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Messer CL, Fox DT. Broken chromosomes heading into mitosis: More than one way to patch a flat tire. J Cell Biol 2024; 223:e202401085. [PMID: 38477879 PMCID: PMC10937182 DOI: 10.1083/jcb.202401085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
A cell dealing with a broken chromosome in mitosis is like a driver dealing with a flat tire on the highway: damage repair must occur under non-ideal circumstances. Mitotic chromosome breaks encounter problems related to structures called micronuclei. These aberrant nuclei are linked to cell death, mutagenesis, and cancer. In the last few years, a flurry of studies illuminated two mechanisms that prevent mitotic problems related to micronuclei. One mechanism prevents micronuclei from forming during mitosis and involves DNA Polymerase Theta, a DNA repair regulator that patches up broken mitotic chromosomes. A second mechanism is activated after micronuclei form and then rupture, and involves CIP2A and TOPBP1 proteins, which patch micronuclear fragments to promote their subsequent mitotic segregation. Here, we review recent progress in this field of mitotic DNA damage and discuss why multiple mechanisms exist. Future studies in this exciting area will reveal new DNA break responses and inform therapeutic strategies.
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Affiliation(s)
- C. Luke Messer
- Department of Biology, St. Bonaventure University, St. Bonaventure, NY, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Donald T. Fox
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, USA
- Duke Regeneration Center, Duke University Medical Center, Durham, NC, USA
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
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2
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Perea J, García JL, Corchete LA, Martí M, Hernández-Villafranca S, Alcázar JA, Álvaro E, Hurtado E, Jiménez-Toscano M, Balaguer F, Ballestero A, López-Rojo I, Jiménez F, Sanz G, Melone S, Brandáriz L, Vivas A, Alvarellos A, González-Sarmiento R. Chromosomal breaks: another differential gap between early-onset and late-onset colorectal cancers. Br J Surg 2024; 111:znae041. [PMID: 38430195 DOI: 10.1093/bjs/znae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 03/03/2024]
Affiliation(s)
- José Perea
- Molecular Medicine Unit-Department of Medicine, Institute of Biomedical Research of Salamanca (IBSAL) and Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-SACYL-CSIC, Salamanca, Spain
- Surgery Department, Vithas Arturo Soria Hospital, Madrid, Spain
| | - Juan Luis García
- Molecular Medicine Unit-Department of Medicine, Institute of Biomedical Research of Salamanca (IBSAL) and Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-SACYL-CSIC, Salamanca, Spain
| | - Luis A Corchete
- Haematology Department, University Hospital of Salamanca, Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
- Cancer Research Centre-IBMCC (USAL-CSIC), Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Marc Martí
- Colorectal Unit, Vall d'Hebrón University Hospital, Barcelona, Spain
| | | | - José A Alcázar
- Surgery Department, Clinic University Hospital, Salamanca, Spain
| | - Edurne Álvaro
- Surgery Department, Infanta Leonor University Hospital, Madrid, Spain
| | - Elena Hurtado
- Surgery Department, Gregorio Marañon University Hospital, Madrid, Spain
| | | | - Francesc Balaguer
- Gastroenterology Department, Clinic University Hospital, Barcelona, Spain
| | | | - Irene López-Rojo
- Surgery Department, MD Anderson Cancer Center Madrid, Madrid, Spain
| | | | - Gonzalo Sanz
- Surgery Department, San Carlos University Hospital, Madrid, Spain
| | - Sirio Melone
- Surgery Department, Alcorcon Foundation Hospital, Madrid, Spain
| | | | - Alfredo Vivas
- Surgery Department, 12 de Octubre University Hospital, Madrid, Spain
| | - Alicia Alvarellos
- Surgery Department, University Clinic of Navarra-Madrid, Madrid, Spain
| | - Rogelio González-Sarmiento
- Molecular Medicine Unit-Department of Medicine, Institute of Biomedical Research of Salamanca (IBSAL) and Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-SACYL-CSIC, Salamanca, Spain
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Manohar S, Gofin Y, Streff H, Vossaert L, Camacho P, Murali CN. A familial deletion of 10p12.1 associated with thrombocytopenia. Am J Med Genet A 2024; 194:77-81. [PMID: 37746810 DOI: 10.1002/ajmg.a.63403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 08/23/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023]
Abstract
Thrombocytopenia can be inherited or acquired from a variety of causes. While hereditary causes of thrombocytopenia are rare, several genes have been associated with the condition. In this report, we describe an 18-year-old man and his mother, both of whom have congenital thrombocytopenia. Exome sequencing in the man revealed a 1006 kb maternally inherited deletion in the 10p12.1 region (arr[GRCh37] 10p12.1(27378928_28384564)x1) of uncertain clinical significance. This deletion in the THC2 locus includes genes ANKRD26, known to be involved in normal megakaryocyte differentiation, and MASTL, which some studies suggest is linked to autosomal dominant thrombocytopenia. In the family presented here, the deletion segregated with the congenital thrombocytopenia phenotype, suggesting that haploinsufficiency of one or both genes may be the cause. To our knowledge, this is the first report of a deletion of the THC2 locus associated with thrombocytopenia. Future functional studies of deletions of the THC2 locus may elucidate the mechanism for this phenotype observed clinically.
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Affiliation(s)
- Sujal Manohar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Yoel Gofin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Pamela Camacho
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Cancer and Hematology Centers, Houston, Texas, USA
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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4
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Petsalaki E, Balafouti S, Kyriazi AA, Zachos G. The abscission checkpoint senses chromatin bridges through Top2α recruitment to DNA knots. J Cell Biol 2023; 222:e202303123. [PMID: 37638884 PMCID: PMC10461104 DOI: 10.1083/jcb.202303123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/13/2023] [Accepted: 08/10/2023] [Indexed: 08/29/2023] Open
Abstract
In response to chromatin bridges, the abscission checkpoint delays completion of cytokinesis to prevent chromosome breakage or tetraploidization. Here, we show that spontaneous or replication stress-induced chromatin bridges exhibit "knots" of catenated and overtwisted DNA next to the midbody. Topoisomerase IIα (Top2α) forms abortive Top2-DNA cleavage complexes (Top2ccs) on DNA knots; furthermore, impaired Top2α-DNA cleavage activity correlates with chromatin bridge breakage in cytokinesis. Proteasomal degradation of Top2ccs is required for Rad17 localization to Top2-generated double-strand DNA ends on DNA knots; in turn, Rad17 promotes local recruitment of the MRN complex and downstream ATM-Chk2-INCENP signaling to delay abscission and prevent chromatin breakage. In contrast, dicentric chromosomes that do not exhibit knotted DNA fail to activate the abscission checkpoint in human cells. These findings are the first to describe a mechanism by which the abscission checkpoint detects chromatin bridges, through generation of abortive Top2ccs on DNA knots, to preserve genome integrity.
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Affiliation(s)
- Eleni Petsalaki
- Department of Biology, University of Crete, Heraklion, Greece
| | - Sofia Balafouti
- Department of Biology, University of Crete, Heraklion, Greece
| | | | - George Zachos
- Department of Biology, University of Crete, Heraklion, Greece
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Li N, Hu DX, Qin X, Zhu YP, Zhou M, He L, Chang LX, Xu XJ, Dai Y, Cao XY, Chen K, Wang HM, Wang CJ, He YL, Qian XW, Xu LP, Chen J. [Diagnosis status and genetic characteristics analysis of Fanconi anemia in China]. Zhonghua Er Ke Za Zhi 2023; 61:889-895. [PMID: 37803855 DOI: 10.3760/cma.j.cn112140-20230606-00383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 10/08/2023]
Abstract
Objective: To analyze the clinical and molecular diagnostic status of Fanconi anemia (FA) in China. Methods: The General situation, clinical manifestations and chromosome breakage test and genetic test results of 107 pediatric FA cases registered in the Chinese Blood and Marrow Transplantation Registry Group (CBMTRG) and the Chinese Children Blood and Marrow Transplantation Registry Group (CCBMTRG) from August 2009 to January 2022 were analyzed retrospectively. Children with FANCA gene variants were divided into mild and severe groups based on the type of variant, and Wilcoxon-test was used to compare the phenotypic differences between groups. Results: Of the 176 registered FA patients, 69 (39.2%) cases were excluded due to lack of definitive genetic diagnosis results, and the remaining 107 children from 15 hospitals were included in the study, including 70 males and 37 females. The age at transplantation treatment were 6 (4, 9) years. The enrolled children were involved in 10 pathogenic genes, including 89 cases of FANCA gene, 7 cases of FANCG gene, 3 cases of FANCB gene, 2 cases of FANCE gene and 1 case each of FANCC, FANCD1, FANCD2, FANCF, FANCJ, and FANCN gene. Compound heterozygous or homozygous of loss-of-function variants account for 69.2% (72/104). Loss-of-function variants account for 79.2% (141/178) in FANCA gene variants, and 20.8% (37/178) were large exon deletions. Fifty-five children (51.4%) had chromosome breakage test records, with a positive rate of 81.8% (45/55). There were 172 congenital malformations in 80 children.Café-au-Lait spots (16.3%, 28/172), thumb deformities (16.3%,28/172), polydactyly (13.9%, 24/172), and short stature (12.2%, 21/172) were the most common congenital malformations in Chinese children with FA. No significant difference was found in the number of congenital malformations between children with severe (50 cases) and mild FANCA variants (26 cases) (Z=-1.33, P=0.185). Conclusions: FANCA gene is the main pathogenic gene in children with FA, where the detection of its exon deletion should be strengthened clinically. There were no phenotypic differences among children with different types of FANCA variants. Chromosome break test is helpful to determine the pathogenicity of variants, but its accuracy needs to be improved.
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Affiliation(s)
- N Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - D X Hu
- Department of Hematology, Children's Hospital of Soochow University,Suzhou 215000, China
| | - X Qin
- Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Y P Zhu
- Department of Pediatrics, West China Second University Hospital of Sichuan University, Chengdu 610041, China
| | - M Zhou
- Department of Hematology, Guangzhou First People's Hospital, Guangzhou 510030, China
| | - L He
- Nanfang-Chunfu Children's Institute of Hematology & Oncology, Dongguan 523000, China
| | - L X Chang
- Department of Pediatrics, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjing 300020, China
| | - X J Xu
- Department of Hematology and Oncology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Y Dai
- Department of Pediatrics, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, China
| | - X Y Cao
- Department of Transplantation, Hebei Yanda Ludaopei Hospital, Langfang, 065201, China
| | - K Chen
- Department of Hematology and Oncology, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200040, China
| | - H M Wang
- Department of Pediatrics, the First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | - C J Wang
- Department of Hematology, Shenzhen Children's Hospital, Shenzhen 518028, China
| | - Y L He
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - X W Qian
- Department of Hematology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - L P Xu
- Department of Hematology, Peking University People's Hospital, Beijing 100044, China
| | - J Chen
- Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
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Serrano‐Benitez A, Wells SE, Drummond‐Clarke L, Russo LC, Thomas JC, Leal GA, Farrow M, Edgerton JM, Balasubramanian S, Yang M, Frezza C, Gautam A, Brazina J, Burdova K, Hoch NC, Jackson SP, Caldecott KW. Unrepaired base excision repair intermediates in template DNA strands trigger replication fork collapse and PARP inhibitor sensitivity. EMBO J 2023; 42:e113190. [PMID: 37492888 PMCID: PMC10505916 DOI: 10.15252/embj.2022113190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 05/17/2023] [Accepted: 07/07/2023] [Indexed: 07/27/2023] Open
Abstract
DNA single-strand breaks (SSBs) disrupt DNA replication and induce chromosome breakage. However, whether SSBs induce chromosome breakage when present behind replication forks or ahead of replication forks is unclear. To address this question, we exploited an exquisite sensitivity of SSB repair-defective human cells lacking PARP activity or XRCC1 to the thymidine analogue 5-chloro-2'-deoxyuridine (CldU). We show that incubation with CldU in these cells results in chromosome breakage, sister chromatid exchange, and cytotoxicity by a mechanism that depends on the S phase activity of uracil DNA glycosylase (UNG). Importantly, we show that CldU incorporation in one cell cycle is cytotoxic only during the following cell cycle, when it is present in template DNA. In agreement with this, while UNG induces SSBs both in nascent strands behind replication forks and in template strands ahead of replication forks, only the latter trigger fork collapse and chromosome breakage. Finally, we show that BRCA-defective cells are hypersensitive to CldU, either alone and/or in combination with PARP inhibitor, suggesting that CldU may have clinical utility.
