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Zhang Y, Liu X, Li Z, Li H, Miao Z, Wan B, Xu X. Advances on the Mechanisms and Therapeutic Strategies in Non-coding CGG Repeat Expansion Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04239-9. [PMID: 38780719 DOI: 10.1007/s12035-024-04239-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Non-coding CGG repeat expansions within the 5' untranslated region are implicated in a range of neurological disorders, including fragile X-associated tremor/ataxia syndrome, oculopharyngeal myopathy with leukodystrophy, and oculopharyngodistal myopathy. This review outlined the general characteristics of diseases associated with non-coding CGG repeat expansions, detailing their clinical manifestations and neuroimaging patterns, which often overlap and indicate shared pathophysiological traits. We summarized the underlying molecular mechanisms of these disorders, providing new insights into the roles that DNA, RNA, and toxic proteins play. Understanding these mechanisms is crucial for the development of targeted therapeutic strategies. These strategies include a range of approaches, such as antisense oligonucleotides, RNA interference, genomic DNA editing, small molecule interventions, and other treatments aimed at correcting the dysregulated processes inherent in these disorders. A deeper understanding of the shared mechanisms among non-coding CGG repeat expansion disorders may hold the potential to catalyze the development of innovative therapies, ultimately offering relief to individuals grappling with these debilitating neurological conditions.
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Affiliation(s)
- Yutong Zhang
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Xuan Liu
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Zeheng Li
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
| | - Hao Li
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China
- Department of Neurology, The Fourth Affiliated Hospital of Soochow University, Suzhou, 215124, China
| | - Zhigang Miao
- The Institute of Neuroscience, Soochow University, Suzhou City, China
| | - Bo Wan
- The Institute of Neuroscience, Soochow University, Suzhou City, China
| | - Xingshun Xu
- Departments of Neurology, The First Affiliated Hospital of Soochow University, Suzhou City, China.
- The Institute of Neuroscience, Soochow University, Suzhou City, China.
- Department of Neurology, The First Affiliated Hospital of Soochow University, Suzhou, 215000, China.
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2
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Hisey JA, Radchenko EA, Mandel NH, McGinty R, Matos-Rodrigues G, Rastokina A, Masnovo C, Ceschi S, Hernandez A, Nussenzweig A, Mirkin S. Pathogenic CANVAS (AAGGG)n repeats stall DNA replication due to the formation of alternative DNA structures. Nucleic Acids Res 2024; 52:4361-4374. [PMID: 38381906 PMCID: PMC11077069 DOI: 10.1093/nar/gkae124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/23/2024] Open
Abstract
CANVAS is a recently characterized repeat expansion disease, most commonly caused by homozygous expansions of an intronic (A2G3)n repeat in the RFC1 gene. There are a multitude of repeat motifs found in the human population at this locus, some of which are pathogenic and others benign. In this study, we conducted structure-functional analyses of the pathogenic (A2G3)n and nonpathogenic (A4G)n repeats. We found that the pathogenic, but not the nonpathogenic, repeat presents a potent, orientation-dependent impediment to DNA polymerization in vitro. The pattern of the polymerization blockage is consistent with triplex or quadruplex formation in the presence of magnesium or potassium ions, respectively. Chemical probing of both repeats in vitro reveals triplex H-DNA formation by only the pathogenic repeat. Consistently, bioinformatic analysis of S1-END-seq data from human cell lines shows preferential H-DNA formation genome-wide by (A2G3)n motifs over (A4G)n motifs. Finally, the pathogenic, but not the nonpathogenic, repeat stalls replication fork progression in yeast and human cells. We hypothesize that the CANVAS-causing (A2G3)n repeat represents a challenge to genome stability by folding into alternative DNA structures that stall DNA replication.
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Affiliation(s)
- Julia A Hisey
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | | | - Ryan J McGinty
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115, USA
| | | | | | - Chiara Masnovo
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | | | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD20892, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA
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3
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Nickens DG, Feng Z, Shen J, Gray SJ, Simmons RH, Niu H, Bochman ML. Cdc13 exhibits dynamic DNA strand exchange in the presence of telomeric DNA. Nucleic Acids Res 2024:gkae265. [PMID: 38613387 DOI: 10.1093/nar/gkae265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/22/2024] [Accepted: 04/01/2024] [Indexed: 04/14/2024] Open
Abstract
Telomerase is the enzyme that lengthens telomeres and is tightly regulated by a variety of means to maintain genome integrity. Several DNA helicases function at telomeres, and we previously found that the Saccharomyces cerevisiae helicases Hrq1 and Pif1 directly regulate telomerase. To extend these findings, we are investigating the interplay between helicases, single-stranded DNA (ssDNA) binding proteins (ssBPs), and telomerase. The yeast ssBPs Cdc13 and RPA differentially affect Hrq1 and Pif1 helicase activity, and experiments to measure helicase disruption of Cdc13/ssDNA complexes instead revealed that Cdc13 can exchange between substrates. Although other ssBPs display dynamic binding, this was unexpected with Cdc13 due to the reported in vitro stability of the Cdc13/telomeric ssDNA complex. We found that the DNA exchange by Cdc13 occurs rapidly at physiological temperatures, requires telomeric repeat sequence DNA, and is affected by ssDNA length. Cdc13 truncations revealed that the low-affinity binding site (OB1), which is distal from the high-affinity binding site (OB3), is required for this intermolecular dynamic DNA exchange (DDE). We hypothesize that DDE by Cdc13 is the basis for how Cdc13 'moves' at telomeres to alternate between modes where it regulates telomerase activity and assists in telomere replication.
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Affiliation(s)
- David G Nickens
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Zhitong Feng
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Jiangchuan Shen
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Spencer J Gray
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Robert H Simmons
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Hengyao Niu
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | - Matthew L Bochman
- Molecular & Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
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4
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Nickens DG, Feng Z, Shen J, Gray SJ, Simmons RH, Niu H, Bochman ML. Cdc13 exhibits dynamic DNA strand exchange in the presence of telomeric DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.04.569902. [PMID: 38105973 PMCID: PMC10723391 DOI: 10.1101/2023.12.04.569902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Telomerase is the enzyme that lengthens telomeres and is tightly regulated by a variety of means to maintain genome integrity. Several DNA helicases function at telomeres, and we previously found that the Saccharomyces cerevisiae helicases Hrq1 and Pif1 directly regulate telomerase. To extend these findings, we are investigating the interplay between helicases, single-stranded DNA (ssDNA) binding proteins (ssBPs), and telomerase. The yeast ssBPs Cdc13 and RPA differentially affect Hrq1 and Pif1 helicase activity, and experiments to measure helicase disruption of Cdc13/ssDNA complexes instead revealed that Cdc13 can exchange between substrates. Although other ssBPs display dynamic binding, this was unexpected with Cdc13 due to the reported in vitro stability of the Cdc13/telomeric ssDNA complex. We found that the DNA exchange by Cdc13 occurs rapidly at physiological temperatures, requires telomeric repeat sequence DNA, and is affected by ssDNA length. Cdc13 truncations revealed that the low-affinity binding site (OB1), which is distal from the high-affinity binding site (OB3), is required for this intermolecular dynamic DNA exchange (DDE). We hypothesize that DDE by Cdc13 is the basis for how Cdc13 'moves' at telomeres to alternate between modes where it regulates telomerase activity and assists in telomere replication.
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5
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Meir A, Raina VB, Rivera CE, Marie L, Symington LS, Greene EC. The separation pin distinguishes the pro- and anti-recombinogenic functions of Saccharomyces cerevisiae Srs2. Nat Commun 2023; 14:8144. [PMID: 38065943 PMCID: PMC10709652 DOI: 10.1038/s41467-023-43918-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Srs2 is an Sf1a helicase that helps maintain genome stability in Saccharomyces cerevisiae through its ability to regulate homologous recombination. Srs2 downregulates HR by stripping Rad51 from single-stranded DNA, and Srs2 is also thought to promote synthesis-dependent strand annealing by unwinding D-loops. However, it has not been possible to evaluate the relative contributions of these two distinct activities to any aspect of recombination. Here, we used a structure-based approach to design an Srs2 separation-of-function mutant that can dismantle Rad51-ssDNA filaments but is incapable of disrupting D-loops, allowing us to assess the relative contributions of these pro- and anti-recombinogenic functions. We show that this separation-of-function mutant phenocopies wild-type SRS2 in vivo, suggesting that the ability of Srs2 to remove Rad51 from ssDNA is its primary role during HR.
