early embryonic arrest in mouse. However, an RNase H2 AGS-related mutant with residual RER activity develops to birth. Estimations of the number of rNMPs in DNA in these two mutants define a ribonucleotide threshold above which p53 induces apoptosis. Below the threshold, rNMPs in DNA trigger an innate immune response. Compound heterozygous cells, containing both defective enzymes, retain rNMPs above the threshold, indicative of competition for RER substrates between active and inactive enzymes, suggesting that patients with compound heterozygous mutations in RNASEH2 genes may not reflect the properties of recombinantly expressed proteins. Uehara et al. use RNase H2 mice with differing activity levels for removal of rNMPs embedded in DNA. Moderate levels of rNMPs lead to perinatal lethality activating the cGAS-Sting DNA sensing innate immune response. Exceeding a threshold, high abundance of rNMPs activates p53-dependent DNA damage, causing early embryonic lethality.
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Affiliation(s)
- Ryo Uehara
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Susana M Cerritelli
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Naushaba Hasin
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Kiran Sakhuja
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Mariya London
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Jaime Iranzo
- NCBI, National Library of Medicine, Bethesda, MD, USA
| | - Hyongi Chon
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Alexander Grinberg
- Mouse Core, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Robert J Crouch
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
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Abstract
RNases H are a family of endonucleases that hydrolyze RNA residues in various nucleic acids. These enzymes are present in all branches of life, and their counterpart domains are also found in reverse transcriptases (RTs) from retroviruses and retroelements. RNases H are divided into two main classes (RNases H1 and H2 or type 1 and type 2 enzymes) with common structural features of the catalytic domain but different range of substrates for enzymatic cleavage. Additionally, a third class is found in some Archaea and bacteria. Besides distinct cellular functions specific for each type of RNases H, this family of proteins is generally involved in the maintenance of genome stability with overlapping and cooperative role in removal of R-loops thus preventing their accumulation. Extensive biochemical and structural studies of RNases H provided not only a comprehensive and complete picture of their mechanism but also revealed key basic principles of nucleic acid recognition and processing. RNase H1 is present in prokaryotes and eukaryotes and cleaves RNA in RNA/DNA hybrids. Its main function is hybrid removal, notably in the context of R-loops. RNase H2, which is also present in all branches of life, can play a similar role but it also has a specialized function in the cleavage of single ribonucleotides embedded in the DNA. RNase H3 is present in Archaea and bacteria and is closely related to RNase H2 in sequence and structure but has RNase H1-like biochemical properties. This review summarizes the mechanisms of substrate recognition and enzymatic cleavage by different classes of RNases H with particular insights into structural features of nucleic acid binding, specificity towards RNA and/or DNA strands and catalysis.
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Affiliation(s)
- Malwina Hyjek
- ProBiostructures, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
| | - Małgorzata Figiel
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
| | - Marcin Nowotny
- ProBiostructures, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland; Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, Warsaw, 02-109, Poland.
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10
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Du WF, Ge JH, Li JJ, Tang LJ, Yu RQ, Jiang JH. Single-step, high-specificity detection of single nucleotide mutation by primer-activatable loop-mediated isothermal amplification (PA-LAMP). Anal Chim Acta 2018; 1050:132-138. [PMID: 30661580 DOI: 10.1016/j.aca.2018.10.068] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 01/08/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a useful platform for nucleic acids detection in point-of-care (POC) situations, and development of single-step, close-tube LAMP reactions for specific detection of single nucleotide mutations (SNMs) remains a challenge. We develop a novel primer-activatable LAMP (PA-LAMP) strategy that enables highly specific and sensitive SNM detection using single-step, close-tube reactions. This strategy designs a terminal-blocked inner primer with a ribonucleotide insertion, which is cleaved and activated specifically to perfectly matched targets by ribonuclease (RNase) H2, to realize efficient amplification of mutant genes. It has shown dynamic responses of mutant target in a linear range from 220 aM to 22 pM with a lowest detectable concentration of 22 aM. It also demonstrates very high specificity in identifying the mutant in a large excess of the wild-type with a discrimination ratio as high as ∼10,000. It has been successfully applied to mutation detection of genomic DNA in tumor cells. The PA-LAMP strategy provides a useful, portable and affordable POC platform for highly sensitive and specific detection of genetic mutations in clinical applications.