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Affiliation(s)
- Almudena Serrano‐Benitez
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- The Wellcome and Cancer Research UK Gurdon Institute and Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Sophie E Wells
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Lylah Drummond‐Clarke
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Lilian C Russo
- Departament of Biochemistry, Chemistry InstituteUniversity of São PauloSão PauloBrazil
| | - John Christopher Thomas
- The Wellcome and Cancer Research UK Gurdon Institute and Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Giovanna A Leal
- Departament of Biochemistry, Chemistry InstituteUniversity of São PauloSão PauloBrazil
| | - Mark Farrow
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | | | - Shankar Balasubramanian
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Yusuf Hamied Department of ChemistryUniversity of CambridgeCambridgeUK
| | - Ming Yang
- CECAD Research Center, Faculty of MedicineUniversity Hospital CologneCologneGermany
| | - Christian Frezza
- CECAD Research Center, Faculty of MedicineUniversity Hospital CologneCologneGermany
| | - Amit Gautam
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Jan Brazina
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Kamila Burdova
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
| | - Nicolas C Hoch
- Departament of Biochemistry, Chemistry InstituteUniversity of São PauloSão PauloBrazil
| | - Stephen P Jackson
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- The Wellcome and Cancer Research UK Gurdon Institute and Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life SciencesUniversity of SussexFalmerUK
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Zagnoli-Vieira G, Brazina J, Van Den Bogaert K, Huybrechts W, Molenaers G, Caldecott KW, Van Esch H. Inactivating TDP2 missense mutation in siblings with congenital abnormalities reminiscent of fanconi anemia. Hum Genet 2023; 142:1417-1427. [PMID: 37558815 PMCID: PMC10449949 DOI: 10.1007/s00439-023-02589-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/15/2023] [Indexed: 08/11/2023]
Abstract
Mutations in TDP2, encoding tyrosyl-DNA phosphodiesterase 2, have been associated with a syndromal form of autosomal recessive spinocerebellar ataxia, type 23 (SCAR23). This is a very rare and progressive neurodegenerative disorder described in only nine patients to date, and caused by splice site or nonsense mutations that result in greatly reduced or absent TDP2 protein. TDP2 is required for the rapid repair of DNA double-strand breaks induced by abortive DNA topoisomerase II (TOP2) activity, important for genetic stability in post-mitotic cells such as neurons. Here, we describe a sibship that is homozygous for the first TDP2 missense mutation (p.Glu152Lys) and which presents with clinical features overlapping both SCAR23 and Fanconi anemia (FA). We show that in contrast to previously reported SCAR23 patients, fibroblasts derived from the current patient retain significant levels of TDP2 protein. However, this protein is catalytically inactive, resulting in reduced rates of repair of TOP2-induced DNA double-strand breaks and cellular hypersensitivity to the TOP2 poison, etoposide. The TDP2-mutated patient-derived fibroblasts do not display increased chromosome breakage following treatment with DNA crosslinking agents, but both TDP2-mutated and FA cells exhibit increased chromosome breakage in response to etoposide. This suggests that the FA pathway is required in response to TOP2-induced DNA lesions, providing a possible explanation for the clinical overlap between FA and the current TDP2-mutated patients. When reviewing the relatively small number of patients with SCAR23 that have been reported, it is clear that the phenotype of such patients can extend beyond neurological features, indicating that the TDP2 protein influences not only neural homeostasis but also other tissues as well.
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Affiliation(s)
- Guido Zagnoli-Vieira
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK.
| | - Jan Brazina
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Wim Huybrechts
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Guy Molenaers
- Pediatric Orthopedics, Department of Orthopedics, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, Herestraat 49, 3000, Louvain, Belgium.
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Florsheim N, Naugolni L, Zahdeh F, Lobel O, Terespolsky B, Michaelson-Cohen R, Gold MY, Goldberg M, Renbaum P, Levy-Lahad E, Zangen D. Loss of function of FIGNL1, a DNA damage response gene, causes human ovarian dysgenesis. Eur J Endocrinol 2023; 189:K7-K14. [PMID: 37740949 DOI: 10.1093/ejendo/lvad127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/18/2023] [Accepted: 08/14/2023] [Indexed: 09/25/2023]
Abstract
Ovarian dysgenesis (OD), an XX disorder of sex development, presents with primary amenorrhea, hypergonadotrophic hypogonadism, and infertility. In an Ashkenazi Jewish patient with OD, whole exome sequencing identified compound heterozygous frameshifts in FIGNL1, a DNA damage response (DDR) gene: c.189del and c.1519_1523del. Chromosomal breakage was significantly increased in patient cells, both spontaneously, and following mitomycin C exposure. Transfection of DYK-tagged FIGNL1 constructs in HEK293 cells showed no detectable protein in FIGNL1c.189del and truncation with reduced expression in FIGNL1c.1519_1523del (64% of wild-type [WT], P = .003). FIGNL1 forms nuclear foci increased by phleomycin treatment (20.6 ± 1.6 vs 14.8 ± 2.4, P = .02). However, mutant constructs showed reduced DYK-FIGNL1 foci formation in non-treated cells (0.8 ± 0.9 and 5.6 ± 1.5 vs 14.8 ± 2.4 in DYK-FIGNL1WT, P < .001) and no increase with phleomycin treatment. In conclusion, FIGNL1 loss of function is a newly characterized OD gene, highlighting the DDR pathway's role in ovarian development and maintenance and suggesting chromosomal breakage as an assessment tool in XX-DSD patients.
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Affiliation(s)
- Natan Florsheim
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Division of Pediatric Endocrinology, Hadassah Medical Center, Jerusalem, Israel
| | - Larisa Naugolni
- Pediatric Endocrinology and Diabetes Institute, Shamir Medical Center, Zerifin, Israel
| | - Fouad Zahdeh
- Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Orit Lobel
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Batel Terespolsky
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Rachel Michaelson-Cohen
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Obstetrics and Gynecology, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Merav Y Gold
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Goldberg
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Paul Renbaum
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Zangen
- Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- Division of Pediatric Endocrinology, Hadassah Medical Center, Jerusalem, Israel
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9
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Hill HJ, Bonser D, Golic KG. Dicentric chromosome breakage in Drosophila melanogaster is influenced by pericentric heterochromatin and occurs in nonconserved hotspots. Genetics 2023; 224:iyad052. [PMID: 37010100 PMCID: PMC10213500 DOI: 10.1093/genetics/iyad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/18/2022] [Accepted: 03/13/2023] [Indexed: 04/04/2023] Open
Abstract
Chromosome breakage plays an important role in the evolution of karyotypes and can produce deleterious effects within a single individual, such as aneuploidy or cancer. Forces that influence how and where chromosomes break are not fully understood. In humans, breakage tends to occur in conserved hotspots called common fragile sites (CFS), especially during replication stress. By following the fate of dicentric chromosomes in Drosophila melanogaster, we find that breakage under tension also tends to occur in specific hotspots. Our experimental approach was to induce sister chromatid exchange in a ring chromosome to generate a dicentric chromosome with a double chromatid bridge. In the following cell division, the dicentric bridges may break. We analyzed the breakage patterns of 3 different ring-X chromosomes. These chromosomes differ by the amount and quality of heterochromatin they carry as well as their genealogical history. For all 3 chromosomes, breakage occurs preferentially in several hotspots. Surprisingly, we found that the hotspot locations are not conserved between the 3 chromosomes: each displays a unique array of breakage hotspots. The lack of hotspot conservation, along with a lack of response to aphidicolin, suggests that these breakage sites are not entirely analogous to CFS and may reveal new mechanisms of chromosome fragility. Additionally, the frequency of dicentric breakage and the durability of each chromosome's spindle attachment vary significantly between the 3 chromosomes and are correlated with the origin of the centromere and the amount of pericentric heterochromatin. We suggest that different centromere strengths could account for this.
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Affiliation(s)
- Hunter J Hill
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Danielle Bonser
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Kent G Golic
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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10
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Rossnerova A, Elzeinova F, Chvojkova I, Honkova K, Sima M, Milcova A, Pastorkova A, Schmuczerova J, Rossner P, Topinka J, Sram RJ. Effects of various environments on epigenetic settings and chromosomal damage. Environ Pollut 2023; 323:121290. [PMID: 36804881 DOI: 10.1016/j.envpol.2023.121290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 02/10/2023] [Accepted: 02/12/2023] [Indexed: 06/18/2023]
Abstract
Air pollution is a dominant environmental exposure factor with significant health consequences. Unexpectedly, research in a heavily polluted region of the Czech Republic, with traditional heavy industry, revealed repeatedly the lowest frequency of micronuclei in the season with the highest concentrations of air pollutants including carcinogenic benzo[a]pyrene (B[a]P). Molecular findings have been collected for more than 10 years from various locations of the Czech Republic, with differing quality of ambient air. Preliminary conclusions have suggested adaptation of the population from the polluted locality (Ostrava, Moravian-Silesian Region (MSR)) to chronic air pollution exposure. In this study we utilize the previous findings and, for the first time, investigate micronuclei (MN) frequency by type: (i) centromere positive (CEN+) MN, representing chromosomal losses, and (ii) centromere negative (CEN-) MN representing chromosomal breaks. As previous results indicated differences between populations in the expression of XRCC5, a gene involved in the non-homologous end-joining (NHEJ) repair pathway, possible variations in epigenetic settings in this gene were also investigated. This new research was conducted in two seasons in the groups from two localities with different air quality levels (Ostrava (OS) and Prague (PG)). The obtained new results show significantly lower frequencies of chromosomal breaks in the OS subjects, related to the highest air pollution levels (p < 0.001). In contrast, chromosomal losses were comparable between both groups. In addition, significantly lower DNA methylation was found in 14.3% of the analyzed CpG loci of XRCC5 in the population from OS. In conclusion, the epigenetic adaptation (hypomethylation) in XRCC5 involved in the NHEJ repair pathway in the population from the polluted region, was suggested as a reason for the reduced level of chromosomal breaks. Further research is needed to explore the additional mechanisms, including genetic adaptation.
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Affiliation(s)
- Andrea Rossnerova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20, Prague 4, Czech Republic; Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20, Prague 4, Czech Republic.
| | - Fatima Elzeinova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20, Prague 4, Czech Republic.
| | - Irena Chvojkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20, Prague 4, Czech Republic.
| | - Katerina Honkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20, Prague 4, Czech Republic.
| | - Michal Sima
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20, Prague 4, Czech Republic.
| | - Alena Milcova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20, Prague 4, Czech Republic.
| | - Anna Pastorkova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20, Prague 4, Czech Republic.
| | - Jana Schmuczerova
- Department of Medical Genetics, L. Pasteur University Hospital, Trieda SNP 1, 040 11, Kosice, Slovakia.
| | - Pavel Rossner
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20, Prague 4, Czech Republic.
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20, Prague 4, Czech Republic.
| | - Radim J Sram
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20, Prague 4, Czech Republic.