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Affiliation(s)
- Aviv Meir
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Vivek B Raina
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Carly E Rivera
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Léa Marie
- Department of Microbiology & Immunology, Columbia University, New York, NY, 10032, USA
- Institute of Pharmacology and Structural Biology (IPBS), French National Centre for Scientific Research (CNRS), Université Toulouse III, Toulouse, France
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University, New York, NY, 10032, USA
- Department of Genetics & Development, Columbia University, New York, NY, 10032, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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Chib S, Griffin WC, Gao J, Proffitt DR, Byrd AK, Raney KD. Pif1 Helicase Mediates Remodeling of Protein-Nucleic Acid Complexes by Promoting Dissociation of Sub1 from G-Quadruplex DNA and Cdc13 from G-Rich Single-Stranded DNA. Biochemistry 2023; 62:3360-3372. [PMID: 37948114 PMCID: PMC10841737 DOI: 10.1021/acs.biochem.3c00441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Pif1 is a molecular motor enzyme that is conserved from yeast to mammals. It translocates on ssDNA with a directional bias (5' → 3') and unwinds duplexes using the energy obtained from ATP hydrolysis. Pif1 is involved in dsDNA break repair, resolution of G-quadruplex (G4) structures, negative regulation of telomeres, and Okazaki fragment maturation. An important property of this helicase is to exert force and disrupt protein-DNA complexes, which may otherwise serve as barriers to various cellular pathways. Previously, Pif1 was reported to displace streptavidin from biotinylated DNA, Rap1 from telomeric DNA, and telomerase from DNA ends. Here, we have investigated the ability of S. cerevisiae Pif1 helicase to disrupt protein barriers from G4 and telomeric sites. Yeast chromatin-associated transcription coactivator Sub1 was characterized as a G4 binding protein. We found evidence for a physical interaction between Pif1 helicase and Sub1 protein. Here, we demonstrate that Pif1 is capable of catalyzing the disruption of Sub1-bound G4 structures in an ATP-dependent manner. We also investigated Pif1-mediated removal of yeast telomere-capping protein Cdc13 from DNA ends. Cdc13 exhibits a high-affinity interaction with an 11-mer derived from the yeast telomere sequence. Our results show that Pif1 uses its translocase activity to enhance the dissociation of this telomere-specific protein from its binding site. The rate of dissociation increased with an increase in the helicase loading site length. Additionally, we examined the biochemical mechanism for Pif1-catalyzed protein displacement by mutating the sequence of the telomeric 11-mer on the 5'-end and the 3'-end. The results support a model whereby Pif1 disrupts Cdc13 from the ssDNA in steps.
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Affiliation(s)
- Shubeena Chib
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - Wezley C. Griffin
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - Jun Gao
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - David R. Proffitt
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - Alicia K. Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
| | - Kevin D. Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205
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Fang P, Xie C, Pan T, Cheng T, Chen W, Xia S, Ding T, Fang J, Zhou Y, Fang L, Wei D, Xiao S. Unfolding of an RNA G-quadruplex motif in the negative strand genome of porcine reproductive and respiratory syndrome virus by host and viral helicases to promote viral replication. Nucleic Acids Res 2023; 51:10752-10767. [PMID: 37739415 PMCID: PMC10602871 DOI: 10.1093/nar/gkad759] [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: 01/02/2023] [Revised: 08/28/2023] [Accepted: 09/07/2023] [Indexed: 09/24/2023] Open
Abstract
G-quadruplex (G4) is a unique secondary structure formed by guanine-rich nucleic acid sequences. Growing studies reported that the genomes of some viruses harbor G4 structures associated with viral replication, opening up a new field to dissect viral infection. Porcine reproductive and respiratory syndrome virus (PRRSV), a representative member of Arteriviridae, is an economically significant pathogen that has devastated the swine industry worldwide for over 30 years. In this study, we identified a highly conserved G-rich sequence with parallel-type G4 structure (named PRRSV-G4) in the negative strand genome RNA of PRRSV. Pyridostatin (PDS), a well-known G4-binding ligand, stabilized the PRRSV-G4 structure and inhibited viral replication. By screening the proteins interacting with PRRSV-G4 in PRRSV-infected cells and single-molecule magnetic tweezers analysis, we found that two helicases, host DDX18 and viral nsp10, interact with and efficiently unwound the PRRSV-G4 structure, thereby facilitating viral replication. Using a PRRSV reverse genetics system, we confirmed that recombinant PRRSV with a G4-disruptive mutation exhibited resistance to PDS treatment, thereby displaying higher replication than wild-type PRRSV. Collectively, these results demonstrate that the PRRSV-G4 structure plays a crucial regulatory role in viral replication, and targeting this structure represents a promising strategy for antiviral therapies.
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Affiliation(s)
- Puxian Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Congbao Xie
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, and Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Ting Pan
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Ting Cheng
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Wei Chen
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Sijin Xia
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Tong Ding
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Junkang Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, and Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yanrong Zhou
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Liurong Fang
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Dengguo Wei
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, and Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Shaobo Xiao
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- The Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
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Hisey JA, Radchenko EA, Ceschi S, Rastokina A, Mandel NH, McGinty RJ, Matos-Rodrigues G, Hernandez A, Nussenzweig A, Mirkin SM. Pathogenic CANVAS (AAGGG) n repeats stall DNA replication due to the formation of alternative DNA structures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550509. [PMID: 37546920 PMCID: PMC10402041 DOI: 10.1101/2023.07.25.550509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
CANVAS is a recently characterized repeat expansion disease, most commonly caused by homozygous expansions of an intronic (A2G3)n repeat in the RFC1 gene. There are a multitude of repeat motifs found in the human population at this locus, some of which are pathogenic and others benign. In this study, we conducted structure-functional analyses of the main pathogenic (A2G3)n and the main nonpathogenic (A4G)n repeats. We found that the pathogenic, but not the nonpathogenic, repeat presents a potent, orientation-dependent impediment to DNA polymerization in vitro. The pattern of the polymerization blockage is consistent with triplex or quadruplex formation in the presence of magnesium or potassium ions, respectively. Chemical probing of both repeats in supercoiled DNA reveals triplex H-DNA formation by the pathogenic repeat. Consistently, bioinformatic analysis of the S1-END-seq data from human cell lines shows preferential H-DNA formation genome-wide by (A2G3)n motifs over (A4G)n motifs in vivo. Finally, the pathogenic, but not the non-pathogenic, repeat stalls replication fork progression in yeast and human cells. We hypothesize that CANVAS-causing (A2G3)n repeat represents a challenge to genome stability by folding into alternative DNA structures that stall DNA replication.
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Affiliation(s)
- Julia A. Hisey
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | - Silvia Ceschi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | | | | | - Ryan J. McGinty
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
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9
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Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
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Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
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10
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Rider SD, Damewood FJ, Gadgil RY, Hitch DC, Alhawach V, Shrestha R, Shanahan M, Zavada N, Leffak M. Suppressors of Break-Induced Replication in Human Cells. Genes (Basel) 2023; 14:genes14020398. [PMID: 36833325 PMCID: PMC9956954 DOI: 10.3390/genes14020398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/23/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Short tandem DNA repeats are drivers of genome instability. To identify suppressors of break-induced mutagenesis human cells, unbiased genetic screens were conducted using a lentiviral shRNA library. The recipient cells possessed fragile non-B DNA that could induce DNA double-strand breaks (DSBs), integrated at an ectopic chromosomal site adjacent to a thymidine kinase marker gene. Mutagenesis of the thymidine kinase gene rendered cells resistant to the nucleoside analog ganciclovir (GCV). The screen identified genes that have established roles in DNA replication and repair, chromatin modification, responses to ionizing radiation, and genes encoding proteins enriched at replication forks. Novel loci implicated in BIR included olfactory receptors, the G0S2 oncogene/tumor suppressor axis, the EIF3H-METTL3 translational regulator, and the SUDS3 subunit of the Sin3A corepressor. Consistent with a role in suppressing BIR, siRNA knockdown of selected candidates increased the frequency of the GCVr phenotype and increased DNA rearrangements near the ectopic non-B DNA. Inverse PCR and DNA sequence analyses showed that hits identified in the screen increased genome instability. Further analysis quantitated repeat-induced hypermutagenesis at the ectopic site and showed that knockdown of a primary hit, COPS2, induced mutagenic hotspots, remodeled the replication fork, and increased nonallelic chromosome template switches.
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11
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Brush GS. Anomalies in dye-terminator DNA sequencing caused by a natural G-quadruplex. PLoS One 2022; 17:e0279423. [PMID: 36574393 PMCID: PMC9794070 DOI: 10.1371/journal.pone.0279423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 11/24/2022] [Indexed: 12/29/2022] Open
Abstract
A G-rich DNA sequence from yeast that can form a non-canonical G-quadruplex structure was cloned into a plasmid vector and subjected to Sanger sequencing using dye-labeled dideoxynucleotides. Two different effects were observed. In one, presence of the G4 sequence on the template strand led to incorrect incorporation of an A residue at an internal position in the G4 sequence. In the other, the nascent strand caused attenuation of the readout coincident with synthesis of the G-rich DNA. The two effects are novel examples of disruption in DNA synthesis caused by a G4 sequence. These results provide a new example of a DNA structure that could influence genomic stability in human cells.
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Affiliation(s)
- George S. Brush
- Department of Oncology, Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine,Detroit, MI, United States of America
- * E-mail:
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12
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Li X, Wang L, Liu X, Zheng Z, Kong D. Cellular regulation and stability of DNA replication forks in eukaryotic cells. DNA Repair (Amst) 2022; 120:103418. [DOI: 10.1016/j.dnarep.2022.103418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 11/03/2022]
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13
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Casas-Delucchi CS, Daza-Martin M, Williams SL, Coster G. The mechanism of replication stalling and recovery within repetitive DNA. Nat Commun 2022; 13:3953. [PMID: 35853874 PMCID: PMC9296464 DOI: 10.1038/s41467-022-31657-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 06/27/2022] [Indexed: 11/09/2022] Open
Abstract
Accurate chromosomal DNA replication is essential to maintain genomic stability. Genetic evidence suggests that certain repetitive sequences impair replication, yet the underlying mechanism is poorly defined. Replication could be directly inhibited by the DNA template or indirectly, for example by DNA-bound proteins. Here, we reconstitute replication of mono-, di- and trinucleotide repeats in vitro using eukaryotic replisomes assembled from purified proteins. We find that structure-prone repeats are sufficient to impair replication. Whilst template unwinding is unaffected, leading strand synthesis is inhibited, leading to fork uncoupling. Synthesis through hairpin-forming repeats is rescued by replisome-intrinsic mechanisms, whereas synthesis of quadruplex-forming repeats requires an extrinsic accessory helicase. DNA-induced fork stalling is mechanistically similar to that induced by leading strand DNA lesions, highlighting structure-prone repeats as an important potential source of replication stress. Thus, we propose that our understanding of the cellular response to replication stress may also be applied to DNA-induced replication stalling.