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Affiliation(s)
- Wen-Fang Du
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Jian-Hui Ge
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Jun-Jie Li
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Li-Juan Tang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China.
| | - Ru-Qin Yu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Jian-Hui Jiang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China.
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11
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Benitez-Guijarro M, Lopez-Ruiz C, Tarnauskaitė Ž, Murina O, Mian Mohammad M, Williams TC, Fluteau A, Sanchez L, Vilar-Astasio R, Garcia-Canadas M, Cano D, Kempen MJH, Sanchez-Pozo A, Heras SR, Jackson AP, Reijns MA, Garcia-Perez JL. RNase H2, mutated in Aicardi-Goutières syndrome, promotes LINE-1 retrotransposition. EMBO J 2018; 37:e98506. [PMID: 29959219 PMCID: PMC6068448 DOI: 10.15252/embj.201798506] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 12/03/2022] Open
Abstract
Long INterspersed Element class 1 (LINE-1) elements are a type of abundant retrotransposons active in mammalian genomes. An average human genome contains ~100 retrotransposition-competent LINE-1s, whose activity is influenced by the combined action of cellular repressors and activators. TREX1, SAMHD1 and ADAR1 are known LINE-1 repressors and when mutated cause the autoinflammatory disorder Aicardi-Goutières syndrome (AGS). Mutations in RNase H2 are the most common cause of AGS, and its activity was proposed to similarly control LINE-1 retrotransposition. It has therefore been suggested that increased LINE-1 activity may be the cause of aberrant innate immune activation in AGS Here, we establish that, contrary to expectations, RNase H2 is required for efficient LINE-1 retrotransposition. As RNase H1 overexpression partially rescues the defect in RNase H2 null cells, we propose a model in which RNase H2 degrades the LINE-1 RNA after reverse transcription, allowing retrotransposition to be completed. This also explains how LINE-1 elements can retrotranspose efficiently without their own RNase H activity. Our findings appear to be at odds with LINE-1-derived nucleic acids driving autoinflammation in AGS.
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Affiliation(s)
- Maria Benitez-Guijarro
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Cesar Lopez-Ruiz
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Žygimantė Tarnauskaitė
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Olga Murina
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Mahwish Mian Mohammad
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Thomas C Williams
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Adeline Fluteau
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Laura Sanchez
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Raquel Vilar-Astasio
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Marta Garcia-Canadas
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - David Cano
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
| | - Marie-Jeanne Hc Kempen
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Antonio Sanchez-Pozo
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Sara R Heras
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Andrew P Jackson
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Martin Am Reijns
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Jose L Garcia-Perez
- GENYO, Centro de Genómica e Investigación Oncológica: Pfizer - Universidad de Granada - Junta de Andalucía, PTS, Granada, Spain
- MRC Human Genetics Unit, MRC, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
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12
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Abstract
Ribonucleotides incorporated into DNA by the DNA polymerases can be incised by Topoisomerase 1 (Top1) to initiate removal of ribonucleotides from the genome. This Top1-dependent ribonucleotide removal has been demonstrated to result in multiple forms of genome instability in yeast. Here, we describe both quantitative and qualitative assays to identify mutations and other forms of DNA damage resulting from Top1-cleavage at unrepaired genomic ribonucleotides.
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13
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Abstract
Ribonucleotides embedded within DNA render the DNA sensitive to the formation of single-stranded breaks under alkali conditions. Here, we describe a next-generation sequencing method called hydrolytic end sequencing (HydEn-seq) to map ribonucleotides inserted into the genome of Saccharomyce cerevisiae strains deficient in ribonucleotide excision repair. We use this method to map several genomic features in wild-type and replicase variant yeast strains.