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11
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Li JSZ, Abbasi A, Kim DH, Lippman SM, Alexandrov LB, Cleveland DW. Chromosomal fragile site breakage by EBV-encoded EBNA1 at clustered repeats. Nature 2023; 616:504-509. [PMID: 37046091 PMCID: PMC10328181 DOI: 10.1038/s41586-023-05923-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 03/07/2023] [Indexed: 04/14/2023]
Abstract
Epstein-Barr virus (EBV) is an oncogenic herpesvirus associated with several cancers of lymphocytic and epithelial origin1-3. EBV encodes EBNA1, which binds to a cluster of 20 copies of an 18-base-pair palindromic sequence in the EBV genome4-6. EBNA1 also associates with host chromosomes at non-sequence-specific sites7, thereby enabling viral persistence. Here we show that the sequence-specific DNA-binding domain of EBNA1 binds to a cluster of tandemly repeated copies of an EBV-like, 18-base-pair imperfect palindromic sequence encompassing a region of about 21 kilobases at human chromosome 11q23. In situ visualization of the repetitive EBNA1-binding site reveals aberrant structures on mitotic chromosomes characteristic of inherently fragile DNA. We demonstrate that increasing levels of EBNA1 binding trigger dose-dependent breakage at 11q23, producing a fusogenic centromere-containing fragment and an acentric distal fragment, with both mis-segregated into micronuclei in the next cell cycles. In cells latently infected with EBV, elevating EBNA1 abundance by as little as twofold was sufficient to trigger breakage at 11q23. Examination of whole-genome sequencing of EBV-associated nasopharyngeal carcinomas revealed that structural variants are highly enriched on chromosome 11. Presence of EBV is also shown to be associated with an enrichment of chromosome 11 rearrangements across 2,439 tumours from 38 cancer types. Our results identify a previously unappreciated link between EBV and genomic instability, wherein EBNA1-induced breakage at 11q23 triggers acquisition of structural variations in chromosome 11.
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MESH Headings
- Humans
- Binding Sites
- DNA/chemistry
- DNA/metabolism
- Herpesvirus 4, Human/genetics
- Herpesvirus 4, Human/metabolism
- Herpesvirus 4, Human/pathogenicity
- Viral Proteins/genetics
- Viral Proteins/metabolism
- DNA Breaks, Double-Stranded
- Chromosomes, Human, Pair 11/chemistry
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 11/metabolism
- Genomic Instability
- Mitosis
- Chromosome Breakage
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Affiliation(s)
- Julia Su Zhou Li
- Ludwig Cancer Research, UC San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
| | - Ammal Abbasi
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Dong Hyun Kim
- Ludwig Cancer Research, UC San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Oncology Research Unit, Pfizer Inc., San Diego, CA, USA
| | | | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
- Department of Bioengineering, UC San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Ludwig Cancer Research, UC San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA.
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12
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Trost H, Merkell A, Lopezcolorado FW, Stark J. Resolution of sequence divergence for repeat-mediated deletions shows a polarity that is mediated by MLH1. Nucleic Acids Res 2023; 51:650-667. [PMID: 36620890 PMCID: PMC9881173 DOI: 10.1093/nar/gkac1240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/07/2022] [Accepted: 01/04/2023] [Indexed: 01/10/2023] Open
Abstract
Repeat-mediated deletions (RMDs) are a type of chromosomal rearrangement between two homologous sequences that causes loss of the sequence between the repeats, along with one of the repeats. Sequence divergence between repeats suppresses RMDs; the mechanisms of such suppression and of resolution of the sequence divergence remains poorly understood. We identified RMD regulators using a set of reporter assays in mouse cells that test two key parameters: repeat sequence divergence and the distances between one repeat and the initiating chromosomal break. We found that the mismatch repair factor MLH1 suppresses RMDs with sequence divergence in the same pathway as MSH2 and MSH6, and which is dependent on residues in MLH1 and its binding partner PMS2 that are important for nuclease activity. Additionally, we found that the resolution of sequence divergence in the RMD product has a specific polarity, where divergent bases that are proximal to the chromosomal break end are preferentially removed. Moreover, we found that the domain of MLH1 that forms part of the MLH1-PMS2 endonuclease is important for polarity of resolution of sequence divergence. We also identified distinctions between MLH1 versus TOP3α in regulation of RMDs. We suggest that MLH1 suppresses RMDs with sequence divergence, while also promoting directional resolution of sequence divergence in the RMD product.
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Affiliation(s)
- Hannah Trost
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Arianna Merkell
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | - Jeremy M Stark
- To whom correspondence should be addressed. Tel: +1 626 218-6346; Fax: +1 626 218 8892;
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13
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Cisneros-Aguirre M, Ping X, Stark JM. To indel or not to indel: Factors influencing mutagenesis during chromosomal break end joining. DNA Repair (Amst) 2022; 118:103380. [PMID: 35926296 PMCID: PMC10105512 DOI: 10.1016/j.dnarep.2022.103380] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 12/16/2022]
Abstract
Chromosomal DNA double-strand breaks (DSBs) are the effective lesion of radiotherapy and other clastogenic cancer therapeutics, and are also the initiating event of many approaches to gene editing. Ligation of the DSBs by end joining (EJ) pathways can restore the broken chromosome, but the repair junctions can have insertion/deletion (indel) mutations. The indel patterns resulting from DSB EJ are likely defined by the initial structure of the DNA ends, how the ends are processed and synapsed prior to ligation, and the factors that mediate the ligation step. In this review, we describe key factors that influence these steps of DSB EJ in mammalian cells, which is significant both for understanding mutagenesis resulting from clastogenic cancer therapeutics, and for developing approaches to manipulating gene editing outcomes.
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Affiliation(s)
- Metztli Cisneros-Aguirre
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Xiaoli Ping
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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14
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Palazzo A, Piccolo I, Minervini CF, Purgato S, Capozzi O, D'Addabbo P, Cumbo C, Albano F, Rocchi M, Catacchio CR. Genome characterization and CRISPR-Cas9 editing of a human neocentromere. Chromosoma 2022; 131:239-251. [PMID: 35978051 DOI: 10.1007/s00412-022-00779-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/20/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022]
Abstract
The maintenance of genome integrity is ensured by proper chromosome inheritance during mitotic and meiotic cell divisions. The chromosomal counterpart responsible for chromosome segregation to daughter cells is the centromere, at which the spindle apparatus attaches through the kinetochore. Although all mammalian centromeres are primarily composed of megabase-long repetitive sequences, satellite-free human neocentromeres have been described. Neocentromeres and evolutionary new centromeres have revolutionized traditional knowledge about centromeres. Over the past 20 years, insights have been gained into their organization, but in spite of these advancements, the mechanisms underlying their formation and evolution are still unclear. Today, through modern and increasingly accessible genome editing and long-read sequencing techniques, research in this area is undergoing a sudden acceleration. In this article, we describe the primary sequence of a previously described human chromosome 3 neocentromere and observe its possible evolution and repair results after a chromosome breakage induced through CRISPR-Cas9 technologies. Our data represent an exciting advancement in the field of centromere/neocentromere evolution and chromosome stability.
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Affiliation(s)
- Antonio Palazzo
- Department of Biology, University of Bari Aldo Moro, Bari, Italy.
| | - Ilaria Piccolo
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Crescenzio Francesco Minervini
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology and Stem Cell Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Stefania Purgato
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Oronzo Capozzi
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Pietro D'Addabbo
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Cosimo Cumbo
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology and Stem Cell Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology and Stem Cell Transplantation Unit, University of Bari Aldo Moro, Bari, Italy
| | - Mariano Rocchi
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
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15
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Zhang Z, An HH, Vege S, Hu T, Zhang S, Mosbruger T, Jayaraman P, Monos D, Westhoff CM, Chou ST. Accurate long-read sequencing allows assembly of the duplicated RHD and RHCE genes harboring variants relevant to blood transfusion. Am J Hum Genet 2022; 109:180-191. [PMID: 34968422 DOI: 10.1016/j.ajhg.2021.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/07/2021] [Indexed: 12/18/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have transformed medical genetics. However, short-read lengths pose a limitation on identification of structural variants, sequencing repetitive regions, phasing of distant nucleotide changes, and distinguishing highly homologous genomic regions. Long-read sequencing technologies may offer improvements in the characterization of genes that are currently difficult to assess. We used a combination of targeted DNA capture, long-read sequencing, and a customized bioinformatics pipeline to fully assemble the RH region, which harbors variation relevant to red cell donor-recipient mismatch, particularly among patients with sickle cell disease. RHD and RHCE are a pair of duplicated genes located within an ∼175 kb region on human chromosome 1 that have high sequence similarity and frequent structural variations. To achieve the assembly, we utilized palindrome repeats in PacBio SMRT reads to obtain consensus sequences of 2.1 to 2.9 kb average length with over 99% accuracy. We used these long consensus sequences to identify 771 assembly markers and to phase the RHD-RHCE region with high confidence. The dataset enabled direct linkage between coding and intronic variants, phasing of distant SNPs to determine RHD-RHCE haplotypes, and identification of known and novel structural variations along with the breakpoints. A limiting factor in phasing is the frequency of heterozygous assembly markers and therefore was most successful in samples from African Black individuals with increased heterogeneity at the RH locus. Overall, this approach allows RH genotyping and de novo assembly in an unbiased and comprehensive manner that is necessary to expand application of NGS technology to high-resolution RH typing.
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Affiliation(s)
- Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hyun Hyung An
- Division of Hematology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sunitha Vege
- Immunohematology and Genomics, New York Blood Center, New York, NY 11101, USA
| | - Taishan Hu
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shiping Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Timothy Mosbruger
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pushkala Jayaraman
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Dimitri Monos
- Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman Schools of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Connie M Westhoff
- Immunohematology and Genomics, New York Blood Center, New York, NY 11101, USA
| | - Stella T Chou
- Division of Hematology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Division of Transfusion Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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16
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Gaimster H, Winterhalter C, Koh A, Murray H. Visualizing the Replisome, Chromosome Breaks, and Replication Restart in Bacillus subtilis. Methods Mol Biol 2022; 2476:263-276. [PMID: 35635709 DOI: 10.1007/978-1-0716-2221-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Research over the last two decades has revealed that bacterial genomes are highly organized and that bacteria have sophisticated mechanisms in place to ensure their correct replication and segregation into progeny cells. Here we discuss techniques that can be used with live bacterial cells to analyze DNA replisome dynamics, double-strand chromosome breaks, and restart of repaired replication forks.
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Affiliation(s)
- Hannah Gaimster
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Charles Winterhalter
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Alan Koh
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Heath Murray
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
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17
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Clay DE, Bretscher HS, Jezuit EA, Bush KB, Fox DT. Persistent DNA damage signaling and DNA polymerase theta promote broken chromosome segregation. J Cell Biol 2021; 220:e202106116. [PMID: 34613334 PMCID: PMC8500225 DOI: 10.1083/jcb.202106116] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/24/2021] [Accepted: 09/14/2021] [Indexed: 01/16/2023] Open
Abstract
Cycling cells must respond to DNA double-strand breaks (DSBs) to avoid genome instability. Missegregation of chromosomes with DSBs during mitosis results in micronuclei, aberrant structures linked to disease. How cells respond to DSBs during mitosis is incompletely understood. We previously showed that Drosophilamelanogaster papillar cells lack DSB checkpoints (as observed in many cancer cells). Here, we show that papillar cells still recruit early acting repair machinery (Mre11 and RPA3) and the Fanconi anemia (FA) protein Fancd2 to DSBs. These proteins persist as foci on DSBs as cells enter mitosis. Repair foci are resolved in a stepwise manner during mitosis. DSB repair kinetics depends on both monoubiquitination of Fancd2 and the alternative end-joining protein DNA polymerase θ. Disruption of either or both of these factors causes micronuclei after DNA damage, which disrupts intestinal organogenesis. This study reveals a mechanism for how cells with inactive DSB checkpoints can respond to DNA damage that persists into mitosis.
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Affiliation(s)
- Delisa E. Clay
- Department of Cell Biology, Duke University School of Medicine, Durham, NC
| | - Heidi S. Bretscher
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC
| | - Erin A. Jezuit
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC
| | - Korie B. Bush
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC
| | - Donald T. Fox
- Department of Cell Biology, Duke University School of Medicine, Durham, NC
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC
- University Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC
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18
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Gándara C, Torres R, Carrasco B, Ayora S, Alonso JC. DisA Restrains the Processing and Cleavage of Reversed Replication Forks by the RuvAB-RecU Resolvasome. Int J Mol Sci 2021; 22:11323. [PMID: 34768753 PMCID: PMC8583203 DOI: 10.3390/ijms222111323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/16/2021] [Indexed: 11/17/2022] Open
Abstract
DNA lesions that impede fork progression cause replisome stalling and threaten genome stability. Bacillus subtilis RecA, at a lesion-containing gap, interacts with and facilitates DisA pausing at these branched intermediates. Paused DisA suppresses its synthesis of the essential c-di-AMP messenger. The RuvAB-RecU resolvasome branch migrates and resolves formed Holliday junctions (HJ). We show that DisA prevents DNA degradation. DisA, which interacts with RuvB, binds branched structures, and reduces the RuvAB DNA-dependent ATPase activity. DisA pre-bound to HJ DNA limits RuvAB and RecU activities, but such inhibition does not occur if the RuvAB- or RecU-HJ DNA complexes are pre-formed. RuvAB or RecU pre-bound to HJ DNA strongly inhibits DisA-mediated synthesis of c-di-AMP, and indirectly blocks cell proliferation. We propose that DisA limits RuvAB-mediated fork remodeling and RecU-mediated HJ cleavage to provide time for damage removal and replication restart in order to preserve genome integrity.