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Affiliation(s)
- Corella S Casas-Delucchi
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Manuel Daza-Martin
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Sophie L Williams
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Gideon Coster
- Genome Replication lab, Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK.
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14
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Radchenko EA, Aksenova AY, Volkov KV, Shishkin AA, Pavlov YI, Mirkin SM. Partners in crime: Tbf1 and Vid22 promote expansions of long human telomeric repeats at an interstitial chromosome position in yeast. PNAS NEXUS 2022; 1:pgac080. [PMID: 35832866 PMCID: PMC9272169 DOI: 10.1093/pnasnexus/pgac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/01/2022] [Indexed: 02/05/2023]
Abstract
In humans, telomeric repeats (TTAGGG)n are known to be present at internal chromosomal sites. These interstitial telomeric sequences (ITSs) are an important source of genomic instability, including repeat length polymorphism, but the molecular mechanisms responsible for this instability remain to be understood. Here, we studied the mechanisms responsible for expansions of human telomeric (Htel) repeats that were artificially inserted inside a yeast chromosome. We found that Htel repeats in an interstitial chromosome position are prone to expansions. The propensity of Htel repeats to expand depends on the presence of a complex of two yeast proteins: Tbf1 and Vid22. These two proteins are physically bound to an interstitial Htel repeat, and together they slow replication fork progression through it. We propose that slow progression of the replication fork through the protein complex formed by the Tbf1 and Vid22 partners at the Htel repeat cause DNA strand slippage, ultimately resulting in repeat expansions.
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Affiliation(s)
| | | | - Kirill V Volkov
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | | | - Youri I Pavlov
- Eppley Institute for Research In Cancer and Allied Diseases, Omaha, NE 68198, USA
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15
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Vicari MR, Bruschi DP, Cabral-de-Mello DC, Nogaroto V. Telomere organization and the interstitial telomeric sites involvement in insects and vertebrates chromosome evolution. Genet Mol Biol 2022; 45:e20220071. [DOI: 10.1590/1678-4685-gmb-2022-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
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16
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Polleys EJ, Freudenreich CH. Homologous recombination within repetitive DNA. Curr Opin Genet Dev 2021; 71:143-153. [PMID: 34464817 DOI: 10.1016/j.gde.2021.08.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 12/16/2022]
Abstract
Many microsatellite DNA sequences are able to form non-B form DNA secondary structures, such as hairpin loops, cruciforms, triplex DNA or G-quadruplexes. These DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks, which can be repaired by homologous recombination (HR). Recent work understanding HR at structure-forming repeats has focused on genetic requirements for replication fork restart, break induced replication (BIR) at broken forks, recombination during and after relocalization of breaks or stalled forks to the nuclear periphery, and how repair pathway choice and kinetics are navigated in the presence of a repeat tract. In this review, we summarize recent developments that illuminate the role of recombination in repairing DNA damage or causing tract length changes within repetitive DNA and its role in maintaining genome stability.
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Affiliation(s)
- Erica J Polleys
- Department of Biology, Tufts University, Medford MA 02155, United States
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford MA 02155, United States; Program in Genetics, Tufts University, Boston MA 02111, United States.
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17
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Shyian M, Shore D. Approaching Protein Barriers: Emerging Mechanisms of Replication Pausing in Eukaryotes. Front Cell Dev Biol 2021; 9:672510. [PMID: 34124054 PMCID: PMC8194067 DOI: 10.3389/fcell.2021.672510] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/03/2021] [Indexed: 11/13/2022] Open
Abstract
During nuclear DNA replication multiprotein replisome machines have to jointly traverse and duplicate the total length of each chromosome during each cell cycle. At certain genomic locations replisomes encounter tight DNA-protein complexes and slow down. This fork pausing is an active process involving recognition of a protein barrier by the approaching replisome via an evolutionarily conserved Fork Pausing/Protection Complex (FPC). Action of the FPC protects forks from collapse at both programmed and accidental protein barriers, thus promoting genome integrity. In addition, FPC stimulates the DNA replication checkpoint and regulates topological transitions near the replication fork. Eukaryotic cells have been proposed to employ physiological programmed fork pausing for various purposes, such as maintaining copy number at repetitive loci, precluding replication-transcription encounters, regulating kinetochore assembly, or controlling gene conversion events during mating-type switching. Here we review the growing number of approaches used to study replication pausing in vivo and in vitro as well as the characterization of additional factors recently reported to modulate fork pausing in different systems. Specifically, we focus on the positive role of topoisomerases in fork pausing. We describe a model where replisome progression is inherently cautious, which ensures general preservation of fork stability and genome integrity but can also carry out specialized functions at certain loci. Furthermore, we highlight classical and novel outstanding questions in the field and propose venues for addressing them. Given how little is known about replisome pausing at protein barriers in human cells more studies are required to address how conserved these mechanisms are.
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Affiliation(s)
- Maksym Shyian
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - David Shore
- Department of Molecular Biology, Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva, Geneva, Switzerland
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18
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Whalen JM, Dhingra N, Wei L, Zhao X, Freudenreich CH. Relocation of Collapsed Forks to the Nuclear Pore Complex Depends on Sumoylation of DNA Repair Proteins and Permits Rad51 Association. Cell Rep 2021; 31:107635. [PMID: 32402281 DOI: 10.1016/j.celrep.2020.107635] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 01/07/2020] [Accepted: 04/21/2020] [Indexed: 10/24/2022] Open
Abstract
Expanded CAG repeats form stem-loop secondary structures that lead to fork stalling and collapse. Previous work has shown that these collapsed forks relocalize to nuclear pore complexes (NPCs) in late S phase in a manner dependent on replication, the nucleoporin Nup84, and the Slx5 protein, which prevents repeat fragility and instability. Here, we show that binding of the Smc5/6 complex to the collapsed fork triggers Mms21-dependent sumoylation of fork-associated DNA repair proteins, and that RPA, Rad52, and Rad59 are the key sumoylation targets that mediate relocation. The SUMO interacting motifs of Slx5 target collapsed forks to the NPC. Notably, Rad51 foci only co-localize with the repeat after it is anchored to the nuclear periphery and Rad51 exclusion from the early collapsed fork is dependent on RPA sumoylation. This pathway may provide a mechanism to constrain recombination at stalled or collapsed forks until it is required for fork restart.
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Affiliation(s)
- Jenna M Whalen
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Nalini Dhingra
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lei Wei
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, MA 02155, USA; Program in Genetics, Tufts University, Boston, MA 02111, USA.
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19
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Drosopoulos WC, Deng Z, Twayana S, Kosiyatrakul ST, Vladimirova O, Lieberman PM, Schildkraut CL. TRF2 Mediates Replication Initiation within Human Telomeres to Prevent Telomere Dysfunction. Cell Rep 2020; 33:108379. [PMID: 33176153 PMCID: PMC7790361 DOI: 10.1016/j.celrep.2020.108379] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/15/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023] Open
Abstract
The telomeric shelterin protein telomeric repeat-binding factor 2 (TRF2) recruits origin recognition complex (ORC) proteins, the foundational building blocks of DNA replication origins, to telomeres. We seek to determine whether TRF2-recruited ORC proteins give rise to functional origins in telomere repeat tracts. We find that reduction of telomeric recruitment of ORC2 by expression of an ORC interaction-defective TRF2 mutant significantly reduces telomeric initiation events in human cells. This reduction in initiation events is accompanied by telomere repeat loss, telomere aberrations and dysfunction. We demonstrate that telomeric origins are activated by induced replication stress to provide a key rescue mechanism for completing compromised telomere replication. Importantly, our studies also indicate that the chromatin remodeler SNF2H promotes telomeric initiation events by providing access for ORC2. Collectively, our findings reveal that active recruitment of ORC by TRF2 leads to formation of functional origins, providing an important mechanism for avoiding telomere dysfunction and rescuing challenged telomere replication.