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Affiliation(s)
- Clinton D Orebaugh
- Genome Integrity and Structural Biology Laboratory, National Institute for Environmental Health Sciences, National Institute of Health (NIH), 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Scott A Lujan
- Genome Integrity and Structural Biology Laboratory, National Institute for Environmental Health Sciences, National Institute of Health (NIH), 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Adam B Burkholder
- Integrative Bioinformatics, National Institute for Environmental Health Sciences, National Institute of Health (NIH), Research Triangle Park, NC, USA
| | - Anders R Clausen
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute for Environmental Health Sciences, National Institute of Health (NIH), 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA.
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14
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Kind B, Wolf C, Engel K, Rapp A, Cristina Cardoso M, Lee-Kirsch MA. Single Cell Gel Electrophoresis for the Detection of Genomic Ribonucleotides. Methods Mol Biol 2018; 1672:311-8. [PMID: 29043632 DOI: 10.1007/978-1-4939-7306-4_21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Single cell gel electrophoresis or comet assay enables the quantification of DNA damage such as single-strand or double-strand breaks on a single cell level. Here, we describe a variant of this method for the detection of ribonucleotides embedded in genomic DNA. Briefly, cells are embedded in agarose on a microscopic slide, lysed under high salt and alkaline conditions and then subjected to in situ treatment with E. coli RNase HII which nicks 5' to a ribonucleotide within the context of a DNA duplex thereby converting genomic ribonucleotides into strand breaks. After unwinding of genomic DNA using a highly alkaline buffer, electrophoresis under mild alkaline conditions is performed resulting in formation of comets due to migration of fragmented DNA toward the anode. Following SYBR Gold staining comets can be visualized by fluorescence microscopy. In this setting, the length and the intensity of comets formed reflect the level of genomic ribonucleotides present in a given cell.
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15
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Zhao H, Zhu M, Limbo O, Russell P. RNase H eliminates R-loops that disrupt DNA replication but is nonessential for efficient DSB repair. EMBO Rep 2018; 19:embr.201745335. [PMID: 29622660 DOI: 10.15252/embr.201745335] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/02/2018] [Accepted: 03/09/2018] [Indexed: 12/12/2022] Open
Abstract
In Saccharomyces cerevisiae, genome stability depends on RNases H1 and H2, which remove ribonucleotides from DNA and eliminate RNA-DNA hybrids (R-loops). In Schizosaccharomyces pombe, RNase H enzymes were reported to process RNA-DNA hybrids produced at a double-strand break (DSB) generated by I-PpoI meganuclease. However, it is unclear if RNase H is generally required for efficient DSB repair in fission yeast, or whether it has other genome protection roles. Here, we show that S. pombe rnh1∆ rnh201∆ cells, which lack the RNase H enzymes, accumulate R-loops and activate DNA damage checkpoints. Their viability requires critical DSB repair proteins and Mus81, which resolves DNA junctions formed during repair of broken replication forks. "Dirty" DSBs generated by ionizing radiation, as well as a "clean" DSB at a broken replication fork, are efficiently repaired in the absence of RNase H. RNA-DNA hybrids are not detected at a reparable DSB formed by fork collapse. We conclude that unprocessed R-loops collapse replication forks in rnh1∆ rnh201∆ cells, but RNase H is not generally required for efficient DSB repair.