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Affiliation(s)
| | | | | | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St, 28049 Madrid, Spain; (C.G.); (R.T.); (B.C.)
| | - Juan C. Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St, 28049 Madrid, Spain; (C.G.); (R.T.); (B.C.)
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19
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Liu D, Loh YHE, Hsieh CL, Lieber MR. Mechanistic basis for chromosomal translocations at the E2A gene and its broader relevance to human B cell malignancies. Cell Rep 2021; 36:109387. [PMID: 34260910 PMCID: PMC8327686 DOI: 10.1016/j.celrep.2021.109387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/31/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022] Open
Abstract
Analysis of translocation breakpoints in human B cell malignancies reveals that DNA double-strand breaks at oncogenes most frequently occur at CpG sites located within 20-600 bp fragile zones and depend on activation-induced deaminase (AID). AID requires single-stranded DNA (ssDNA) to act, but it has been unclear why or how this region transiently acquires a ssDNA state. Here, we demonstrate the ssDNA state in the 23 bp E2A fragile zone using several methods, including native bisulfite DNA structural analysis in live human pre-B cells. AID deamination within the E2A fragile zone does not require but is increased upon transcription. High C-string density, nascent RNA tails, and direct DNA sequence repeats prolong the ssDNA state of the E2A fragile zone and increase AID deamination at overlapping AID hotspots that contain the CpG sites at which breaks occur in patients. These features provide key insights into lymphoid fragile zones generally.
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Affiliation(s)
- Di Liu
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Yong-Hwee Eddie Loh
- USC Libraries Bioinformatics Services, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Chih-Lin Hsieh
- Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
| | - Michael R Lieber
- Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA.
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20
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Jo A, Li S, Shin JW, Zhao X, Cho Y. Structure Basis for Shaping the Nse4 Protein by the Nse1 and Nse3 Dimer within the Smc5/6 Complex. J Mol Biol 2021; 433:166910. [PMID: 33676928 PMCID: PMC8173833 DOI: 10.1016/j.jmb.2021.166910] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/01/2021] [Accepted: 02/23/2021] [Indexed: 12/01/2022]
Abstract
The Smc5/6 complex facilitates chromosome replication and DNA break repair. Within this complex, a subcomplex composed of Nse1, Nse3 and Nse4 is thought to play multiple roles through DNA binding and regulating ATP-dependent activities of the complex. However, how the Nse1-Nse3-Nse4 subcomplex carries out these multiple functions remain unclear. To address this question, we determine the crystal structure of the Xenopus laevis Nse1-Nse3-Nse4 subcomplex at 1.7 Å resolution and examine how it interacts with DNA. Our structural analyses show that the Nse1-Nse3 dimer adopts a closed conformation and forms three interfaces with a segment of Nse4, forcing it into a Z-shaped conformation. The Nse1-Nse3-Nse4 structure provides an explanation for how the lung disease immunodeficiency and chromosome breakage syndrome-causing mutations could dislodge Nse4 from Nse1-Nse3. Our DNA binding and mutational analyses reveal that the N-terminal and the middle region of Nse4 contribute to DNA interaction and cell viability. Integrating our data with previous crosslink mass spectrometry data, we propose potential roles of the Nse1-Nse3-Nse4 complex in binding DNA within the Smc5/6 complex.
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Affiliation(s)
- Aera Jo
- Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Shibai Li
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jin Woo Shin
- Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yunje Cho
- Department of Life Science, Pohang University of Science and Technology, Pohang, Republic of Korea.
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21
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van den Akker J, Hon L, Ondov A, Mahkovec Z, O'Connor R, Chan RC, Lock J, Zimmer AD, Rostamianfar A, Ginsberg J, Leon A, Topper S. Intronic Breakpoint Signatures Enhance Detection and Characterization of Clinically Relevant Germline Structural Variants. J Mol Diagn 2021; 23:612-629. [PMID: 33621668 DOI: 10.1016/j.jmoldx.2021.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/14/2020] [Accepted: 01/27/2021] [Indexed: 12/16/2022] Open
Abstract
The relevance of large copy number variants (CNVs) to hereditary disorders has been long recognized, and population sequencing efforts have chronicled many common structural variants (SVs). However, limited data are available on the clinical contribution of rare germline SVs. Here, a detailed characterization of SVs identified using targeted next-generation sequencing was performed. Across 50 genes associated with hereditary cancer and cardiovascular disorders, a minimum of 828 unique SVs were reported, including 584 fully characterized SVs. Almost 40% of CNVs were <5 kb, with one in three deletions impacting a single exon. Additionally, 36 mid-range deletions/duplications (50 to 250 bp), 21 mobile element insertions, 6 inversions, and 27 complex rearrangements were detected. This data set was used to model SV detection in a bioinformatics pipeline solely relying on read depth, which revealed that genome sequencing (30×) allows detection of 71%, a 500× panel only targeting coding regions 53%, and exome sequencing (100×) <20% of characterized SVs. SVs accounted for 14.1% of all unique pathogenic variants, supporting the importance of SVs in hereditary disorders. Robust SV detection requires an ensemble of variant-calling algorithms that utilize sequencing of intronic regions. These algorithms should use distinct data features representative of each class of mutational mechanism, including recombination between two sequences sharing high similarity, covariants inserted between CNV breakpoints, and complex rearrangements containing inverted sequences.
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22
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Shah A, George M, Dhangar S, Rajendran A, Mohan S, Vundinti BR. Severe telomere shortening in Fanconi anemia complementation group L. Mol Biol Rep 2021; 48:585-593. [PMID: 33394227 DOI: 10.1007/s11033-020-06101-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/16/2020] [Indexed: 01/18/2023]
Abstract
Fanconi Anemia (FA) is a rare genetic disease with the incidence of 1 in 360,000 and is characterised by bone marrow failure, physical abnormalities, pancytopenia, and high frequency of chromosomal breakage and increased risk of evolving into malignancy. Telomere plays an important role in genomic stability, ageing process and cancers. Telomere shortening has been reported in FA. We studied telomere length in FA subjects and compared with complementation groups. Chromosomal breakage analysis from PHA stimulated, MMC induced peripheral blood culture was carried out in 37 clinically diagnosed FA. Molecular study of FANCA, G, and L was done through Sanger sequencing and next generation sequencing. Telomere length was estimated using real time quantitative polymerase chain reaction (qPCR) method. Student t-test was applied to test the significance. A high frequency of chromosomal breakage was observed in all the patients compared to healthy controls. We found significantly shorter telomere length in all the three complementation groups compare to age matched healthy controls. Among all complementation groups, FANCL showed severe telomere shortening (P value 0.0001). A negative correlation was observed between telomere length and chromosomal breakage frequency (R = -0.3116). Telomere shortening is not uncommon in FA subjects. However the telomere length shortening is different in complementation groups as FANCL showed severe telomere shortening in FA subjects. Though BM transplantation is essential for the management of the FA subjects, the telomere length can be considered as biological marker to understand the prognosis of the disease as FA subjects primarily treated with androgens.
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Affiliation(s)
- Anjali Shah
- Department of Cytogenetics, ICMR-National Institute of Immunohematology, 13th floor, New Multistoried Building, K.E.M. Hospital Campus, Mumbai, Maharashtra, 400012, India
| | - Merin George
- Department of Cytogenetics, ICMR-National Institute of Immunohematology, 13th floor, New Multistoried Building, K.E.M. Hospital Campus, Mumbai, Maharashtra, 400012, India
| | - Somprakash Dhangar
- Department of Cytogenetics, ICMR-National Institute of Immunohematology, 13th floor, New Multistoried Building, K.E.M. Hospital Campus, Mumbai, Maharashtra, 400012, India
| | - Aruna Rajendran
- Department of Hematology, Institute of Child Health and Hospital for Children, Egmore, Chennai, Tamil Nadu, India
| | - Sheila Mohan
- Pediatric Haematology Department, Apollo Children's Hospital, Chennai, Tamil Nadu, India
| | - Babu Rao Vundinti
- Department of Cytogenetics, ICMR-National Institute of Immunohematology, 13th floor, New Multistoried Building, K.E.M. Hospital Campus, Mumbai, Maharashtra, 400012, India.
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23
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Zaksauskaite R, Thomas RC, van Eeden F, El-Khamisy SF. Tdp1 protects from topoisomerase 1-mediated chromosomal breaks in adult zebrafish but is dispensable during larval development. Sci Adv 2021; 7:7/5/eabc4165. [PMID: 33514542 PMCID: PMC7846158 DOI: 10.1126/sciadv.abc4165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Deficiency in the DNA end-processing enzyme, tyrosyl-DNA phosphodiesterase 1 (TDP1), causes progressive neurodegeneration in humans. Here, we generated a tdp1 knockout zebrafish and confirmed the lack of TDP1 activity. In adulthood, homozygotes exhibit hypersensitivity to topoisomerase 1 (Top1) poisons and a very mild locomotion defect. Unexpectedly, embryonic tdp1 -/- zebrafish were not hypersensitive to Top1 poisons and did not exhibit increased Top1-DNA breaks. This is in contrast to the hypersensitivity of Tdp1-deficient vertebrate models reported to date. Tdp1 is dispensable in the zebrafish embryo with transcript levels down-regulated in response to Top1-DNA damage. In contrast, apex2 and ercc4 (xpf) transcripts were up-regulated. These findings identify the tdp1-/- zebrafish embryo as the first vertebrate model that does not require Tdp1 to protect from Top1-DNA damage and identify apex2 and ercc4 (xpf) as putative players fulfilling this role. It highlights the requirement of distinct DNA repair factors across the life span of vertebrates.
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Affiliation(s)
- Ringaile Zaksauskaite
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Ruth C Thomas
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
- Bateson Centre, Department of Biomedical Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Freek van Eeden
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
- Bateson Centre, Department of Biomedical Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Sherif F El-Khamisy
- Healthy Lifespan Institute, Sheffield Institute for Neuroscience, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
- The Institute of Cancer Therapeutics, University of Bradford, Bradford BD7 1DP, UK
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24
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Macheret M, Bhowmick R, Sobkowiak K, Padayachy L, Mailler J, Hickson ID, Halazonetis TD. High-resolution mapping of mitotic DNA synthesis regions and common fragile sites in the human genome through direct sequencing. Cell Res 2020; 30:997-1008. [PMID: 32561860 PMCID: PMC7784693 DOI: 10.1038/s41422-020-0358-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/31/2020] [Indexed: 12/22/2022] Open
Abstract
DNA replication stress, a feature of human cancers, often leads to instability at specific genomic loci, such as the common fragile sites (CFSs). Cells experiencing DNA replication stress may also exhibit mitotic DNA synthesis (MiDAS). To understand the physiological function of MiDAS and its relationship to CFSs, we mapped, at high resolution, the genomic sites of MiDAS in cells treated with the DNA polymerase inhibitor aphidicolin. Sites of MiDAS were evident as well-defined peaks that were largely conserved between cell lines and encompassed all known CFSs. The MiDAS peaks mapped within large, transcribed, origin-poor genomic regions. In cells that had been treated with aphidicolin, these regions remained unreplicated even in late S phase; MiDAS then served to complete their replication after the cells entered mitosis. Interestingly, leading and lagging strand synthesis were uncoupled in MiDAS, consistent with MiDAS being a form of break-induced replication, a repair mechanism for collapsed DNA replication forks. Our results provide a better understanding of the mechanisms leading to genomic instability at CFSs and in cancer cells.