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Affiliation(s)
- William C Drosopoulos
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
| | - Zhong Deng
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Shyam Twayana
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Settapong T Kosiyatrakul
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Olga Vladimirova
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Paul M Lieberman
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Carl L Schildkraut
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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20
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Mosbach V, Viterbo D, Descorps-Declère S, Poggi L, Vaysse-Zinkhöfer W, Richard GF. Resection and repair of a Cas9 double-strand break at CTG trinucleotide repeats induces local and extensive chromosomal deletions. PLoS Genet 2020; 16:e1008924. [PMID: 32673314 PMCID: PMC7413560 DOI: 10.1371/journal.pgen.1008924] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 08/07/2020] [Accepted: 06/10/2020] [Indexed: 12/26/2022] Open
Abstract
Microsatellites are short tandem repeats, ubiquitous in all eukaryotes and represent ~2% of the human genome. Among them, trinucleotide repeats are responsible for more than two dozen neurological and developmental disorders. Targeting microsatellites with dedicated DNA endonucleases could become a viable option for patients affected with dramatic neurodegenerative disorders. Here, we used the Streptococcus pyogenes Cas9 to induce a double-strand break within the expanded CTG repeat involved in myotonic dystrophy type 1, integrated in a yeast chromosome. Repair of this double-strand break generated unexpected large chromosomal deletions around the repeat tract. These deletions depended on RAD50, RAD52, DNL4 and SAE2, and both non-homologous end-joining and single-strand annealing pathways were involved. Resection and repair of the double-strand break (DSB) were totally abolished in a rad50Δ strain, whereas they were impaired in a sae2Δ mutant, only on the DSB end containing most of the repeat tract. This observation demonstrates that Sae2 plays significant different roles in resecting a DSB end containing a repeated and structured sequence as compared to a non-repeated DSB end. In addition, we also discovered that gene conversion was less efficient when the DSB could be repaired using a homologous template, suggesting that the trinucleotide repeat may interfere with gene conversion too. Altogether, these data show that SpCas9 may not be the best choice when inducing a double-strand break at or near a microsatellite, especially in mammalian genomes that contain many more dispersed repeated elements than the yeast genome. With the discovery of highly specific DNA endonucleases such as TALEN and CRISPR-Cas systems, gene editing has become an attractive approach to address genetic disorders. Myotonic dystrophy type 1 (Steinert disease) is due to a large expansion of a CTG trinucleotide repeat in the DMPK gene. At the present time, despite numerous therapeutic attempts, this dramatic neurodegenerative disorder still has no cure. In the present work, we tried to use the Cas9 endonuclease to induce a double-strand break within the expanded CTG repeat of the DMPK gene integrated in the yeast genome. Surprisingly, this break induced chromosomal deletions around the repeat tract. These deletions were local and involved non-homologous joining of the two DNA ends, or more extensive involving homologous recombination between repeated elements upstream and downstream the break. Using yeast genetics, we investigated the genetic requirements for these deletions and found that the triplet repeat tract altered the capacity of the repair machinery to faithfully repair the double-strand break. These results have implications for future gene therapy approaches in human patients.
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Affiliation(s)
| | | | - Stéphane Descorps-Declère
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Institut Pasteur, Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI), Paris, France
| | - Lucie Poggi
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Sorbonne Universités, Collège doctoral, Paris, France
| | - Wilhelm Vaysse-Zinkhöfer
- Institut Pasteur, CNRS, UMR3525, Paris, France
- Sorbonne Universités, Collège doctoral, Paris, France
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21
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Khristich AN, Mirkin SM. On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. J Biol Chem 2020; 295:4134-4170. [PMID: 32060097 PMCID: PMC7105313 DOI: 10.1074/jbc.rev119.007678] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Expansions of simple tandem repeats are responsible for almost 50 human diseases, the majority of which are severe, degenerative, and not currently treatable or preventable. In this review, we first describe the molecular mechanisms of repeat-induced toxicity, which is the connecting link between repeat expansions and pathology. We then survey alternative DNA structures that are formed by expandable repeats and review the evidence that formation of these structures is at the core of repeat instability. Next, we describe the consequences of the presence of long structure-forming repeats at the molecular level: somatic and intergenerational instability, fragility, and repeat-induced mutagenesis. We discuss the reasons for gender bias in intergenerational repeat instability and the tissue specificity of somatic repeat instability. We also review the known pathways in which DNA replication, transcription, DNA repair, and chromatin state interact and thereby promote repeat instability. We then discuss possible reasons for the persistence of disease-causing DNA repeats in the genome. We describe evidence suggesting that these repeats are a payoff for the advantages of having abundant simple-sequence repeats for eukaryotic genome function and evolvability. Finally, we discuss two unresolved fundamental questions: (i) why does repeat behavior differ between model systems and human pedigrees, and (ii) can we use current knowledge on repeat instability mechanisms to cure repeat expansion diseases?
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Affiliation(s)
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, Massachusetts 02155.
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22
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Viterbo D, Richard GF. Quantifying Replication Fork Progression at CTG Repeats by 2D Gel Electrophoresis. Methods Mol Biol 2020; 2056:69-81. [PMID: 31586341 DOI: 10.1007/978-1-4939-9784-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Physical separation of branched DNA from linear molecules is based on the difference of mobility of linear versus branched DNA during two-dimensional agarose gel electrophoresis. Structured DNA migrates as slower species when compared to linear DNA of similar molecular weight. Metabolic processes such as S phase replication or double strand-break repair may generate branched DNA molecules. Trinucleotide repeats are naturally prone to form secondary structures that can modify their migration through an agarose gel matrix. These structures may also interfere in vivo with replication, by slowing down replication-fork progression, transiently stalling forks, possibly leading to secondary structure such as Holliday junctions or hemicatenanes. Alternatively, reversed replication forks may occur following fork stalling, disrupting replication dynamics and modifying DNA migration on agarose gel. So although two-dimensional agarose gel electrophoresis theoretically allows to resolve a mixture of structured DNA molecules and quantify them by radioactive hybridization, its practical application to trinucleotide repeats faces some serious technical challenges.
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Affiliation(s)
- David Viterbo
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France.
| | - Guy-Franck Richard
- Department Genomes & Genetics, Institut Pasteur, CNRS, UMR3525, Paris, France
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23
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Gellon L, Kaushal S, Cebrián J, Lahiri M, Mirkin SM, Freudenreich CH. Mrc1 and Tof1 prevent fragility and instability at long CAG repeats by their fork stabilizing function. Nucleic Acids Res 2019; 47:794-805. [PMID: 30476303 PMCID: PMC6344861 DOI: 10.1093/nar/gky1195] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/13/2018] [Indexed: 12/14/2022] Open
Abstract
Fork stabilization at DNA impediments is key to maintaining replication fork integrity and preventing chromosome breaks. Mrc1 and Tof1 are two known stabilizers that travel with the replication fork. In addition to a structural role, Mrc1 has a DNA damage checkpoint function. Using a yeast model system, we analyzed the role of Mrc1 and Tof1 at expanded CAG repeats of medium and long lengths, which are known to stall replication forks and cause trinucleotide expansion diseases such as Huntington's disease and myotonic dystrophy. We demonstrate that the fork stabilizer but not the checkpoint activation function of Mrc1 is key for preventing DNA breakage and death of cells containing expanded CAG tracts. In contrast, both Mrc1 functions are important in preventing repeat length instability. Mrc1 has a general fork protector role that is evident at forks traversing both repetitive and non-repetitive DNA, though it becomes crucial at long CAG repeat lengths. In contrast, the role of Tof1 in preventing fork breakage is specific to long CAG tracts of 85 or more repeats. Our results indicate that long CAG repeats have a particular need for Tof1 and highlight the importance of fork stabilizers in maintaining fork integrity during replication of structure-forming repeats.
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Affiliation(s)
- Lionel Gellon
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Simran Kaushal
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Jorge Cebrián
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Mayurika Lahiri
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave, Medford, MA 02155, USA
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24
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Dahan D, Tsirkas I, Dovrat D, Sparks MA, Singh SP, Galletto R, Aharoni A. Pif1 is essential for efficient replisome progression through lagging strand G-quadruplex DNA secondary structures. Nucleic Acids Res 2019; 46:11847-11857. [PMID: 30395308 PMCID: PMC6294490 DOI: 10.1093/nar/gky1065] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/18/2018] [Indexed: 12/27/2022] Open
Abstract
Pif1 DNA helicase is a potent unwinder of G-quadruplex (G4) structures in vitro and functions to maintain genome stability at G4 sequences in Saccharomyces cerevisiae. Here, we developed and utilized a live-cell imaging approach to quantitatively measure the progression rates of single replication forks through different G4 containing sequences in individual yeast cells. We show that in the absence of Pif1, replication rates through specific lagging strand G4 sequences in vivo is significantly decreased. In contrast, we found that in the absence of Pif1, replication rates through the same G4s on the leading strand are not decreased relative to the respective WT strains, showing that Pif1 is essential only for efficient replication through lagging strand G4s. Additionally, we show that a canonical PIP sequence in Pif1 interacts with PCNA and that replication through G4 structures is significantly slower in the absence of this interaction in vitro and in vivo. Thus, Pif1–PCNA interaction is essential for optimal replisome progression through G4 sequences, highlighting the importance of coupling between Pif1 activity and replisome progression during yeast genome replication.
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Affiliation(s)
- Danielle Dahan
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Ioannis Tsirkas
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Daniel Dovrat
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Melanie A Sparks
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Saurabh P Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amir Aharoni
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
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25
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Aksenova AY, Mirkin SM. At the Beginning of the End and in the Middle of the Beginning: Structure and Maintenance of Telomeric DNA Repeats and Interstitial Telomeric Sequences. Genes (Basel) 2019; 10:genes10020118. [PMID: 30764567 PMCID: PMC6410037 DOI: 10.3390/genes10020118] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Tandem DNA repeats derived from the ancestral (TTAGGG)n run were first detected at chromosome ends of the majority of living organisms, hence the name telomeric DNA repeats. Subsequently, it has become clear that telomeric motifs are also present within chromosomes, and they were suitably called interstitial telomeric sequences (ITSs). It is well known that telomeric DNA repeats play a key role in chromosome stability, preventing end-to-end fusions and precluding the recurrent DNA loss during replication. Recent data suggest that ITSs are also important genomic elements as they confer its karyotype plasticity. In fact, ITSs appeared to be among the most unstable microsatellite sequences as they are highly length polymorphic and can trigger chromosomal fragility and gross chromosomal rearrangements. Importantly, mechanisms responsible for their instability appear to be similar to the mechanisms that maintain the length of genuine telomeres. This review compares the mechanisms of maintenance and dynamic properties of telomeric repeats and ITSs and discusses the implications of these dynamics on genome stability.