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Affiliation(s)
- Hongchang Zhao
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Min Zhu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Oliver Limbo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Paul Russell
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
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16
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Bartsch K, Damme M, Regen T, Becker L, Garrett L, Hölter SM, Knittler K, Borowski C, Waisman A, Glatzel M, Fuchs H, Gailus-Durner V, Hrabe de Angelis M, Rabe B. RNase H2 Loss in Murine Astrocytes Results in Cellular Defects Reminiscent of Nucleic Acid-Mediated Autoinflammation. Front Immunol 2018; 9:587. [PMID: 29662492 PMCID: PMC5890188 DOI: 10.3389/fimmu.2018.00587] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/08/2018] [Indexed: 11/13/2022] Open
Abstract
Aicardi-Goutières syndrome (AGS) is a rare early onset childhood encephalopathy caused by persistent neuroinflammation of autoimmune origin. AGS is a genetic disorder and >50% of affected individuals bear hypomorphic mutations in ribonuclease H2 (RNase H2). All available RNase H2 mouse models so far fail to mimic the prominent CNS involvement seen in AGS. To establish a mouse model recapitulating the human disease, we deleted RNase H2 specifically in the brain, the most severely affected organ in AGS. Although RNase H2ΔGFAP mice lacked the nuclease in astrocytes and a majority of neurons, no disease signs were apparent in these animals. We additionally confirmed these results in a second, neuron-specific RNase H2 knockout mouse line. However, when astrocytes were isolated from brains of RNase H2ΔGFAP mice and cultured under mitogenic conditions, they showed signs of DNA damage and premature senescence. Enhanced expression of interferon-stimulated genes (ISGs) represents the most reliable AGS biomarker. Importantly, primary RNase H2ΔGFAP astrocytes displayed significantly increased ISG transcript levels, which we failed to detect in in vivo in brains of RNase H2ΔGFAP mice. Isolated astrocytes primed by DNA damage, including RNase H2-deficiency, exhibited a heightened innate immune response when exposed to bacterial or viral antigens. Taken together, we established a valid cellular AGS model that utilizes the very cell type responsible for disease pathology, the astrocyte, and phenocopies major molecular defects observed in AGS patient cells.
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Affiliation(s)
- Kareen Bartsch
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Markus Damme
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Tommy Regen
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Lillian Garrett
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sabine M Hölter
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Katharina Knittler
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christopher Borowski
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Björn Rabe
- Medical Faculty, Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
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17
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Williams JS, Gehle DB, Kunkel TA. The role of RNase H2 in processing ribonucleotides incorporated during DNA replication. DNA Repair (Amst) 2017; 53:52-8. [PMID: 28325498 DOI: 10.1016/j.dnarep.2017.02.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/31/2017] [Accepted: 02/01/2017] [Indexed: 12/17/2022]
Abstract
Saccharomyces cerevisiae RNase H2 resolves RNA-DNA hybrids formed during transcription and it incises DNA at single ribonucleotides incorporated during nuclear DNA replication. To distinguish between the roles of these two activities in maintenance of genome stability, here we investigate the phenotypes of a mutant of yeast RNase H2 (rnh201-RED; ribonucleotide excision defective) that retains activity on RNA-DNA hybrids but is unable to cleave single ribonucleotides that are stably incorporated into the genome. The rnh201-RED mutant was expressed in wild type yeast or in a strain that also encodes a mutant allele of DNA polymerase ε (pol2-M644G) that enhances ribonucleotide incorporation during DNA replication. Similar to a strain that completely lacks RNase H2 (rnh201Δ), the pol2-M644G rnh201-RED strain exhibits replication stress and checkpoint activation. Moreover, like its null mutant counterpart, the double mutant pol2-M644G rnh201-RED strain and the single mutant rnh201-RED strain delete 2-5 base pairs in repetitive sequences at a high rate that is topoisomerase 1-dependent. The results highlight an important role for RNase H2 in maintaining genome integrity by removing single ribonucleotides incorporated during DNA replication.
