1
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Bugallo A, Sánchez M, Fernández-García M, Segurado M. S-phase checkpoint prevents leading strand degradation from strand-associated nicks at stalled replication forks. Nucleic Acids Res 2024; 52:5121-5137. [PMID: 38520409 PMCID: PMC11109941 DOI: 10.1093/nar/gkae192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 03/25/2024] Open
Abstract
The S-phase checkpoint is involved in coupling DNA unwinding with nascent strand synthesis and is critical to maintain replication fork stability in conditions of replicative stress. However, its role in the specific regulation of leading and lagging strands at stalled forks is unclear. By conditionally depleting RNaseH2 and analyzing polymerase usage genome-wide, we examine the enzymology of DNA replication during a single S-phase in the presence of replicative stress and show that there is a differential regulation of lagging and leading strands. In checkpoint proficient cells, lagging strand replication is down-regulated through an Elg1-dependent mechanism. Nevertheless, when checkpoint function is impaired we observe a defect specifically at the leading strand, which was partially dependent on Exo1 activity. Further, our genome-wide mapping of DNA single-strand breaks reveals that strand discontinuities highly accumulate at the leading strand in HU-treated cells, whose dynamics are affected by checkpoint function and Exo1 activity. Our data reveal an unexpected role of Exo1 at the leading strand and support a model of fork stabilization through prevention of unrestrained Exo1-dependent resection of leading strand-associated nicks after fork stalling.
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Affiliation(s)
- Alberto Bugallo
- Instituto de Biología Funcional y Genómica (CSIC/USAL), Campus Miguel de Unamuno, Salamanca 37007, Spain
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica (CSIC/USAL), Campus Miguel de Unamuno, Salamanca 37007, Spain
| | - María Fernández-García
- Instituto de Biología Funcional y Genómica (CSIC/USAL), Campus Miguel de Unamuno, Salamanca 37007, Spain
| | - Mónica Segurado
- Instituto de Biología Funcional y Genómica (CSIC/USAL), Campus Miguel de Unamuno, Salamanca 37007, Spain
- Departamento de Microbiología y Genética (USAL), Campus Miguel de Unamuno, Salamanca 37007, Spain
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2
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Xie X, Chen C, Liang Q, Wu X, Wang X, Wu W, Ding Q. Characterization of two large duplications of
F9
associated with mild and severe haemophilia B, respectively. Haemophilia 2019; 25:475-483. [PMID: 30866119 DOI: 10.1111/hae.13704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/06/2018] [Accepted: 01/23/2019] [Indexed: 02/01/2023]
Affiliation(s)
- Xiaoling Xie
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Changming Chen
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Qian Liang
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Xi Wu
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
| | - Wenman Wu
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
- Faculty of Medical Laboratory Science, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital Shanghai Jiaotong University School of Medicine Shanghai China
- Collaborative Innovation Center of Hematology Shanghai Jiaotong University School of Medicine Shanghai China
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3
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Beck CR, Carvalho CMB, Akdemir ZC, Sedlazeck FJ, Song X, Meng Q, Hu J, Doddapaneni H, Chong Z, Chen ES, Thornton PC, Liu P, Yuan B, Withers M, Jhangiani SN, Kalra D, Walker K, English AC, Han Y, Chen K, Muzny DM, Ira G, Shaw CA, Gibbs RA, Hastings PJ, Lupski JR. Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2. Cell 2019; 176:1310-1324.e10. [PMID: 30827684 PMCID: PMC6438178 DOI: 10.1016/j.cell.2019.01.045] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 11/06/2018] [Accepted: 01/25/2019] [Indexed: 01/16/2023]
Abstract
DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. Evidence for an increased rate of clustered single-nucleotide variant (SNV) mutation in cis with non-recurrent rearrangements was found. Indel and SNV formation are associated with both copy-number gains and losses of 17p11.2, occur up to ∼1 Mb away from the breakpoint junctions, and favor C > G transversion substitutions; results suggest that single-stranded DNA is formed during the genesis of the SV and provide compelling support for a microhomology-mediated break-induced replication (MMBIR) mechanism for SV formation. Our data show an additional mutational burden of MMBIR consisting of hypermutation confined to the locus and manifesting as SNVs and indels predominantly within genes.