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Affiliation(s)
- Anna Y Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02421, USA.
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26
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Kaushal S, Freudenreich CH. The role of fork stalling and DNA structures in causing chromosome fragility. Genes Chromosomes Cancer 2019; 58:270-283. [PMID: 30536896 DOI: 10.1002/gcc.22721] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/13/2018] [Accepted: 12/03/2018] [Indexed: 12/19/2022] Open
Abstract
Alternative non-B form DNA structures, also called secondary structures, can form in certain DNA sequences under conditions that produce single-stranded DNA, such as during replication, transcription, and repair. Direct links between secondary structure formation, replication fork stalling, and genomic instability have been found for many repeated DNA sequences that cause disease when they expand. Common fragile sites (CFSs) are known to be AT-rich and break under replication stress, yet the molecular basis for their fragility is still being investigated. Over the past several years, new evidence has linked both the formation of secondary structures and transcription to fork stalling and fragility of CFSs. How these two events may synergize to cause fragility and the role of nuclease cleavage at secondary structures in rare and CFSs are discussed here. We also highlight evidence for a new hypothesis that secondary structures at CFSs not only initiate fragility but also inhibit healing, resulting in their characteristic appearance.
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Affiliation(s)
- Simran Kaushal
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, Massachusetts.,Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts
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27
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Flamand L. Chromosomal Integration by Human Herpesviruses 6A and 6B. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1045:209-226. [PMID: 29896669 DOI: 10.1007/978-981-10-7230-7_10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Upon infection and depending on the infected cell type, human herpesvirus 6A (HHV-6A) and 6B (HHV-6B) can replicate or enter a state of latency. HHV-6A and HHV-6B can integrate their genomes into host chromosomes as one way to establish latency. Viral integration takes place near the subtelomeric/telomeric junction of chromosomes. When HHV-6 infection and integration occur in gametes, the virus can be genetically transmitted. Inherited chromosomally integrated HHV-6 (iciHHV-6)-positive individuals carry one integrated HHV-6 copy per somatic cell. The prevalence of iciHHV-6+ individuals varies between 0.6% and 2%, depending on the geographical region sampled. In this chapter, the mechanisms leading to viral integration and reactivation from latency, as well as some of the biological and medical consequences associated with iciHHV-6, were discussed.
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Affiliation(s)
- Louis Flamand
- Division of Infectious and Immune Diseases, CHU de Québec Research Center, QC, Quebec, Canada. .,Department of Microbiology, Infectious Disease and Immunology, Faculty of Medicine, Université Laval, QC, Quebec, Canada.
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The Main Role of Srs2 in DNA Repair Depends on Its Helicase Activity, Rather than on Its Interactions with PCNA or Rad51. mBio 2018; 9:mBio.01192-18. [PMID: 30018112 PMCID: PMC6050964 DOI: 10.1128/mbio.01192-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Homologous recombination (HR) is a mechanism that repairs a variety of DNA lesions. Under certain circumstances, however, HR can generate intermediates that can interfere with other cellular processes such as DNA transcription or replication. Cells have therefore developed pathways that abolish undesirable HR intermediates. The Saccharomyces cerevisiae yeast Srs2 helicase has a major role in one of these pathways. Srs2 also works during DNA replication and interacts with the clamp PCNA. The relative importance of Srs2’s helicase activity, Rad51 removal function, and PCNA interaction in genome stability remains unclear. We created a new SRS2 allele [srs2(1-850)] that lacks the whole C terminus, containing the interaction site for Rad51 and PCNA and interactions with many other proteins. Thus, the new allele encodes an Srs2 protein bearing only the activity of the DNA helicase. We find that the interactions of Srs2 with Rad51 and PCNA are dispensable for the main role of Srs2 in the repair of DNA damage in vegetative cells and for proper completion of meiosis. On the other hand, it has been shown that in cells impaired for the DNA damage tolerance (DDT) pathways, Srs2 generates toxic intermediates that lead to DNA damage sensitivity; we show that this negative Srs2 activity requires the C terminus of Srs2. Dissection of the genetic interactions of the srs2(1-850) allele suggest a role for Srs2’s helicase activity in sister chromatid cohesion. Our results also indicate that Srs2’s function becomes more central in diploid cells. Homologous recombination (HR) is a key mechanism that repairs damaged DNA. However, this process has to be tightly regulated; failure to regulate it can lead to genome instability. The Srs2 helicase is considered a regulator of HR; it was shown to be able to evict the recombinase Rad51 from DNA. Cells lacking Srs2 exhibit sensitivity to DNA-damaging agents, and in some cases, they display defects in DNA replication. The relative roles of the helicase and Rad51 removal activities of Srs2 in genome stability remain unclear. To address this question, we created a new Srs2 mutant which has only the DNA helicase domain. Our study shows that only the DNA helicase domain is needed to deal with DNA damage and assist in DNA replication during vegetative growth and in meiosis. Thus, our findings shift the view on the role of Srs2 in the maintenance of genome integrity.
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29
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GC content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2018; 115:E7109-E7118. [PMID: 29987035 PMCID: PMC6064992 DOI: 10.1073/pnas.1807334115] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The chromosomes of many eukaryotes have regions of high GC content interspersed with regions of low GC content. In the yeast Saccharomyces cerevisiae, high-GC regions are often associated with high levels of meiotic recombination. In this study, we constructed URA3 genes that differ substantially in their base composition [URA3-AT (31% GC), URA3-WT (43% GC), and URA3-GC (63% GC)] but encode proteins with the same amino acid sequence. The strain with URA3-GC had an approximately sevenfold elevated rate of ura3 mutations compared with the strains with URA3-WT or URA3-AT About half of these mutations were single-base substitutions and were dependent on the error-prone DNA polymerase ζ. About 30% were deletions or duplications between short (5-10 base) direct repeats resulting from DNA polymerase slippage. The URA3-GC gene also had elevated rates of meiotic and mitotic recombination relative to the URA3-AT or URA3-WT genes. Thus, base composition has a substantial effect on the basic parameters of genome stability and evolution.
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30
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McGinty RJ, Mirkin SM. Cis- and Trans-Modifiers of Repeat Expansions: Blending Model Systems with Human Genetics. Trends Genet 2018; 34:448-465. [PMID: 29567336 PMCID: PMC5959756 DOI: 10.1016/j.tig.2018.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/15/2018] [Accepted: 02/19/2018] [Indexed: 12/30/2022]
Abstract
Over 30 hereditary diseases are caused by the expansion of microsatellite repeats. The length of the expandable repeat is the main hereditary determinant of these disorders. They are also affected by numerous genomic variants that are either nearby (cis) or physically separated from (trans) the repetitive locus, which we review here. These genetic variants have largely been elucidated in model systems using gene knockouts, while a few have been directly observed as single-nucleotide polymorphisms (SNPs) in patients. There is a notable disconnect between these two bodies of knowledge: knockouts poorly approximate the SNP-level variation in human populations that gives rise to medically relevant cis- and trans-modifiers, while the rarity of these diseases limits the statistical power of SNP-based analysis in humans. We propose that high-throughput SNP-based screening in model systems could become a useful approach to quickly identify and characterize modifiers of clinical relevance for patients.
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Affiliation(s)
- Ryan J McGinty
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
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31
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Schwindt E, Paeschke K. Mms1 is an assistant for regulating G-quadruplex DNA structures. Curr Genet 2018; 64:535-540. [PMID: 29098365 PMCID: PMC5948289 DOI: 10.1007/s00294-017-0773-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/24/2017] [Accepted: 10/26/2017] [Indexed: 12/25/2022]
Abstract
The preservation of genome stability is fundamental for every cell. Genomic integrity is constantly challenged. Among those challenges are also non-canonical nucleic acid structures. In recent years, scientists became aware of the impact of G-quadruplex (G4) structures on genome stability. It has been shown that folded G4-DNA structures cause changes in the cell, such as transcriptional up/down-regulation, replication stalling, or enhanced genome instability. Multiple helicases have been identified to regulate G4 structures and by this preserve genome stability. Interestingly, although these helicases are mostly ubiquitous expressed, they show specificity for G4 regulation in certain cellular processes (e.g., DNA replication). To this date, it is not clear how this process and target specificity of helicases are achieved. Recently, Mms1, an ubiquitin ligase complex protein, was identified as a novel G4-DNA-binding protein that supports genome stability by aiding Pif1 helicase binding to these regions. In this perspective review, we discuss the question if G4-DNA interacting proteins are fundamental for helicase function and specificity at G4-DNA structures.
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Affiliation(s)
- Eike Schwindt
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Katrin Paeschke
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands.
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32
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Genetic Control of Genomic Alterations Induced in Yeast by Interstitial Telomeric Sequences. Genetics 2018; 209:425-438. [PMID: 29610215 PMCID: PMC5972418 DOI: 10.1534/genetics.118.300950] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 03/27/2018] [Indexed: 11/23/2022] Open
Abstract
In many organisms, telomeric sequences can be located internally on the chromosome in addition to their usual positions at the ends of the chromosome. In humans, such interstitial telomeric sequences (ITSs) are nonrandomly associated with translocation breakpoints in tumor cells and with chromosome fragile sites (regions of the chromosome that break in response to perturbed DNA replication). We previously showed that ITSs in yeast generated several different types of instability, including terminal inversions (recombination between the ITS and the “true” chromosome telomere) and point mutations in DNA sequences adjacent to the ITS. In the current study, we examine the genetic control of these events. We show that the terminal inversions occur by the single-strand annealing pathway of DNA repair following the formation of a double-stranded DNA break within the ITS. The point mutations induced by the ITS require the error-prone DNA polymerase ζ. Unlike the terminal inversions, these events are not initiated by a double-stranded DNA break, but likely result from the error-prone repair of a single-stranded DNA gap or recruitment of DNA polymerase ζ in the absence of DNA damage.