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18
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Cornelio DA, Sedam HNC, Ferrarezi JA, Sampaio NMV, Argueso JL. Both R-loop removal and ribonucleotide excision repair activities of RNase H2 contribute substantially to chromosome stability. DNA Repair (Amst) 2017; 52:110-114. [PMID: 28268090 DOI: 10.1016/j.dnarep.2017.02.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/12/2017] [Accepted: 02/14/2017] [Indexed: 12/11/2022]
Abstract
Cells carrying deletions of genes encoding H-class ribonucleases display elevated rates of chromosome instability. The role of these enzymes is to remove RNA-DNA associations including persistent mRNA-DNA hybrids (R-loops) formed during transcription, and ribonucleotides incorporated into DNA during replication. RNases H1 and H2 can degrade the RNA component of R-loops, but only RNase H2 can initiate accurate ribonucleotide excision repair (RER). In order to examine the specific contributions of these activities to chromosome stability, we measured rates of loss-of-heterozygosity (LOH) in diploid Saccharomyces cerevisiae yeast strains carrying the rnh201-RED separation-of-function allele, encoding a version of RNase H2 that is RER-defective, but partly retains its other activity. The LOH rate in rnh201-RED was intermediate between RNH201 and rnh201Δ. In strains carrying a mutant version of DNA polymerase ε (pol2-M644G) that incorporates more ribonucleotides than normal, the LOH rate in rnh201-RED was as high as the rate measured in rnh201Δ. Topoisomerase 1 cleavage at sites of ribonucleotide incorporation has been recently shown to produce DNA double strand breaks. Accordingly, in both the POL2 and pol2-M644G backgrounds, the LOH elevation in rnh201-RED was suppressed by top1Δ. In contrast, in strains that incorporate fewer ribonucleotides (pol2-M644L) the LOH rate in rnh201-RED was low and independent of topoisomerase 1. These results suggest that both R-loop removal and RER contribute substantially to chromosome stability, and that their relative contributions may be variable across different regions of the genome. In this scenario, a prominent contribution of R-loop removal may be expected at highly transcribed regions, whereas RER may play a greater role at hotspots of ribonucleotide incorporation.
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Affiliation(s)
- Deborah A Cornelio
- Department of Environmental and Radiological Health Sciences and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA
| | - Hailey N C Sedam
- Department of Environmental and Radiological Health Sciences and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA; Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Jessica A Ferrarezi
- Department of Environmental and Radiological Health Sciences and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA
| | - Nadia M V Sampaio
- Department of Environmental and Radiological Health Sciences and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA; Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences and Institute for Genome Architecture and Function, Colorado State University, Fort Collins, CO 80523, USA; Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523, USA.
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19
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Huang SYN, Williams JS, Arana ME, Kunkel TA, Pommier Y. Topoisomerase I-mediated cleavage at unrepaired ribonucleotides generates DNA double-strand breaks. EMBO J 2016; 36:361-373. [PMID: 27932446 DOI: 10.15252/embj.201592426] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/28/2016] [Accepted: 11/04/2016] [Indexed: 01/02/2023] Open
Abstract
Ribonuclease activity of topoisomerase I (Top1) causes DNA nicks bearing 2',3'-cyclic phosphates at ribonucleotide sites. Here, we provide genetic and biochemical evidence that DNA double-strand breaks (DSBs) can be directly generated by Top1 at sites of genomic ribonucleotides. We show that RNase H2-deficient yeast cells displayed elevated frequency of Rad52 foci, inactivation of RNase H2 and RAD52 led to synthetic lethality, and combined loss of RNase H2 and RAD51 induced slow growth and replication stress. Importantly, these phenotypes were rescued upon additional deletion of TOP1, implicating homologous recombination for the repair of Top1-induced damage at ribonuclelotide sites. We demonstrate biochemically that irreversible DSBs are generated by subsequent Top1 cleavage on the opposite strand from the Top1-induced DNA nicks at ribonucleotide sites. Analysis of Top1-linked DNA from pull-down experiments revealed that Top1 is covalently linked to the end of DNA in RNase H2-deficient yeast cells, supporting this model. Taken together, these results define Top1 as a source of DSBs and genome instability when ribonucleotides incorporated by the replicative polymerases are not removed by RNase H2.