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Affiliation(s)
- Morgane Macheret
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Rahul Bhowmick
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Katarzyna Sobkowiak
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Laura Padayachy
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Jonathan Mailler
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark.
| | - Thanos D Halazonetis
- Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland.
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25
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Tsai L, Lopezcolorado F, Bhargava R, Mendez-Dorantes C, Jahanshir E, Stark J. RNF8 has both KU-dependent and independent roles in chromosomal break repair. Nucleic Acids Res 2020; 48:6032-6052. [PMID: 32427332 PMCID: PMC7293022 DOI: 10.1093/nar/gkaa380] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/10/2020] [Accepted: 04/30/2020] [Indexed: 12/19/2022] Open
Abstract
Chromosomal double strand breaks (DSBs) can initiate several signaling events, such as ubiquitination, however the precise influence of such signaling on DSB repair outcomes remains poorly understood. With an RNA interference screen, we found that the E3 ubiquitin ligase RNF8 suppresses a deletion rearrangement mediated by canonical non-homologous end joining (C-NHEJ). We also found that RNF8 suppresses EJ without insertion/deletion mutations, which is a hallmark of C-NHEJ. Conversely, RNF8 promotes alternative EJ (ALT-EJ) events involving microhomology that is embedded from the edge of the DSB. These ALT-EJ events likely require limited end resection, whereas RNF8 is not required for single-strand annealing repair involving extensive end resection. Thus, RNF8 appears to specifically facilitate repair events requiring limited end resection, which we find is dependent on the DSB end protection factor KU. However, we also find that RNF8 is important for homology-directed repair (HDR) independently of KU, which appears linked to promoting PALB2 function. Finally, the influence of RNF8 on EJ is distinct from 53BP1 and the ALT-EJ factor, POLQ. We suggest that RNF8 mediates both ALT-EJ and HDR, but via distinct mechanisms, since only the former is dependent on KU.
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Affiliation(s)
- Linda Jillianne Tsai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | - Ragini Bhargava
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Carlos Mendez-Dorantes
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Eva Jahanshir
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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26
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Kaushal S, Wollmuth CE, Das K, Hile SE, Regan SB, Barnes RP, Haouzi A, Lee SM, House NCM, Guyumdzhyan M, Eckert KA, Freudenreich CH. Sequence and Nuclease Requirements for Breakage and Healing of a Structure-Forming (AT)n Sequence within Fragile Site FRA16D. Cell Rep 2020; 27:1151-1164.e5. [PMID: 31018130 DOI: 10.1016/j.celrep.2019.03.103] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 02/07/2019] [Accepted: 03/27/2019] [Indexed: 01/20/2023] Open
Abstract
Common fragile sites (CFSs) are genomic regions that display gaps and breaks in human metaphase chromosomes under replication stress and are often deleted in cancer cells. We studied an ∼300-bp subregion (Flex1) of human CFS FRA16D in yeast and found that it recapitulates characteristics of CFS fragility in human cells. Flex1 fragility is dependent on the ability of a variable-length AT repeat to form a cruciform structure that stalls replication. Fragility at Flex1 is initiated by structure-specific endonuclease Mus81-Mms4 acting together with the Slx1-4/Rad1-10 complex, whereas Yen1 protects Flex1 against breakage. Sae2 is required for healing of Flex1 after breakage. Our study shows that breakage within a CFS can be initiated by nuclease cleavage at forks stalled at DNA structures. Furthermore, our results suggest that CFSs are not just prone to breakage but also are impaired in their ability to heal, and this deleterious combination accounts for their fragility.
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Affiliation(s)
- Simran Kaushal
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Charles E Wollmuth
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Kohal Das
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Suzanne E Hile
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Samantha B Regan
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Ryan P Barnes
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Alice Haouzi
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Soo Mi Lee
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Nealia C M House
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Michael Guyumdzhyan
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA
| | - Kristin A Eckert
- Department of Pathology, The Jake Gittlen Laboratories for Cancer Research, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Suite 4700, 200 Boston Ave., Medford, MA 02155, USA; Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, MA 02111, USA.
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27
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Ngo K, Epum EA, Friedman KL. Emerging non-canonical roles for the Rad51-Rad52 interaction in response to double-strand breaks in yeast. Curr Genet 2020; 66:917-926. [PMID: 32399607 DOI: 10.1007/s00294-020-01081-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/24/2022]
Abstract
DNA double-strand break repair allows cells to survive both exogenous and endogenous insults to the genome. In yeast, the recombinases Rad51 and Rad52 are central to multiple forms of homology-dependent repair. Classically, Rad51 and Rad52 are thought to act cooperatively, with formation of the functional Rad51 nucleofilament facilitated by the mediator function of Rad52. Several studies have now identified functions for the interaction between Rad51 and Rad52 that are independent of the mediator function of Rad52 and affect a seemingly diverse array of functions in de novo telomere addition, global chromosome mobility following DNA damage, Rad51 nucleofilament stability, checkpoint adaptation, and microhomology-mediated chromosome rearrangements. Here, we review these functions with an emphasis on our recent discovery that the Rad51-Rad52 interaction influences the probability of de novo telomere addition at sites preferentially targeted by telomerase following a double-strand break (DSB). We present data addressing the prevalence of sites within the yeast genome that are capable of stimulating de novo telomere addition following a DSB and speculate about the potential role such sites may play in genome stability.
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Affiliation(s)
- Katrina Ngo
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Esther A Epum
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Biology, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA, USA
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28
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Umbreit NT, Zhang CZ, Lynch LD, Blaine LJ, Cheng AM, Tourdot R, Sun L, Almubarak HF, Judge K, Mitchell TJ, Spektor A, Pellman D. Mechanisms generating cancer genome complexity from a single cell division error. Science 2020; 368:eaba0712. [PMID: 32299917 PMCID: PMC7347108 DOI: 10.1126/science.aba0712] [Citation(s) in RCA: 224] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/04/2020] [Indexed: 12/12/2022]
Abstract
The chromosome breakage-fusion-bridge (BFB) cycle is a mutational process that produces gene amplification and genome instability. Signatures of BFB cycles can be observed in cancer genomes alongside chromothripsis, another catastrophic mutational phenomenon. We explain this association by elucidating a mutational cascade that is triggered by a single cell division error-chromosome bridge formation-that rapidly increases genomic complexity. We show that actomyosin forces are required for initial bridge breakage. Chromothripsis accumulates, beginning with aberrant interphase replication of bridge DNA. A subsequent burst of DNA replication in the next mitosis generates extensive DNA damage. During this second cell division, broken bridge chromosomes frequently missegregate and form micronuclei, promoting additional chromothripsis. We propose that iterations of this mutational cascade generate the continuing evolution and subclonal heterogeneity characteristic of many human cancers.
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Affiliation(s)
- Neil T Umbreit
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cheng-Zhong Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Luke D Lynch
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Logan J Blaine
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anna M Cheng
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Richard Tourdot
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lili Sun
- Single-Cell Sequencing Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hannah F Almubarak
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kim Judge
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Alexander Spektor
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David Pellman
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
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29
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Carvajal-Garcia J, Cho JE, Carvajal-Garcia P, Feng W, Wood RD, Sekelsky J, Gupta GP, Roberts SA, Ramsden DA. Mechanistic basis for microhomology identification and genome scarring by polymerase theta. Proc Natl Acad Sci U S A 2020; 117:8476-8485. [PMID: 32234782 PMCID: PMC7165422 DOI: 10.1073/pnas.1921791117] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
DNA polymerase theta mediates an end joining pathway (TMEJ) that repairs chromosome breaks. It requires resection of broken ends to generate long, 3' single-stranded DNA tails, annealing of complementary sequence segments (microhomologies) in these tails, followed by microhomology-primed synthesis sufficient to resolve broken ends. The means by which microhomologies are identified is thus a critical step in this pathway, but is not understood. Here we show microhomologies are identified by a scanning mechanism initiated from the 3' terminus and favoring bidirectional progression into flanking DNA, typically to a maximum of 15 nucleotides into each flank. Polymerase theta is frequently insufficiently processive to complete repair of breaks in microhomology-poor, AT-rich regions. Aborted synthesis leads to one or more additional rounds of microhomology search, annealing, and synthesis; this promotes complete repair in part because earlier rounds of synthesis generate microhomologies de novo that are sufficiently long that synthesis is more processive. Aborted rounds of synthesis are evident in characteristic genomic scars as insertions of 3 to 30 bp of sequence that is identical to flanking DNA ("templated" insertions). Templated insertions are present at higher levels in breast cancer genomes from patients with germline BRCA1/2 mutations, consistent with an addiction to TMEJ in these cancers. Our work thus describes the mechanism for microhomology identification and shows how it both mitigates limitations implicit in the microhomology requirement and generates distinctive genomic scars associated with pathogenic genome instability.
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Affiliation(s)
- Juan Carvajal-Garcia
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Jang-Eun Cho
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Pablo Carvajal-Garcia
- Departamento de Ingeniería Geológica y Minera, Universidad Politécnica de Madrid, 28003 Madrid, Spain
| | - Wanjuan Feng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78957
| | - Jeff Sekelsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Integrative Program in Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164
| | - Dale A Ramsden
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599;
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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30
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Faramarz A, Balk JA, van Schie JJM, Oostra AB, Ghandour CA, Rooimans MA, Wolthuis RMF, de Lange J. Non-redundant roles in sister chromatid cohesion of the DNA helicase DDX11 and the SMC3 acetyl transferases ESCO1 and ESCO2. PLoS One 2020; 15:e0220348. [PMID: 31935221 PMCID: PMC6959578 DOI: 10.1371/journal.pone.0220348] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 12/30/2019] [Indexed: 12/30/2022] Open
Abstract
In a process linked to DNA replication, duplicated chromosomes are entrapped in large, circular cohesin complexes and functional sister chromatid cohesion (SCC) is established by acetylation of the SMC3 cohesin subunit. Roberts Syndrome (RBS) and Warsaw Breakage Syndrome (WABS) are rare human developmental syndromes that are characterized by defective SCC. RBS is caused by mutations in the SMC3 acetyltransferase ESCO2, whereas mutations in the DNA helicase DDX11 lead to WABS. We found that WABS-derived cells predominantly rely on ESCO2, not ESCO1, for residual SCC, growth and survival. Reciprocally, RBS-derived cells depend on DDX11 to maintain low levels of SCC. Synthetic lethality between DDX11 and ESCO2 correlated with a prolonged delay in mitosis, and was rescued by knockdown of the cohesin remover WAPL. Rescue experiments using human or mouse cDNAs revealed that DDX11, ESCO1 and ESCO2 act on different but related aspects of SCC establishment. Furthermore, a DNA binding DDX11 mutant failed to correct SCC in WABS cells and DDX11 deficiency reduced replication fork speed. We propose that DDX11, ESCO1 and ESCO2 control different fractions of cohesin that are spatially and mechanistically separated.
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Affiliation(s)
- Atiq Faramarz
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Jesper A. Balk
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Janne J. M. van Schie
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Anneke B. Oostra
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Cherien A. Ghandour
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Martin A. Rooimans
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Rob M. F. Wolthuis
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Job de Lange
- Cancer Center Amsterdam, Department of Clinical Genetics, section Oncogenetics, Amsterdam University Medical Centers, Amsterdam, the Netherlands
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Abstract
DNA-strand breaks influence structure and function of chromosomes in diverse ways, and it is essential to analyze the lesions to understand behaviors of genetic information. For researchers in a wide array of fields including recombination, repair, and DNA damage response, efficient and easy detection of DNA breaks is of paramount importance. Among several procedures suitable for this purpose, a method to directly observe broken chromosomes by pulsed-field gel electrophoresis, using the fission yeast Schizosaccharomyces pombe as a model organism, is described in this chapter. Because S. pombe chromosomes are megabase-size, careful attention should be paid to maintain DNA as intact as possible. The protocol includes induction of DNA breaks, preparation of chromosomes, and separation of chromosomal DNA by PFGE. This procedure can be applicable to other species as well as other experiments handling large-size DNA molecules.
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Affiliation(s)
- Takatomi Yamada
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan.