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33
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Qiu Y, Koh HR, Myong S. Probing Dynamic Assembly and Disassembly of Rad51 Tuned by Srs2 Using smFRET. Methods Enzymol 2018; 600:321-345. [PMID: 29458765 DOI: 10.1016/bs.mie.2018.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The integrity of DNA is critical for sustaining the life of any living organism, as DNA is a reservoir of its genetic information. However, DNA is continuously damaged by either normal metabolic pathways or environmental insults such as ultraviolet exposure or chemicals. Double-stranded DNA break is one of the most common types of DNA damage that requires activation of homologous recombination (HR) pathway mediated by Rad51 in eukaryotes (Paques & Haber, 1999; Symington, 2002). Rad51 protein forms a helical nucleoprotein filament on resected DNA to initiate homology search but also can interact with other single-stranded DNA (ssDNA)-binding proteins including Srs2. Srs2, a well-known antirecombinase in HR, is an ATP-dependent 3'-5' DNA helicase in the budding yeast Saccharomyces cerevisiae as well as an ssDNA translocase. It disrupts Rad51 filaments, preventing HR (Krejci et al., 2003; Le Breton et al., 2008; Veaute et al., 2003). In the following text, we provide detailed experimental platforms employed to investigate the activity of Rad51 and Srs2 using single-molecule Forster resonance energy transfer and protein-induced fluorescence enhancement. First, we demonstrate how to detect Rad51 filament formation to address the binding site size binding kinetic of the Rad51, as well as the directionality of the filament formation. Next, we explain how to visualize ATP-dependent translocation and unwinding activities of Srs2 on DNA. Lastly, we demonstrate the filament forming activity by Rad51 which is counteracted by the filament removal activity of Srs2.
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Affiliation(s)
- Yupeng Qiu
- Johns Hopkins University, Baltimore, MD, United States
| | - Hye Ran Koh
- Johns Hopkins University, Baltimore, MD, United States; Chung-Ang University, Seoul, South Korea
| | - Sua Myong
- Johns Hopkins University, Baltimore, MD, United States.
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34
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Shubernetskaya O, Skvortsov D, Evfratov S, Rubtsova M, Belova E, Strelkova O, Cherepaninets V, Zhironkina O, Olovnikov A, Zvereva M, Dontsova O, Kireev I. Interstitial telomeric repeats-associated DNA breaks. Nucleus 2017; 8:641-653. [PMID: 28914588 PMCID: PMC5788545 DOI: 10.1080/19491034.2017.1356501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 06/28/2017] [Accepted: 07/04/2017] [Indexed: 02/08/2023] Open
Abstract
During a cell's lifespan, DNA break formation is a common event, associated with many processes, from replication to apoptosis. Most of DNA breaks are readily repaired, but some are meant to persist in time, such as the chromosome ends, protected by telomeres. Besides them, eukaryotic genomes comprise shorter stretches of interstitial telomeric repeats. We assumed that the latter may also be associated with the formation of DNA breaks meant to persist in time. In zebrafish and mouse embryos, cells containing numerous breakage foci were identified. These breaks were not associated with apoptosis or replication, nor did they seem to activate DNA damage response machinery. Unlike short-living, accidental sparse breaks, the ones we found seem to be closely associated, forming discrete break foci. A PCR-based method was developed, allowing specific amplification of DNA regions located between inverted telomeric repeats associated with breaks. The cloning and sequencing of such DNA fragments were found to denote some specificity in their distribution for different tissue types and development stages.
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Affiliation(s)
- Olga Shubernetskaya
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry Skvortsov
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Sergey Evfratov
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Maria Rubtsova
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Elena Belova
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Olga Strelkova
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Varvara Cherepaninets
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Oxana Zhironkina
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | | | - Maria Zvereva
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Olga Dontsova
- Chemistry Department, M.V. Lomonosov Moscow State University, Moscow, Russia
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia
| | - Igor Kireev
- A.N. Belozersky Institute of Physico-chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
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35
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Structure and function of Pif1 helicase. Biochem Soc Trans 2017; 45:1159-1171. [PMID: 28900015 DOI: 10.1042/bst20170096] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/18/2022]
Abstract
Pif1 family helicases have multiple roles in the maintenance of nuclear and mitochondrial DNA in eukaryotes. Saccharomyces cerevisiae Pif1 is involved in replication through barriers to replication, such as G-quadruplexes and protein blocks, and reduces genetic instability at these sites. Another Pif1 family helicase in S. cerevisiae, Rrm3, assists in fork progression through replication fork barriers at the rDNA locus and tRNA genes. ScPif1 (Saccharomyces cerevisiae Pif1) also negatively regulates telomerase, facilitates Okazaki fragment processing, and acts with polymerase δ in break-induced repair. Recent crystal structures of bacterial Pif1 helicases and the helicase domain of human PIF1 combined with several biochemical and biological studies on the activities of Pif1 helicases have increased our understanding of the function of these proteins. This review article focuses on these structures and the mechanism(s) proposed for Pif1's various activities on DNA.
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36
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Nguyen JHG, Viterbo D, Anand RP, Verra L, Sloan L, Richard GF, Freudenreich CH. Differential requirement of Srs2 helicase and Rad51 displacement activities in replication of hairpin-forming CAG/CTG repeats. Nucleic Acids Res 2017; 45:4519-4531. [PMID: 28175398 PMCID: PMC5416882 DOI: 10.1093/nar/gkx088] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 01/31/2017] [Indexed: 12/25/2022] Open
Abstract
Trinucleotide repeats are a source of genome instability, causing replication fork stalling, chromosome fragility, and impaired repair. Specialized helicases play an important role in unwinding DNA structures to maintain genome stability. The Srs2 helicase unwinds DNA hairpins, facilitates replication, and prevents repeat instability and fragility. However, since Srs2 is a multifunctional protein with helicase activity and the ability to displace Rad51 recombinase, it was unclear which functions were required for its various protective roles. Here, using SRS2 separation-of-function alleles, we show that in the absence of Srs2 recruitment to PCNA or in helicase-deficient mutants, breakage at a CAG/CTG repeat increases. We conclude that Srs2 interaction with PCNA allows the helicase activity to unwind fork-blocking CAG/CTG hairpin structures to prevent breaks. Independently of PCNA binding, Srs2 also displaces Rad51 from nascent strands to prevent recombination-dependent repeat expansions and contractions. By 2D gel electrophoresis, we detect two different kinds of structured intermediates or joint molecules (JMs). Some JMs are Rad51-independent and exhibit properties of reversed forks, including being processed by the Exo1 nuclease. In addition, in a helicase-deficient mutant, Rad51-dependent JMs are detected, probably corresponding to recombination between sisters. These results clarify the many roles of Srs2 in facilitating replication through fork-blocking hairpin lesions.
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Affiliation(s)
| | - David Viterbo
- Institut Pasteur, Department Genomes & Genetics, CNRS, UMR3525, Université Pierre et Marie Curie, UFR927, 25 rue du Dr Roux, F-75015 Paris, France
| | - Ranjith P Anand
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Lauren Verra
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Laura Sloan
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Guy-Franck Richard
- Institut Pasteur, Department Genomes & Genetics, CNRS, UMR3525, Université Pierre et Marie Curie, UFR927, 25 rue du Dr Roux, F-75015 Paris, France
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37
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Niu H, Klein HL. Multifunctional roles of Saccharomyces cerevisiae Srs2 protein in replication, recombination and repair. FEMS Yeast Res 2017; 17:fow111. [PMID: 28011904 DOI: 10.1093/femsyr/fow111] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 12/22/2016] [Indexed: 11/12/2022] Open
Abstract
The Saccharomyces cerevisiae Srs2 DNA helicase has important roles in DNA replication, recombination and repair. In replication, Srs2 aids in repair of gaps by repair synthesis by preventing gaps from being used to initiate recombination. This is considered to be an anti-recombination role. In recombination, Srs2 plays both prorecombination and anti-recombination roles to promote the synthesis-dependent strand annealing recombination pathway and to inhibit gaps from initiating homologous recombination. In repair, the Srs2 helicase actively promotes gap repair through an interaction with the Exo1 nuclease to enlarge a gap for repair and to prevent Rad51 protein from accumulating on single-stranded DNA. Finally, Srs2 helicase can unwind hairpin-forming repeat sequences to promote replication and prevent repeat instability. The Srs2 activities can be controlled by phosphorylation, SUMO modification and interaction with key partners at DNA damage or lesions sites, which include PCNA and Rad51. These interactions can also limit DNA polymerase function during recombinational repair independent of the Srs2 translocase or helicase activity, further highlighting the importance of the Srs2 protein in regulating recombination. Here we review the myriad roles of Srs2 that have been documented in genome maintenance and distinguish between the translocase, helicase and additional functions of the Srs2 protein.