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Affiliation(s)
- Shar-Yin N Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jessica S Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Mercedes E Arana
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
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20
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Epshtein A, Potenski CJ, Klein HL. Increased Spontaneous Recombination in RNase H2-Deficient Cells Arises From Multiple Contiguous rNMPs and Not From Single rNMP Residues Incorporated by DNA Polymerase Epsilon. Microb Cell 2016; 3:248-254. [PMID: 28203566 PMCID: PMC5305187 DOI: 10.15698/mic2016.06.506] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Ribonucleotides can become embedded in DNA from insertion by DNA polymerases,
failure to remove Okazaki fragment primers, R-loops that can prime replication,
and RNA/cDNA-mediated recombination. RNA:DNA hybrids are removed by RNase H
enzymes. Single rNMPs in DNA are removed by RNase H2 and if they remain on the
leading strand, can lead to mutagenesis in a Top1-dependent pathway. rNMPs in
DNA can also stimulate genome instability, among which are homologous
recombination gene conversion events. We previously found that, similar to the
rNMP-stimulated mutagenesis, rNMP-stimulated recombination was also
Top1-dependent. However, in contrast to mutagenesis, we report here that
recombination is not stimulated by rNMPs incorporated by the replicative
polymerase epsilon. Instead, recombination seems to be stimulated by multiple
contiguous rNMPs, which may arise from R-loops or replication priming
events.
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Affiliation(s)
- Anastasiya Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, USA
| | | | - Hannah L Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 First Avenue, New York, New York 10016, USA
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21
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Cerritelli SM, Crouch RJ. The Balancing Act of Ribonucleotides in DNA. Trends Biochem Sci 2016; 41:434-445. [PMID: 26996833 DOI: 10.1016/j.tibs.2016.02.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/01/2016] [Accepted: 02/09/2016] [Indexed: 11/28/2022]
Abstract
The abundance of ribonucleotides in DNA remained undetected until recently because they are efficiently removed by the ribonucleotide excision repair (RER) pathway, a process similar to Okazaki fragment (OF) processing after incision by Ribonuclease H2 (RNase H2). All DNA polymerases incorporate ribonucleotides during DNA synthesis. How many, when, and why they are incorporated has been the focus of intense work during recent years by many labs. In this review, we discuss recent advances in ribonucleotide incorporation by eukaryotic DNA polymerases that suggest an evolutionarily conserved role for ribonucleotides in DNA. We also review the data that indicate that removal of ribonucleotides has an important role in maintaining genome stability.
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Affiliation(s)
- Susana M Cerritelli
- Section on Formation of RNA, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Crouch
- Section on Formation of RNA, Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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22
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Donigan KA, Cerritelli SM, McDonald JP, Vaisman A, Crouch RJ, Woodgate R. Unlocking the steric gate of DNA polymerase η leads to increased genomic instability in Saccharomyces cerevisiae. DNA Repair (Amst) 2015; 35:1-12. [PMID: 26340535 PMCID: PMC4651834 DOI: 10.1016/j.dnarep.2015.07.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/18/2015] [Accepted: 07/21/2015] [Indexed: 11/26/2022]
Abstract
DNA polymerase η (pol η) is best characterized for its ability to perform accurate and efficient translesion DNA synthesis (TLS) through cyclobutane pyrimidine dimers (CPDs). To ensure accurate bypass the polymerase is not only required to select the correct base, but also discriminate between NTPs and dNTPs. Most DNA polymerases have a conserved "steric gate" residue which functions to prevent incorporation of NMPs during DNA synthesis. Here, we demonstrate that the Phe35 residue of Saccharomyces cerevisiae pol η functions as a steric gate to limit the use of ribonucleotides during polymerization both in vitro and in vivo. Unlike the related pol ι enzyme, wild-type pol η does not readily incorporate NMPs in vitro. In contrast, a pol η F35A mutant incorporates NMPs on both damaged and undamaged DNA in vitro with a high degree of base selectivity. An S.cerevisiae strain expressing pol η F35A (rad30-F35A) that is also deficient for nucleotide excision repair (rad1Δ) and the TLS polymerase, pol ζ (rev3Δ), is extremely sensitive to UV-light. The sensitivity is due, in part, to RNase H2 activity, as an isogenic rnh201Δ strain is roughly 50-fold more UV-resistant than its RNH201(+) counterpart. Interestingly the rad1Δ rev3Δ rad30-F35A rnh201Δ strain exhibits a significant increase in the extent of spontaneous mutagenesis with a spectrum dominated by 1bp deletions at runs of template Ts. We hypothesize that the increased mutagenesis is due to rA incorporation at these sites and that the short poly rA tract is subsequently repaired in an error-prone manner by a novel repair pathway that is specifically targeted to polyribonucleotide tracks. These data indicate that under certain conditions, pol η can compete with the cell's replicases and gain access to undamaged genomic DNA. Such observations are consistent with a role for pol η in replicating common fragile sites (CFS) in human cells.