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
| | - Hiroshi Murakami
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Kunihiro Ohta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
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32
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Affiliation(s)
- Hannah L Klein
- From the New York University Medical Center, Department of Biochemistry and Molecular Pharmacology, New York, NY
| | - Lorraine S Symington
- From the New York University Medical Center, Department of Biochemistry and Molecular Pharmacology, New York, NY
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33
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Canela A, Maman Y, Huang SYN, Wutz G, Tang W, Zagnoli-Vieira G, Callen E, Wong N, Day A, Peters JM, Caldecott KW, Pommier Y, Nussenzweig A. Topoisomerase II-Induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity. Mol Cell 2019; 75:252-266.e8. [PMID: 31202577 PMCID: PMC8170508 DOI: 10.1016/j.molcel.2019.04.030] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/22/2019] [Accepted: 04/21/2019] [Indexed: 12/24/2022]
Abstract
Topoisomerase II (TOP2) relieves torsional stress by forming transient cleavage complex intermediates (TOP2ccs) that contain TOP2-linked DNA breaks (DSBs). While TOP2ccs are normally reversible, they can be "trapped" by chemotherapeutic drugs such as etoposide and subsequently converted into irreversible TOP2-linked DSBs. Here, we have quantified etoposide-induced trapping of TOP2ccs, their conversion into irreversible TOP2-linked DSBs, and their processing during DNA repair genome-wide, as a function of time. We find that while TOP2 chromatin localization and trapping is independent of transcription, it requires pre-existing binding of cohesin to DNA. In contrast, the conversion of trapped TOP2ccs to irreversible DSBs during DNA repair is accelerated 2-fold at transcribed loci relative to non-transcribed loci. This conversion is dependent on proteasomal degradation and TDP2 phosphodiesterase activity. Quantitative modeling shows that only two features of pre-existing chromatin structure-namely, cohesin binding and transcriptional activity-can be used to predict the kinetics of TOP2-induced DSBs.
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Affiliation(s)
- Andres Canela
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA; The Hakubi Center for Advanced Research and Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Shar-Yin N Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, NIH, Bethesda, MD, USA
| | - Gordana Wutz
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Wen Tang
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Guido Zagnoli-Vieira
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Amanda Day
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Keith W Caldecott
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, 142 20 Prague, 4, Czech Republic
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, NIH, Bethesda, MD, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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34
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Bhandari J, Karg T, Golic KG. Homolog-Dependent Repair Following Dicentric Chromosome Breakage in Drosophila melanogaster. Genetics 2019; 212:615-630. [PMID: 31053594 PMCID: PMC6614899 DOI: 10.1534/genetics.119.302247] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022] Open
Abstract
Double-strand DNA breaks are repaired by one of several mechanisms that rejoin two broken ends. However, cells are challenged when asked to repair a single broken end and respond by: (1) inducing programmed cell death; (2) healing the broken end by constructing a new telomere; (3) adapting to the broken end and resuming the mitotic cycle without repair; and (4) using information from the sister chromatid or homologous chromosome to restore a normal chromosome terminus. During one form of homolog-dependent repair in yeast, termed break-induced replication (BIR), a template chromosome can be copied for hundreds of kilobases. BIR efficiency depends on Pif1 helicase and Pol32, a nonessential subunit of DNA polymerase δ. To date, there is little evidence that BIR can be used for extensive chromosome repair in higher eukaryotes. We report that a dicentric chromosome broken in mitosis in the male germline of Drosophila melanogaster is usually repaired by healing, but can also be repaired in a homolog-dependent fashion, restoring at least 1.3 Mb of terminal sequence information. This mode of repair is significantly reduced in pif1 and pol32 mutants. Formally, the repaired chromosomes are recombinants. However, the absence of reciprocal recombinants and the dependence on Pif1 and Pol32 strongly support the hypothesis that BIR is the mechanism for restoration of the chromosome terminus. In contrast to yeast, pif1 mutants in Drosophila exhibit a reduced rate of chromosome healing, likely owing to fundamental differences in telomeres between these organisms.
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Affiliation(s)
- Jayaram Bhandari
- School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112
| | - Travis Karg
- School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112
| | - Kent G Golic
- School of Biological Sciences, University of Utah, Salt Lake City, Utah 84112
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35
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Pamplona-Silva MT, Gonçalves LC, Marin-Morales MA. Genetic toxicity of water contaminated by microcystins collected during a cyanobacteria bloom. Ecotoxicol Environ Saf 2018; 166:223-230. [PMID: 30269018 DOI: 10.1016/j.ecoenv.2018.09.090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/10/2018] [Accepted: 09/21/2018] [Indexed: 06/08/2023]
Abstract
Microcystin-LR (MCLR) is a toxin mainly produced by Microcystis aeruginosa, cyanobacteria most commonly found in eutrophic environments. Cyanobacteria blooms have affected Salto Grande reservoir (Americana, State of São Paulo/Brazil) for several decades, often observed during periods of drought. In this study, the genotoxic effects of MCLR (95% purity) and water samples contaminated by this toxin were evaluated during cyanobacteria bloom using assays with the test organism Allium cepa. The results showed genotoxic action for pure microcystin and cytotoxic, genotoxic and mutagenic action for water samples collected during flowering. Chromosomal aberration assays have shown that MCLR induces chromosomal breaks that persist in the daughter cells as MN. Therefore, it is possible to infer a clastogenic action for this toxin. The MCLR present in the environmental samples was shown to be more cytogenotoxic for the cells than the different concentrations tested in this study with the pure substance. This amplified toxic action can be related to a synergistic effect between the MCLR and other compounds present in the environmental samples. The genotoxicity studies with MCLR show inconsistent and inconclusive results, so this toxin needs to be better investigated in order to obtain further information about the action mode of it is on the biological system.
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Affiliation(s)
- Maria Tereza Pamplona-Silva
- São Paulo State University (Unesp), Institute of Bioscience, Rio Claro. Av. 24-A, 1515, 13.506-900 Rio Claro, SP, Brazil.
| | - Letícia Cristina Gonçalves
- São Paulo State University (Unesp), Institute of Bioscience, Rio Claro. Av. 24-A, 1515, 13.506-900 Rio Claro, SP, Brazil.
| | - Maria Aparecida Marin-Morales
- São Paulo State University (Unesp), Institute of Bioscience, Rio Claro. Av. 24-A, 1515, 13.506-900 Rio Claro, SP, Brazil.
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36
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Pryor JM, Conlin MP, Carvajal-Garcia J, Luedeman ME, Luthman AJ, Small GW, Ramsden DA. Ribonucleotide incorporation enables repair of chromosome breaks by nonhomologous end joining. Science 2018; 361:1126-1129. [PMID: 30213916 PMCID: PMC6252249 DOI: 10.1126/science.aat2477] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/31/2018] [Accepted: 07/20/2018] [Indexed: 11/02/2022]
Abstract
The nonhomologous end-joining (NHEJ) pathway preserves genome stability by ligating the ends of broken chromosomes together. It employs end-processing enzymes, including polymerases, to prepare ends for ligation. We show that two such polymerases incorporate primarily ribonucleotides during NHEJ-an exception to the central dogma of molecular biology-both during repair of chromosome breaks made by Cas9 and during V(D)J recombination. Moreover, additions of ribonucleotides but not deoxynucleotides effectively promote ligation. Repair kinetics suggest that ribonucleotide-dependent first-strand ligation is followed by complementary strand repair with deoxynucleotides, then by replacement of ribonucleotides embedded in the first strand with deoxynucleotides. Our results indicate that as much as 65% of cellular NHEJ products have transiently embedded ribonucleotides, which promote flexibility in repair at the cost of more fragile intermediates.
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Affiliation(s)
- John M Pryor
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael P Conlin
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Juan Carvajal-Garcia
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Megan E Luedeman
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Adam J Luthman
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - George W Small
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dale A Ramsden
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics and Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA.
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37
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Dandoulaki M, Petsalaki E, Sumpton D, Zanivan S, Zachos G. Src activation by Chk1 promotes actin patch formation and prevents chromatin bridge breakage in cytokinesis. J Cell Biol 2018; 217:3071-3089. [PMID: 29954829 PMCID: PMC6122982 DOI: 10.1083/jcb.201802102] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/16/2018] [Accepted: 06/03/2018] [Indexed: 12/23/2022] Open
Abstract
In cytokinesis with chromatin bridges, cells delay abscission and retain actin patches at the intercellular canal to prevent chromosome breakage. In this study, we show that inhibition of Src, a protein-tyrosine kinase that regulates actin dynamics, or Chk1 kinase correlates with chromatin breakage and impaired formation of actin patches but not with abscission in the presence of chromatin bridges. Chk1 is required for optimal localization and complete activation of Src. Furthermore, Chk1 phosphorylates human Src at serine 51, and phosphorylated Src localizes to actin patches, the cell membrane, or the nucleus. Nonphosphorylatable mutation of S51 to alanine reduces Src catalytic activity and impairs formation of actin patches, whereas expression of a phosphomimicking Src-S51D protein rescues actin patches and prevents chromatin breakage in Chk1-deficient cells. We propose that Chk1 phosphorylates Src-S51 to fully induce Src kinase activity and that phosphorylated Src promotes formation of actin patches and stabilizes chromatin bridges. These results identify proteins that regulate formation of actin patches in cytokinesis.
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Affiliation(s)
| | - Eleni Petsalaki
- Department of Biology, University of Crete, Heraklion, Greece
| | - David Sumpton
- Cancer Research UK Beatson Institute, Glasgow, Scotland, UK
| | - Sara Zanivan
- Cancer Research UK Beatson Institute, Glasgow, Scotland, UK
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, Scotland, UK
| | - George Zachos
- Department of Biology, University of Crete, Heraklion, Greece
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38
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Bhargava R, Sandhu M, Muk S, Lee G, Vaidehi N, Stark JM. C-NHEJ without indels is robust and requires synergistic function of distinct XLF domains. Nat Commun 2018; 9:2484. [PMID: 29950655 PMCID: PMC6021437 DOI: 10.1038/s41467-018-04867-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/25/2018] [Indexed: 01/17/2023] Open
Abstract
To investigate the fidelity of canonical non-homologous end joining (C-NHEJ), we developed an assay to detect EJ between distal ends of two Cas9-induced chromosomal breaks that are joined without causing insertion/deletion mutations (indels). Here we find that such EJ requires several core C-NHEJ factors, including XLF. Using variants of this assay, we find that C-NHEJ is required for EJ events that use 1-2, but not ≥3, nucleotides of terminal microhomology. We also investigated XLF residues required for EJ without indels, finding that one of two binding domains is essential (L115 or C-terminal lysines that bind XRCC4 and KU/DNA, respectively), and that disruption of one of these domains sensitizes XLF to mutations that affect its dimer interface, which we examined with molecular dynamic simulations. Thus, C-NHEJ, including synergistic function of distinct XLF domains, is required for EJ of chromosomal breaks without indels.
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Affiliation(s)
- Ragini Bhargava
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA, 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA, 91010, USA
| | - Manbir Sandhu
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA, 91010, USA
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA, 91010, USA
| | - Sanychen Muk
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA, 91010, USA
| | - Gabriella Lee
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA, 91010, USA
| | - Nagarajan Vaidehi
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA, 91010, USA
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA, 91010, USA
| | - Jeremy M Stark
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA, 91010, USA.
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1500 E Duarte Rd., Duarte, CA, 91010, USA.
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39
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Kesrouani C, Zemoura L, Laé M. [A peculiar intra-uterine lesion: Inflammatory myofibroblastic tumor (IMT)]. Ann Pathol 2018; 38:143-146. [PMID: 29397221 DOI: 10.1016/j.annpat.2017.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 10/22/2017] [Accepted: 12/13/2017] [Indexed: 11/19/2022]
Abstract
A 25-year-old woman presented with a spontaneous vaginal expulsion of a 4cm well-circumscribed nodule a few weeks after delivery. An inflammatory myofibroblastic tumor diagnosis was made by morphologic, immunohistochemistry and FISH analysis of the nodule.