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Affiliation(s)
- Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Hannah L Klein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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38
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Abstract
In this review, we discuss how two evolutionarily conserved pathways at the interface of DNA replication and repair, template switching and break-induced replication, lead to the deleterious large-scale expansion of trinucleotide DNA repeats that cause numerous hereditary diseases. We highlight that these pathways, which originated in prokaryotes, may be subsequently hijacked to maintain long DNA microsatellites in eukaryotes. We suggest that the negative mutagenic outcomes of these pathways, exemplified by repeat expansion diseases, are likely outweighed by their positive role in maintaining functional repetitive regions of the genome such as telomeres and centromeres.
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Affiliation(s)
| | - Jane C Kim
- Department of Biological Sciences, California State University San Marcos, San Marcos, CA, USA
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Rowlands H, Dhavarasa P, Cheng A, Yankulov K. Forks on the Run: Can the Stalling of DNA Replication Promote Epigenetic Changes? Front Genet 2017; 8:86. [PMID: 28690636 PMCID: PMC5479891 DOI: 10.3389/fgene.2017.00086] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/06/2017] [Indexed: 11/13/2022] Open
Abstract
Built of DNA polymerases and multiple associated factors, the replication fork steadily progresses along the DNA template and faithfully replicates DNA. This model can be found in practically every textbook of genetics, with the more complex situation of chromatinized DNA in eukaryotes often viewed as a variation. However, the replication-coupled disassembly/reassembly of chromatin adds significant complexity to the whole replication process. During the course of eukaryotic DNA replication the forks encounter various conditions and numerous impediments. These include nucleosomes with a variety of post-translational modifications, euchromatin and heterochromatin, differentially methylated DNA, tightly bound proteins, active gene promoters and DNA loops. At such positions the forks slow down or even stall. Dedicated factors stabilize the fork and prevent its rotation or collapse, while other factors resolve the replication block and facilitate the resumption of elongation. The fate of histones during replication stalling and resumption is not well understood. In this review we briefly describe recent advances in our understanding of histone turnover during DNA replication and focus on the possible mechanisms of nucleosome disassembly/reassembly at paused replication forks. We propose that replication pausing provides opportunities for an epigenetic change of the associated locus.
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Affiliation(s)
- Hollie Rowlands
- Department of Molecular and Cellular Biology, University of Guelph, GuelphON, Canada
| | - Piriththiv Dhavarasa
- Department of Molecular and Cellular Biology, University of Guelph, GuelphON, Canada
| | - Ashley Cheng
- Department of Molecular and Cellular Biology, University of Guelph, GuelphON, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, GuelphON, Canada
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40
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Abstract
Eukaryotic genomes contain many repetitive DNA sequences that exhibit size instability. Some repeat elements have the added complication of being able to form secondary structures, such as hairpin loops, slipped DNA, triplex DNA or G-quadruplexes. Especially when repeat sequences are long, these DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks. In turn, repair or replication fork restart attempts within the repeat DNA can lead to addition or removal of repeat elements, which can sometimes lead to disease. One important DNA repair mechanism to maintain genomic integrity is recombination. Though early studies dismissed recombination as a mechanism driving repeat expansion and instability, recent results indicate that mitotic recombination is a key pathway operating within repetitive DNA. The action is two-fold: first, it is an important mechanism to repair nicks, gaps, breaks, or stalled forks to prevent chromosome fragility and protect cell health; second, recombination can cause repeat expansions or contractions, which can be deleterious. In this review, we summarize recent developments that illuminate the role of recombination in maintaining genome stability at DNA repeats.
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41
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Wyse B, Oshidari R, Rowlands H, Abbasi S, Yankulov K. RRM3 regulates epigenetic conversions in Saccharomyces cerevisiae in conjunction with Chromatin Assembly Factor I. Nucleus 2017; 7:405-14. [PMID: 27645054 DOI: 10.1080/19491034.2016.1212796] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Chromatin structures are transmitted to daughter cells through a complex system of nucleosome disassembly and re-assembly at the advancing replication forks. However, the role of replication pausing in the transmission and perturbation of chromatin structures has not been addressed. RRM3 encodes a DNA helicase, which facilitates replication at sites covered with non-histone protein complexes (tRNA genes, active gene promoters, telomeres) in Saccharomyces cerevisiae. In this report we show that the deletion of RRM3 reduces the frequency of epigenetic conversions in the subtelomeric regions of the chromosomes. This phenotype is strongly dependent on 2 histone chaperones, CAF-I and ASF1, which are involved in the reassembly of nucleosomes behind replication forks, but not on the histone chaperone HIR1. We also show that the deletion of RRM3 increases the spontaneous mutation rates in conjunction with CAF-I and ASF1, but not HIR1. Finally, we demonstrate that Rrm3p and CAF-I compete for the binding to the DNA replication clamp PCNA (Proliferating Cell Nuclear Antigen). We propose that the stalling of DNA replication predisposes to epigenetic conversions and that RRM3 and CAF-I play key roles in this process.
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Affiliation(s)
- Brandon Wyse
- a Department of Molecular and Cellular Biology , University of Guelph , Ontario , Canada
| | - Roxanne Oshidari
- a Department of Molecular and Cellular Biology , University of Guelph , Ontario , Canada
| | - Hollie Rowlands
- a Department of Molecular and Cellular Biology , University of Guelph , Ontario , Canada
| | - Sanna Abbasi
- a Department of Molecular and Cellular Biology , University of Guelph , Ontario , Canada
| | - Krassimir Yankulov
- a Department of Molecular and Cellular Biology , University of Guelph , Ontario , Canada
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42
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Effects of Replication and Transcription on DNA Structure-Related Genetic Instability. Genes (Basel) 2017; 8:genes8010017. [PMID: 28067787 PMCID: PMC5295012 DOI: 10.3390/genes8010017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/21/2016] [Accepted: 12/26/2016] [Indexed: 12/20/2022] Open
Abstract
Many repetitive sequences in the human genome can adopt conformations that differ from the canonical B-DNA double helix (i.e., non-B DNA), and can impact important biological processes such as DNA replication, transcription, recombination, telomere maintenance, viral integration, transposome activation, DNA damage and repair. Thus, non-B DNA-forming sequences have been implicated in genetic instability and disease development. In this article, we discuss the interactions of non-B DNA with the replication and/or transcription machinery, particularly in disease states (e.g., tumors) that can lead to an abnormal cellular environment, and how such interactions may alter DNA replication and transcription, leading to potential conflicts at non-B DNA regions, and eventually result in genetic stability and human disease.
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43
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Madireddy A, Gerhardt J. Replication Through Repetitive DNA Elements and Their Role in Human Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:549-581. [PMID: 29357073 DOI: 10.1007/978-981-10-6955-0_23] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human cells contain various repetitive DNA sequences, which can be a challenge for the DNA replication machinery to travel through and replicate correctly. Repetitive DNA sequence can adopt non-B DNA structures, which could block the DNA replication. Prolonged stalling of the replication fork at the endogenous repeats in human cells can have severe consequences such as genome instability that includes repeat expansions, contractions, and chromosome fragility. Several neurological and muscular diseases are caused by a repeat expansion. Furthermore genome instability is the major cause of cancer. This chapter describes some of the important classes of repetitive DNA sequences in the mammalian genome, their ability to form secondary DNA structures, their contribution to replication fork stalling, and models for repeat expansion as well as chromosomal fragility. Included in this chapter are also some of the strategies currently employed to detect changes in DNA replication and proteins that could prevent the repeat-mediated disruption of DNA replication in human cells. Additionally summarized are the consequences of repeat-associated perturbation of the DNA replication, which could lead to specific human diseases.
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Larcher MV, Pasquier E, MacDonald RS, Wellinger RJ. Ku Binding on Telomeres Occurs at Sites Distal from the Physical Chromosome Ends. PLoS Genet 2016; 12:e1006479. [PMID: 27930670 PMCID: PMC5145143 DOI: 10.1371/journal.pgen.1006479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 11/14/2016] [Indexed: 01/28/2023] Open
Abstract
The Ku complex binds non-specifically to DNA breaks and ensures repair via NHEJ. However, Ku is also known to bind directly to telomeric DNA ends and its presence there is associated with telomere capping, but avoiding NHEJ. How the complex discriminates between a DNA break and a telomeric extremity remains unknown. Our results using a tagged Ku complex, or a chromosome end capturing method, in budding yeast show that yKu association with telomeres can occur at sites distant from the physical end, on sub-telomeric elements, as well as on interstitial telomeric repeats. Consistent with previous studies, our results also show that yKu associates with telomeres in two distinct and independent ways: either via protein-protein interactions between Yku80 and Sir4 or via direct DNA binding. Importantly, yKu associates with the new sites reported here via both modes. Therefore, in sir4Δ cells, telomere bound yKu molecules must have loaded from a DNA-end near the transition of non-telomeric to telomeric repeat sequences. Such ends may have been one sided DNA breaks that occur as a consequence of stalled replication forks on or near telomeric repeat DNA. Altogether, the results predict a new model for yKu function at telomeres that involves yKu binding at one-sided DNA breaks caused by replication stalling. On telomere proximal chromatin, this binding is not followed by initiation of non-homologous end-joining, but rather by break-induced replication or repeat elongation by telomerase. After repair, the yKu-distal portion of telomeres is bound by Rap1, which in turn reduces the potential for yKu to mediate NHEJ. These results thus propose a solution to a long-standing conundrum, namely how to accommodate the apparently conflicting functions of Ku on telomeres. The Ku complex binds to and mediates the rejoining of two DNA ends that were generated by a double-stranded DNA break in the genome. However, Ku is known to be present at telomeres as well. If it would induce end-to-end joining there, it would create chromosome end-fusions that inevitably will lead to gross chromosome rearrangements and genome instability, common hallmarks for cancer initiation. Our results here show that Ku actually is associated with sites on telomeric regions that are distant from the physical ends of the chromosomes. We propose that this association serves to rescue DNA replication that has difficulty passing through telomeric chromatin. If so called one-sided breaks occur near or in telomeric repeats, they will generate critically short telomeres that need to be elongated. The binding of Ku may thus either facilitate the establishment of a specialized end-copying mechanism, called break induced replication or aid in recruiting telomerase to the short ends. These findings thus propose ways to potential solutions for the major conceptual problem that arose with the finding that Ku is associated with telomeres.