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Affiliation(s)
- Katherine A Donigan
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Susana M Cerritelli
- Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - John P McDonald
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
| | - Robert J Crouch
- Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA.
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23
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Abstract
Research indicates that the transient contamination of DNA with ribonucleotides exceeds all other known types of DNA damage combined. The consequences of ribose incorporation into DNA, and the identity of protein factors operating in this RNA-DNA realm to protect genomic integrity from RNA-triggered events are emerging. Left unrepaired, the presence of ribonucleotides in genomic DNA impacts cellular proliferation and is associated with chromosome instability, gross chromosomal rearrangements, mutagenesis, and production of previously unrecognized forms of ribonucleotide-triggered DNA damage. Here, we highlight recent findings on the nature and structure of DNA damage arising from ribonucleotides in DNA, and the identification of cellular factors acting in an RNA-DNA damage response (RDDR) to counter RNA-triggered DNA damage.
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Affiliation(s)
- Bret D Wallace
- a Genome Integrity and Structural Biology Laboratory; National Institute of Environmental Health Sciences; NIH; DHHS ; Research Triangle Park , NC USA
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O'Connell K, Jinks-Robertson S, Petes TD. Elevated Genome-Wide Instability in Yeast Mutants Lacking RNase H Activity. Genetics 2015; 201:963-75. [PMID: 26400613 DOI: 10.1534/genetics.115.182725] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 11/18/2022] Open
Abstract
Two types of RNA:DNA associations can lead to genome instability: the formation of R-loops during transcription and the incorporation of ribonucleotide monophosphates (rNMPs) into DNA during replication. Both ribonuclease (RNase) H1 and RNase H2 degrade the RNA component of R-loops, whereas only RNase H2 can remove one or a few rNMPs from DNA. We performed high-resolution mapping of mitotic recombination events throughout the yeast genome in diploid strains of Saccharomyces cerevisiae lacking RNase H1 (rnh1Δ), RNase H2 (rnh201Δ), or both RNase H1 and RNase H2 (rnh1Δ rnh201Δ). We found little effect on recombination in the rnh1Δ strain, but elevated recombination in both the rnh201Δ and the double-mutant strains; levels of recombination in the double mutant were ∼50% higher than in the rnh201 single-mutant strain. An rnh201Δ mutant that additionally contained a mutation that reduces rNMP incorporation by DNA polymerase ε (pol2-M644L) had a level of instability similar to that observed in the presence of wild-type Pol ε. This result suggests that the elevated recombination observed in the absence of only RNase H2 is primarily a consequence of R-loops rather than misincorporated rNMPs.