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MESH Headings
- Activin Receptors, Type II/analysis
- Activin Receptors, Type II/genetics
- Adult
- Chromosome Breakage
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Human, Pair 2/ultrastructure
- Diagnosis, Differential
- Female
- Granuloma, Plasma Cell/diagnosis
- Humans
- In Situ Hybridization, Fluorescence
- Inflammation
- Neoplasm Proteins/analysis
- Neoplasm Proteins/genetics
- Neoplasms, Muscle Tissue/chemistry
- Neoplasms, Muscle Tissue/diagnosis
- Neoplasms, Muscle Tissue/genetics
- Neoplasms, Muscle Tissue/pathology
- Oncogene Proteins, Fusion/analysis
- Oncogene Proteins, Fusion/genetics
- Prognosis
- Puerperal Disorders/diagnosis
- Puerperal Disorders/genetics
- Puerperal Disorders/pathology
- Uterine Neoplasms/chemistry
- Uterine Neoplasms/diagnosis
- Uterine Neoplasms/genetics
- Uterine Neoplasms/pathology
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Affiliation(s)
- Carole Kesrouani
- Service de pathologie, Hôtel-Dieu de France, boulevard Alfred-Naccache, Beyrouth, Liban; Service de pathologie, institut Curie-Paris, 26, rue d'Ulm, 75248 Paris, France.
| | - Leila Zemoura
- Service de pathologie, hôpital Foch, 40, rue Worth, 92150 Suresnes, France
| | - Marick Laé
- Service de pathologie, institut Curie-Paris, 26, rue d'Ulm, 75248 Paris, France
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40
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Chan YW, Fugger K, West SC. Unresolved recombination intermediates lead to ultra-fine anaphase bridges, chromosome breaks and aberrations. Nat Cell Biol 2018; 20:92-103. [PMID: 29255170 PMCID: PMC5742284 DOI: 10.1038/s41556-017-0011-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 11/16/2017] [Indexed: 01/21/2023]
Abstract
The resolution of joint molecules that link recombining sister chromatids is essential for chromosome segregation. Here, we determine the fate of unresolved recombination intermediates arising in cells lacking two nucleases required for resolution (GEN1 -/- knockout cells depleted of MUS81). We find that intermediates persist until mitosis and form a distinct class of anaphase bridges, which we term homologous recombination ultra-fine bridges (HR-UFBs). HR-UFBs are distinct from replication stress-associated UFBs, which arise at common fragile sites, and from centromeric UFBs. HR-UFBs are processed by BLM helicase to generate single-stranded RPA-coated bridges that are broken during mitosis. In the next cell cycle, DNA breaks activate the DNA damage checkpoint response, and chromosome fusions arise by non-homologous end joining. Consequently, the cells undergo cell cycle delay and massive cell death. These results lead us to present a model detailing how unresolved recombination intermediates can promote DNA damage and chromosomal instability.
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41
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Zaninetti C, Santini V, Tiniakou M, Barozzi S, Savoia A, Pecci A. Inherited thrombocytopenia caused by ANKRD26 mutations misdiagnosed and treated as myelodysplastic syndrome: report on two cases. J Thromb Haemost 2017; 15:2388-2392. [PMID: 28976612 DOI: 10.1111/jth.13855] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Indexed: 08/31/2023]
Abstract
Essentials Thrombocytopenia 2 (THC2) is an inherited thrombocytopenia (IT) with dysmegakaryopoiesis. Physicians often do not suspect the genetic origin of thrombocytopenia in patients with THC2. We report two THC2 patients misdiagnosed with myelodysplasia and treated with chemotherapy. IT should be always considered in patients with isolated thrombocytopenia and dysmegakaryopoiesis. SUMMARY Thrombocytopenia 2 (THC2) is an autosomal-dominant disorder caused by point substitutions in the 5'UTR of the ANKRD26 gene. Patients have congenital thrombocytopenia, normal platelet morphology and function, and dysmegakaryopoiesis. Thrombocytopenia is frequently discovered only in adulthood and physicians often do not suspect its genetic origin. We describe two unrelated patients referred to two different institutions for investigation of thrombocytopenia. Based on the finding of dysmegakaryopoiesis at bone marrow examination, patients were diagnosed with myelodysplastic syndrome (MDS) (refractory thrombocytopenia) and treated with several courses of 5-azacytidine. Subsequently, demonstration of thrombocytopenia in their relatives eventually led to molecular diagnosis of THC2 in both families. These cases highlight that patients with THC2 are at risk of being misdiagnosed with MDS and receiving undue myelosuppressive treatments. Because dysmegakaryopoiesis is a feature also of other forms of inherited thrombocytopenia, a genetic disorder must always be considered when a patient presents with isolated thrombocytopenia and dysmegakaryopoiesis.
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Affiliation(s)
- C Zaninetti
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - V Santini
- Division of Hematology, Careggi Hospital and University of Florence, Firenze, Italy
| | - M Tiniakou
- Division of Hematology, Department of Internal Medicine, University of Patras Medical School, Patras, Greece
| | - S Barozzi
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
| | - A Savoia
- Department of Medical, Surgical and Health Sciences, IRCCS Burlo Garofolo and University of Trieste, Trieste, Italy
| | - A Pecci
- Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Pavia, Italy
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42
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Sanchez JC, Kwan EX, Pohl TJ, Amemiya HM, Raghuraman MK, Brewer BJ. Defective replication initiation results in locus specific chromosome breakage and a ribosomal RNA deficiency in yeast. PLoS Genet 2017; 13:e1007041. [PMID: 29036220 PMCID: PMC5658192 DOI: 10.1371/journal.pgen.1007041] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 10/26/2017] [Accepted: 09/21/2017] [Indexed: 01/23/2023] Open
Abstract
A form of dwarfism known as Meier-Gorlin syndrome (MGS) is caused by recessive mutations in one of six different genes (ORC1, ORC4, ORC6, CDC6, CDT1, and MCM5). These genes encode components of the pre-replication complex, which assembles at origins of replication prior to S phase. Also, variants in two additional replication initiation genes have joined the list of causative mutations for MGS (Geminin and CDC45). The identity of the causative MGS genetic variants strongly suggests that some aspect of replication is amiss in MGS patients; however, little evidence has been obtained regarding what aspect of chromosome replication is faulty. Since the site of one of the missense mutations in the human ORC4 alleles is conserved between humans and yeast, we sought to determine in what way this single amino acid change affects the process of chromosome replication, by introducing the comparable mutation into yeast (orc4Y232C). We find that yeast cells with the orc4Y232C allele have a prolonged S-phase, due to compromised replication initiation at the ribosomal DNA (rDNA) locus located on chromosome XII. The inability to initiate replication at the rDNA locus results in chromosome breakage and a severely reduced rDNA copy number in the survivors, presumably helping to ensure complete replication of chromosome XII. Although reducing rDNA copy number may help ensure complete chromosome replication, orc4Y232C cells struggle to meet the high demand for ribosomal RNA synthesis. This finding provides additional evidence linking two essential cellular pathways-DNA replication and ribosome biogenesis.
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Affiliation(s)
- Joseph C. Sanchez
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Elizabeth X. Kwan
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Thomas J. Pohl
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Haley M. Amemiya
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - Bonita J. Brewer
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, United States of America
- Department of Genome Sciences, University of Washington, Seattle, WA, United States of America
- * E-mail:
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43
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Luaces JP, Rossi LF, Chirino MG, Browne M, Merani MS, Mudry MD. Genotoxic effects of Roundup Full II® on lymphocytes of Chaetophractus villosus (Xenarthra, Mammalia): In vitro studies. PLoS One 2017; 12:e0182911. [PMID: 28817615 PMCID: PMC5560724 DOI: 10.1371/journal.pone.0182911] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 07/17/2017] [Indexed: 01/26/2023] Open
Abstract
In Argentina, Chaetophractus villosus has a wide distribution that overlaps with agricultural areas where soybean is the predominant crop. In such areas the pesticide Roundup Full II® (RU) is widely applied. The genotoxic effect of its active ingredient glyphosate (RU is 66.2% glyphosate) on the peripheral blood lymphocytes of C. villosus was tested over a range of concentrations (280, 420, 560, 1120 μmol/L). Culture medium without glyphosate served as negative control, while medium containing mitomycin C served as positive control. Genetic damage was characterized in terms of the percentage of cells with chromosome aberrations (CA), the mean number of sister chromatid exchanges (SCE) per cell, and the modification of cell proliferation kinetics via the calculation of the replication index. Significant increases (p < 0.0001) were seen in the CA frequency and the mean number of SCEs per cell compared to negative controls at all the RU concentrations tested. Chromatid breaks, the only form of CA observed, under the 560 μmol/L RU conditions and in presence of mitomycin C were four to five times more common than at lower concentrations, while no viable cells were seen in the 1120 μmol/L treatment. The mean number of SCEs per cell was significantly higher under the 280 μmol/L RU conditions than the 420 or 560 μmol/L RU conditions; cells cultivated in the presence of MMC also showed significantly more SCEs. All the RU concentrations tested (except in the 1120 μmol/L RU treatment [no viable cells]) induced a significant reduction in the replication index (p < 0.0001). The present results confirm the genotoxic effects of RU on C. villosus lymphocytes in vitro, strongly suggesting that exposure to RU could induce DNA damage in C. villosus wildlife.
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Affiliation(s)
- Juan Pablo Luaces
- Laboratorio de Biología Cromosómica, Facultad de Medicina, Universidad de Buenos Aires, Paraguay, Piso 10 Lab. 6, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Ciudad Autónoma de Buenos Aires, Argentina
| | - Luis Francisco Rossi
- Laboratorio de Biología Cromosómica, Facultad de Medicina, Universidad de Buenos Aires, Paraguay, Piso 10 Lab. 6, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mónica Gabriela Chirino
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Ciudad Autónoma de Buenos Aires, Argentina
- Grupo de Citogenética de Insectos, Depto. Ecología, Genética y Evolución, FCENyN-UBA. Instituto de Ecología, Genética y Evolución de Buenos Aires. IEGEBA-CONICET. Lab. 110. Piso 4 –Pabellón II—Ciudad Universitaria, Intendente Güiraldes, Ciudad Autónoma de Buenos Aires, Argentina
| | - Melanie Browne
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Susana Merani
- Laboratorio de Biología Cromosómica, Facultad de Medicina, Universidad de Buenos Aires, Paraguay, Piso 10 Lab. 6, Ciudad Autónoma de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marta Dolores Mudry
- Consejo Nacional de Investigaciones Científicas y Técnicas, Godoy Cruz, Ciudad Autónoma de Buenos Aires, Argentina
- Grupo de Investigación en Biología Evolutiva (GIBE), Depto. Ecología Genética y Evolución, FCEyN-UBA. Instituto de Ecología, Genética y Evolución de Buenos Aires. IEGEBA-CONICET. Labs. 43–46. Piso 4—Pabellón II- Ciudad Universitaria, Intendente Güiraldes, Ciudad Autónoma de Buenos Aires, Argentina
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44
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Abstract
Ever since initial suggestions that instability at common fragile sites (CFSs) could be responsible for chromosome rearrangements in cancers, CFSs and associated genes have been the subject of numerous studies, leading to questions and controversies about their role and importance in cancer. It is now clear that CFSs are not frequently involved in translocations or other cancer-associated recurrent gross chromosome rearrangements. However, recent studies have provided new insights into the mechanisms of CFS instability, their effect on genome instability, and their role in generating focal copy number alterations that affect the genomic landscape of many cancers.
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Affiliation(s)
- Thomas W Glover
- Department of Human Genetics; the Department of Pathology; and the Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics; and the Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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45
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Abstract
The manufacturing and storage of cefotaxime produces different impurities of various concentrations, which may influence the efficacy and safety of the drugs. Because no report of toxicity data is available on the impurities of cefotaxime, the present acute and genotoxicity studies were designed and conducted to provide the information for establishing the safety profile and qualification of the dimeric impurity. Histidine-requiring mutants of Salmonella typhimurium TA97a, TA98, TA100, TA102, and TA1535 strains, with or without metabolic activation (S-9), were used for point-mutation tests. Neither increase in numbers of revertants, indicative of mutagenic activity, nor inhibition of bacterial growth, indicative of cytotoxicity, was observed when the dimeric impurity of cefotaxime at concentrations of 0.62, 1.85, 5.56, 16.67, and 50 μg/plate was incorporated into plates containing S. typhimurium bacterial strains. Cultures of Chinese hamster ovary (CHO) cells at a cell density of 2 × 105 cells per culture were exposed to the dimeric impurity of cefotaxime at the concentration of 11.25, 22.5, and 45 mg per culture, with or without metabolic activation, and harvested at 18 h after exposure. No chromosomal aberrations in the cultured mammalian cells were recorded. Acute intramuscular administration of the dimeric impurity of cefotaxime in Sprague-Dawley rats did not result in any clinical signs and gross pathological changes up to 2000 mg/kg-body weight. The results of these studies indicated that the dimeric impurity of cefotaxime is nonmutagenic in Ames test, nonclastogenic in vitro, and acutely nontoxic in rats.