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Affiliation(s)
- Mélanie V. Larcher
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Emeline Pasquier
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - R. Stephen MacDonald
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Raymund J. Wellinger
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
- * E-mail:
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Beyer T, Weinert T. Ontogeny of Unstable Chromosomes Generated by Telomere Error in Budding Yeast. PLoS Genet 2016; 12:e1006345. [PMID: 27716774 PMCID: PMC5065131 DOI: 10.1371/journal.pgen.1006345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/07/2016] [Indexed: 11/19/2022] Open
Abstract
DNA replication errors at certain sites in the genome initiate chromosome instability that ultimately leads to stable genomic rearrangements. Where instability begins is often unclear. And, early instability may form unstable chromosome intermediates whose transient nature also hinders mechanistic understanding. We report here a budding yeast model that reveals the genetic ontogeny of genome rearrangements, from initial replication error to unstable chromosome formation to their resolution. Remarkably, the initial error often arises in or near the telomere, and frequently forms unstable chromosomes. Early unstable chromosomes may then resolve to an internal "collection site" where a dicentric forms and resolves to an isochromosome (other outcomes are possible at each step). The initial telomere-proximal unstable chromosome is increased in mutants in telomerase subunits, Tel1, and even Rad9, with no known telomere-specific function. Defects in Tel1 and in Rrm3, a checkpoint protein kinase with a role in telomere maintenance and a DNA helicase, respectively, synergize dramatically to generate unstable chromosomes, further illustrating the consequence of replication error in the telomere. Collectively, our results suggest telomeric replication errors may be a common cause of seemingly unrelated genomic rearrangements located hundreds of kilobases away.
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Affiliation(s)
- Tracey Beyer
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
| | - Ted Weinert
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
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Miller JRC, Lo KK, Andre R, Hensman Moss DJ, Träger U, Stone TC, Jones L, Holmans P, Plagnol V, Tabrizi SJ. RNA-Seq of Huntington's disease patient myeloid cells reveals innate transcriptional dysregulation associated with proinflammatory pathway activation. Hum Mol Genet 2016; 25:2893-2904. [PMID: 27170315 PMCID: PMC5181590 DOI: 10.1093/hmg/ddw142] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/03/2016] [Accepted: 05/03/2016] [Indexed: 12/21/2022] Open
Abstract
Innate immune activation beyond the central nervous system is emerging as a vital component of the pathogenesis of neurodegeneration. Huntington's disease (HD) is a fatal neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene. The systemic innate immune system is thought to act as a modifier of disease progression; however, the molecular mechanisms remain only partially understood. Here we use RNA-sequencing to perform whole transcriptome analysis of primary monocytes from thirty manifest HD patients and thirty-three control subjects, cultured with and without a proinflammatory stimulus. In contrast with previous studies that have required stimulation to elicit phenotypic abnormalities, we demonstrate significant transcriptional differences in HD monocytes in their basal, unstimulated state. This includes previously undetected increased resting expression of genes encoding numerous proinflammatory cytokines, such as IL6 Further pathway analysis revealed widespread resting enrichment of proinflammatory functional gene sets, while upstream regulator analysis coupled with Western blotting suggests that abnormal basal activation of the NFĸB pathway plays a key role in mediating these transcriptional changes. That HD myeloid cells have a proinflammatory phenotype in the absence of stimulation is consistent with a priming effect of mutant huntingtin, whereby basal dysfunction leads to an exaggerated inflammatory response once a stimulus is encountered. These data advance our understanding of mutant huntingtin pathogenesis, establish resting myeloid cells as a key source of HD immune dysfunction, and further demonstrate the importance of systemic immunity in the potential treatment of HD and the wider study of neurodegeneration.
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Affiliation(s)
- James R C Miller
- Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Kitty K Lo
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Ralph Andre
- Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Davina J Hensman Moss
- Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Ulrike Träger
- Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Timothy C Stone
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Vincent Plagnol
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Sarah J Tabrizi
- Department of Neurodegenerative Disease, UCL Institute of Neurology, University College London, London, WC1N 3BG, UK
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47
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Viterbo D, Michoud G, Mosbach V, Dujon B, Richard GF. Replication stalling and heteroduplex formation within CAG/CTG trinucleotide repeats by mismatch repair. DNA Repair (Amst) 2016; 42:94-106. [DOI: 10.1016/j.dnarep.2016.03.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/01/2016] [Accepted: 03/11/2016] [Indexed: 10/22/2022]
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Koc KN, Singh SP, Stodola JL, Burgers PM, Galletto R. Pif1 removes a Rap1-dependent barrier to the strand displacement activity of DNA polymerase δ. Nucleic Acids Res 2016; 44:3811-9. [PMID: 27001517 PMCID: PMC4856994 DOI: 10.1093/nar/gkw181] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 03/08/2016] [Indexed: 11/13/2022] Open
Abstract
Using an in vitro reconstituted system in this work we provide direct evidence that the yeast repressor/activator protein 1 (Rap1), tightly bound to its consensus site, forms a strong non-polar barrier for the strand displacement activity of DNA polymerase δ. We propose that relief of inhibition may be mediated by the activity of an accessory helicase. To this end, we show that Pif1, a 5'-3' helicase, not only stimulates the strand displacement activity of Pol δ but it also allows efficient replication through the block, by removing bound Rap1 in front of the polymerase. This stimulatory activity of Pif1 is not limited to the displacement of a single Rap1 molecule; Pif1 also allows Pol δ to carry out DNA synthesis across an array of bound Rap1 molecules that mimics a telomeric DNA-protein assembly. This activity of Pif1 represents a novel function of this helicase during DNA replication.
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Affiliation(s)
- Katrina N Koc
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Saurabh P Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Joseph L Stodola
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Peter M Burgers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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49
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Singh SP, Koc KN, Stodola JL, Galletto R. A Monomer of Pif1 Unwinds Double-Stranded DNA and It Is Regulated by the Nature of the Non-Translocating Strand at the 3'-End. J Mol Biol 2016; 428:1053-1067. [PMID: 26908222 DOI: 10.1016/j.jmb.2016.02.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/12/2016] [Accepted: 02/14/2016] [Indexed: 11/17/2022]
Abstract
Using a DNA polymerase coupled assay and FRET (Förster resonance energy transfer)-based helicase assays, in this work, we show that a monomer of Saccharomyces cerevisiae Pif1 can unwind dsDNA (double-stranded DNA). The helicase activity of a Pif1 monomer is modulated by the nature of the 3'-ssDNA (single-stranded DNA) tail of the substrate and its effect on a Pif1-dependent re-winding activity that is coupled to the opening of dsDNA. We propose that, in addition to the ssDNA site on the protein that interacts with the translocating strand, Pif1 has a second site that binds the 3'-ssDNA of the substrate. Interaction of DNA with this site modulates the degree to which re-winding counteracts unwinding. Depending on the nature of the 3'-tail and the length of the duplex DNA to be unwound, this activity is sufficiently strong to mask the helicase activity of a monomer. In excess Pif1 over the DNA, the Pif1-dependent re-winding of the opened DNA strongly limits unwinding, independent of the 3'-tail. We propose that, in this case, binding of DNA to the second site is precluded and modulation of the Pif1-dependent re-winding activity is largely lost.
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Affiliation(s)
- Saurabh P Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Katrina N Koc
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Joseph L Stodola
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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50
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Aksenova AY, Han G, Shishkin AA, Volkov KV, Mirkin SM. Expansion of Interstitial Telomeric Sequences in Yeast. Cell Rep 2015; 13:1545-51. [PMID: 26586439 DOI: 10.1016/j.celrep.2015.10.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 08/07/2015] [Accepted: 10/08/2015] [Indexed: 11/18/2022] Open
Abstract
Telomeric repeats located within chromosomes are called interstitial telomeric sequences (ITSs). They are polymorphic in length and are likely hotspots for initiation of chromosomal rearrangements that have been linked to human disease. Using our S. cerevisiae system to study repeat-mediated genome instability, we have previously shown that yeast telomeric (Ytel) repeats induce various gross chromosomal rearrangements (GCR) when their G-rich strands serve as the lagging strand template for replication (G orientation). Here, we show that interstitial Ytel repeats in the opposite C orientation prefer to expand rather than cause GCR. A tract of eight Ytel repeats expands at a rate of 4 × 10(-4) per replication, ranking them among the most expansion-prone DNA microsatellites. A candidate-based genetic analysis implicates both post-replication repair and homologous recombination pathways in the expansion process. We propose a model for Ytel repeat expansions and discuss its applications for genome instability and alternative telomere lengthening (ALT).
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Affiliation(s)
- Anna Y Aksenova
- Department of Biology, Tufts University, Medford, MA 02155, USA; Department of Genetics, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Gil Han
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | | | - Kirill V Volkov
- Department of Genetics, St. Petersburg State University, St. Petersburg 199034, Russia
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02155, USA.
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