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Lim YW, Sanz LA, Xu X, Hartono SR, Chédin F. Genome-wide DNA hypomethylation and RNA:DNA hybrid accumulation in Aicardi-Goutières syndrome. eLife 2015; 4. [PMID: 26182405 PMCID: PMC4528086 DOI: 10.7554/elife.08007] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/15/2015] [Indexed: 12/17/2022] Open
Abstract
Aicardi–Goutières syndrome (AGS) is a severe childhood inflammatory disorder that shows clinical and genetic overlap with systemic lupus erythematosus (SLE). AGS is thought to arise from the accumulation of incompletely metabolized endogenous nucleic acid species owing to mutations in nucleic acid-degrading enzymes TREX1 (AGS1), RNase H2 (AGS2, 3 and 4), and SAMHD1 (AGS5). However, the identity and source of such immunogenic nucleic acid species remain undefined. Using genome-wide approaches, we show that fibroblasts from AGS patients with AGS1-5 mutations are burdened by excessive loads of RNA:DNA hybrids. Using MethylC-seq, we show that AGS fibroblasts display pronounced and global loss of DNA methylation and demonstrate that AGS-specific RNA:DNA hybrids often occur within DNA hypomethylated regions. Altogether, our data suggest that RNA:DNA hybrids may represent a common immunogenic form of nucleic acids in AGS and provide the first evidence of epigenetic perturbations in AGS, furthering the links between AGS and SLE. DOI:http://dx.doi.org/10.7554/eLife.08007.001 The immune system protects the body from attack by bacteria, viruses, and other microbes. A key feature of this system is the ability to discriminate between the body's own cells and potential foreign invaders. Occasionally, this process can go wrong and the immune system starts attacking its own tissues, which can lead to arthritis, diabetes, lupus, and other ‘autoimmune’ diseases. Aicardi–Goutières syndrome (AGS) is an autoimmune disease that leads to severe mental and physical symptoms. Recent research has revealed that the disease is caused by mutations in genes that make enzymes called nucleases. In healthy people, these enzymes destroy DNA molecules and other nucleic acids. In AGS patients, the failure of the nucleases to act is thought to lead to the accumulation of unwanted DNA and RNA molecules. These molecules, in turn, are thought to be mistakenly identified by the immune system as ‘foreign’ and to cause an autoimmune response. However, it is not clear how this works. Here, Lim et al. studied skin cells called fibroblasts from patients with Aicardi–Goutières syndrome. The experiments found that the patients' cells had excessive numbers of RNA molecules binding to sections of matching DNA. These unusual DNA–RNA ‘hybrids’ accumulated in regions of the genome that do not contain many genes, perhaps as a result of breaks in the DNA. It is possible that they may mimic nucleic acids from viruses and could trigger an autoimmune response. In healthy individuals, small ‘methyl’ groups are often attached to DNA in a process known as DNA methylation. This serves to maintain the stability of the genome and controls the activity of genes. Unexpectedly, Lim et al. found that the DNA in AGS patients had far fewer methyl groups, especially in areas where the DNA–RNA hybrids had accumulated. This may lead to genome destabilization, alterations in gene activity, and may mean that the DNA in these regions may be mistaken for foreign DNA by the immune system. Altogether, Lim et al.'s findings suggest that Aicardi–Goutières syndrome may be caused by immune responses triggered by the accumulation of RNA–DNA hybrids and lower levels of DNA methylation. These findings may aid the development of new therapies to treat Aicardi–Goutières syndrome, lupus, and other similar diseases. DOI:http://dx.doi.org/10.7554/eLife.08007.002
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Affiliation(s)
- Yoong Wearn Lim
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Xiaoqin Xu
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Stella R Hartono
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
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26
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Abstract
Because of their sessile lifestyle, plants have developed extensive mechanisms to safeguard their genetic information from one generation to the next. The WEE1 kinase is one of the guardians of genome integrity, being important during S-phase progression under replication stress. Knock-out plants for WEE1 (WEE1(KO)) show a hypersensitive response when grown on replication-inhibiting drugs. Recently, we reported the identification of a mutant in the RNase H2A gene that could partially complement this replication phenotype. Here, we present the identification of a second member of the RNase H2 complex, RNase H2B, being able to complement the root growth phenotype of WEE1(KO) plants. We additionally show that deletion of a conserved domain in RNase H2B leads to loss of interaction with the RNase H2C subunit, likely explaining the loss of activity of the RNase H2 complex.
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Affiliation(s)
- Thomas Eekhout
- Department of Plant Systems Biology; Flanders Institute for Biotechnology (VIB); Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Ghent, Belgium
| | - Pooneh Kalhorzadeh
- Department of Plant Systems Biology; Flanders Institute for Biotechnology (VIB); Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Systems Biology; Flanders Institute for Biotechnology (VIB); Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Ghent, Belgium
- Correspondence to: Lieven De Veylder;
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