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Affiliation(s)
- Shiv Kumar Agarwal
- Olchid Chemicals and Pharmaceuticals Ltd., R&D Centre, Sholinganallur, Chennai, India.
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46
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Daga A, Ansari A, Pandya M, Shah K, Patel S, Rawal R, Umrania V. Significant Role of Segmental Duplications and SIDD Sites in Chromosomal Translocations of Hematological Malignancies: A Multi-parametric Bioinformatic Analysis. Interdiscip Sci 2016; 10:467-475. [PMID: 27896663 DOI: 10.1007/s12539-016-0203-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 11/12/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022]
Abstract
Recurrent non-random chromosomal translocations are hallmark characteristics of leukemogenesis, and however, molecular mechanisms underlying these rearrangements are less explored. The fundamental question is, why and how chromosomes break and reunite so precisely in the genome. Meticulous understanding of mechanism leading to chromosomal rearrangement can be achieved by characterizing breakpoints. To address this hypothesis, a novel multi-parametric computational approach for characterization of major leukemic translocations within and around breakpoint region was performed. To best of our knowledge, this bioinformatic analysis is unique in finding the presence of segmental duplications (SDs) flanking breakpoints of all major leukemic translocation. Breakpoint islands (BpIs) were analyzed for stress-induced duplex destabilization (SIDD) sites along with other complex genomic architecture and physicochemical properties. Our study distinctly emphasizes on the probable correlative role of SDs, SIDD sites and various genomic features in the occurrence of breakpoints. Further, it also highlights potential features which may be playing a crucial role in causing double-strand breaks, leading to translocation.
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Affiliation(s)
- Aditi Daga
- Department of Microbiology, MVM Science College, Saurashtra University, Near Under Bridge, Kalawad Road, Rajkot, Gujarat, 360007, India
| | - Afzal Ansari
- BIT Virtual Institute of Bioinformatics (GCRI Node), GSBTM, Gandhinagar, Gujarat, India
- BIT Virtual Institute of Bioinformatics (GCRI Node), Division of Medicinal Chemistry and Pharmacogenomics, The Gujarat Cancer and Research Institute, NCH Campus, Asarwa, Ahmedabad, Gujarat, 380016, India
| | - Medha Pandya
- Department of Bioinformatics, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, 364022, India
- Department of Physics, Maharaja Krishnakumarsinhji Bhavnagar University, Bhavnagar, Gujarat, 364022, India
| | - Krupa Shah
- Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology, The Gujarat Cancer and Research Institute, NCH Campus, Asarwa, Ahmedabad, Gujarat, 380016, India
| | - Shanaya Patel
- Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology, The Gujarat Cancer and Research Institute, NCH Campus, Asarwa, Ahmedabad, Gujarat, 380016, India
| | - Rakesh Rawal
- Division of Medicinal Chemistry and Pharmacogenomics, Department of Cancer Biology, The Gujarat Cancer and Research Institute, NCH Campus, Asarwa, Ahmedabad, Gujarat, 380016, India.
| | - Valentina Umrania
- Department of Microbiology, MVM Science College, Saurashtra University, Near Under Bridge, Kalawad Road, Rajkot, Gujarat, 360007, India
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47
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Lin CYG, Lin IT, Yao MC. Programmed Minichromosome Elimination as a Mechanism for Somatic Genome Reduction in Tetrahymena thermophila. PLoS Genet 2016; 12:e1006403. [PMID: 27806059 PMCID: PMC5091840 DOI: 10.1371/journal.pgen.1006403] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/04/2016] [Indexed: 01/12/2023] Open
Abstract
The maintenance of chromosome integrity is crucial for genetic stability. However, programmed chromosome fragmentations are known to occur in many organisms, and in the ciliate Tetrahymena the five germline chromosomes are fragmented into hundreds of minichromosomes during somatic nuclear differentiation. Here, we showed that there are different fates of these minichromosomes after chromosome breakage. Among the 326 somatic minichromosomes identified using genomic data, 50 are selectively eliminated from the mature somatic genome. Interestingly, many and probably most of these minichromosomes are eliminated during the growth period between 6 and 20 doublings right after conjugation. Genes with potential conjugation-specific functions are found in these minichromosomes. This study revealed a new mode of programmed DNA elimination in ciliates similar to those observed in parasitic nematodes, which could play a role in developmental gene regulation.
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Affiliation(s)
- Chih-Yi Gabriela Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
| | - I-Ting Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Meng-Chao Yao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University, Taipei, Taiwan
- * E-mail:
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48
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Chumki SA, Dunn MK, Coates TF, Mishler JD, Younkin EM, Casper AM. Remarkably Long-Tract Gene Conversion Induced by Fragile Site Instability in Saccharomyces cerevisiae. Genetics 2016; 204:115-28. [PMID: 27343237 PMCID: PMC5012379 DOI: 10.1534/genetics.116.191205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/23/2016] [Indexed: 01/29/2023] Open
Abstract
Replication stress causes breaks at chromosomal locations called common fragile sites. Deletions causing loss of heterozygosity (LOH) in human tumors are strongly correlated with common fragile sites, but the role of gene conversion in LOH at fragile sites in tumors is less well studied. Here, we investigated gene conversion stimulated by instability at fragile site FS2 in the yeast Saccharomyces cerevisiae In our screening system, mitotic LOH events near FS2 are identified by production of red/white sectored colonies. We analyzed single nucleotide polymorphisms between homologs to determine the cause and extent of LOH. Instability at FS2 increases gene conversion 48- to 62-fold, and conversions unassociated with crossover represent 6-7% of LOH events. Gene conversion can result from repair of mismatches in heteroduplex DNA during synthesis-dependent strand annealing (SDSA), double-strand break repair (DSBR), and from break-induced replication (BIR) that switches templates [double BIR (dBIR)]. It has been proposed that SDSA and DSBR typically result in shorter gene-conversion tracts than dBIR. In cells under replication stress, we found that bidirectional tracts at FS2 have a median length of 40.8 kb and a wide distribution of lengths; most of these tracts are not crossover-associated. Tracts that begin at the fragile site FS2 and extend only distally are significantly shorter. The high abundance and long length of noncrossover, bidirectional gene-conversion tracts suggests that dBIR is a prominent mechanism for repair of lesions at FS2, thus this mechanism is likely to be a driver of common fragile site-stimulated LOH in human tumors.
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Affiliation(s)
- Shahana A Chumki
- Department of Biology, Eastern Michigan University, Ypsilanti, Michigan 48197
| | - Mikael K Dunn
- Department of Biology, Eastern Michigan University, Ypsilanti, Michigan 48197
| | - Thomas F Coates
- Department of Biology, Eastern Michigan University, Ypsilanti, Michigan 48197
| | - Jeanmarie D Mishler
- Department of Biology, Eastern Michigan University, Ypsilanti, Michigan 48197
| | - Ellen M Younkin
- Department of Biology, Eastern Michigan University, Ypsilanti, Michigan 48197
| | - Anne M Casper
- Department of Biology, Eastern Michigan University, Ypsilanti, Michigan 48197
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49
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Wyatt DW, Feng W, Conlin MP, Yousefzadeh MJ, Roberts SA, Mieczkowski P, Wood RD, Gupta GP, Ramsden DA. Essential Roles for Polymerase θ-Mediated End Joining in the Repair of Chromosome Breaks. Mol Cell 2016; 63:662-673. [PMID: 27453047 PMCID: PMC4992412 DOI: 10.1016/j.molcel.2016.06.020] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/20/2016] [Accepted: 06/14/2016] [Indexed: 01/04/2023]
Abstract
DNA polymerase theta (Pol θ)-mediated end joining (TMEJ) has been implicated in the repair of chromosome breaks, but its cellular mechanism and role relative to canonical repair pathways are poorly understood. We show that it accounts for most repairs associated with microhomologies and is made efficient by coupling a microhomology search to removal of non-homologous tails and microhomology-primed synthesis across broken ends. In contrast to non-homologous end joining (NHEJ), TMEJ efficiently repairs end structures expected after aborted homology-directed repair (5' to 3' resected ends) or replication fork collapse. It typically does not compete with canonical repair pathways but, in NHEJ-deficient cells, is engaged more frequently and protects against translocation. Cell viability is also severely impaired upon combined deficiency in Pol θ and a factor that antagonizes end resection (Ku or 53BP1). TMEJ thus helps to sustain cell viability and genome stability by rescuing chromosome break repair when resection is misregulated or NHEJ is compromised.
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Affiliation(s)
- David W Wyatt
- Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Wanjuan Feng
- Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Radiation Oncology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Michael P Conlin
- Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Matthew J Yousefzadeh
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78597, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
| | - Piotr Mieczkowski
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX 78597, USA
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Radiation Oncology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dale A Ramsden
- Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
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50
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Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HA, Marchetto MCN, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang WJ, Ventura M, Banci L, Antonacci F, Akey JM, Amemiya CT, Gage FH, Reymond A, Eichler EE. Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. Nature 2016; 536:205-9. [PMID: 27487209 PMCID: PMC4988886 DOI: 10.1038/nature19075] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 07/02/2016] [Indexed: 12/31/2022]
Abstract
Genetic differences that specify unique aspects of human evolution have typically been identified by comparative analyses between the genomes of humans and closely related primates, including more recently the genomes of archaic hominins. Not all regions of the genome, however, are equally amenable to such study. Recurrent copy number variation (CNV) at chromosome 16p11.2 accounts for approximately 1% of cases of autism and is mediated by a complex set of segmental duplications, many of which arose recently during human evolution. Here we reconstruct the evolutionary history of the locus and identify bolA family member 2 (BOLA2) as a gene duplicated exclusively in Homo sapiens. We estimate that a 95-kilobase-pair segment containing BOLA2 duplicated across the critical region approximately 282 thousand years ago (ka), one of the latest among a series of genomic changes that dramatically restructured the locus during hominid evolution. All humans examined carried one or more copies of the duplication, which nearly fixed early in the human lineage--a pattern unlikely to have arisen so rapidly in the absence of selection (P < 0.0097). We show that the duplication of BOLA2 led to a novel, human-specific in-frame fusion transcript and that BOLA2 copy number correlates with both RNA expression (r = 0.36) and protein level (r = 0.65), with the greatest expression difference between human and chimpanzee in experimentally derived stem cells. Analyses of 152 patients carrying a chromosome 16p11. rearrangement show that more than 96% of breakpoints occur within the H. sapiens-specific duplication. In summary, the duplicative transposition of BOLA2 at the root of the H. sapiens lineage about 282 ka simultaneously increased copy number of a gene associated with iron homeostasis and predisposed our species to recurrent rearrangements associated with disease.
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Affiliation(s)
- Xander Nuttle
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Michael H. Duyzend
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Joshua G. Schraiber
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Iñigo Narvaiza
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Peter H. Sudmant
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Osnat Penn
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Maika Malig
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Chris Benner
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Francesca Camponeschi
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
| | - Simone Ciofi-Baffoni
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Holly A.F. Stessman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Maria C. N. Marchetto
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Laura Denman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Lana Harshman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Archana Raja
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Kelsi Penewit
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Nicolette Janke
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - W. Joyce Tang
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Mario Ventura
- Department of Biology, University of Bari, Bari, Italy
| | - Lucia Banci
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Florence, Italy
| | | | - Joshua M. Akey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Chris T. Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Fred H. Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
- Center for Academic Research and Training in Anthropogeny (CARTA), 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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