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Affiliation(s)
- Christine R Beck
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | | | - Zeynep C Akdemir
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | | | - Xiaofei Song
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | | | - Zechen Chong
- Department of Genetics and the Informatics Institute, the University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Edward S Chen
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Philip C Thornton
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Marjorie Withers
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | | | - Divya Kalra
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | | | - Adam C English
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - P J Hastings
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX 77030, USA.
| | - James R Lupski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA; Department of Pediatrics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, BCM, Houston, TX 77030, USA.
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4
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Pronounced maternal parent-of-origin bias for type-1 NF1 microdeletions. Hum Genet 2018; 137:365-373. [PMID: 29730711 DOI: 10.1007/s00439-018-1888-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/24/2018] [Indexed: 01/02/2023]
Abstract
Neurofibromatosis type 1 (NF1) is caused, in 4.7-11% of cases, by large deletions encompassing the NF1 gene and its flanking regions within 17q11.2. Different types of large NF1 deletion occur which are distinguishable by their breakpoint location and underlying mutational mechanism. Most common are the type-1 NF1 deletions of 1.4 Mb which exhibit recurrent breakpoints caused by nonallelic homologous recombination (NAHR), also termed unequal crossover. Here, we analyzed 37 unrelated families of patients with de novo type-1 NF1 deletions by means of short tandem repeat (STR) profiling to determine the parental origin of the deletions. We observed that 33 of the 37 type-1 deletions were of maternal origin (89.2% of cases; p < 0.0001). Analysis of the patients' siblings indicated that, in 14 informative cases, ten (71.4%) deletions resulted from interchromosomal unequal crossover during meiosis I. Our findings indicate a strong maternal parent-of-origin bias for type-1 NF1 deletions. A similarly pronounced maternal transmission bias has been reported for recurrent copy number variants (CNVs) within 16p11.2 associated with autism, but not so far for any other NAHR-mediated pathogenic CNVs. Region-specific genomic features are likely to be responsible for the maternal bias in the origin of both the 16p11.2 CNVs and type-1 NF1 deletions.
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5
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Carvalho CMB, Lupski JR. Mechanisms underlying structural variant formation in genomic disorders. Nat Rev Genet 2016; 17:224-38. [PMID: 26924765 DOI: 10.1038/nrg.2015.25] [Citation(s) in RCA: 406] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the recent burst of technological developments in genomics, and the clinical implementation of genome-wide assays, our understanding of the molecular basis of genomic disorders, specifically the contribution of structural variation to disease burden, is evolving quickly. Ongoing studies have revealed a ubiquitous role for genome architecture in the formation of structural variants at a given locus, both in DNA recombination-based processes and in replication-based processes. These reports showcase the influence of repeat sequences on genomic stability and structural variant complexity and also highlight the tremendous plasticity and dynamic nature of our genome in evolution, health and disease susceptibility.
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Affiliation(s)
- Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, MG 30190-002, Brazil
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA.,Texas Children's Hospital, Houston, Texas 77030, USA
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6
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Polymerase δ replicates both strands after homologous recombination-dependent fork restart. Nat Struct Mol Biol 2015; 22:932-8. [PMID: 26436826 PMCID: PMC4655445 DOI: 10.1038/nsmb.3100] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/28/2015] [Indexed: 12/16/2022]
Abstract
To maintain genetic stability DNA must be replicated only once and replication completed even when individual replication forks are inactivated. Because fork inactivation is common, the passive convergence of an adjacent fork is insufficient to rescue all inactive forks. Thus, eukaryotic cells have evolved homologous recombination-dependent mechanisms to restart persistent inactive forks. Completing DNA synthesis via Homologous Recombination Restarted Replication (HoRReR) ensures cell survival, but at a cost. One such cost is increased mutagenesis caused by HoRReR being more error prone than canonical replication. This increased error rate implies that the HoRReR mechanism is distinct from that of a canonical fork. Here we exploit the fission yeast Schizosaccharomyces pombe to demonstrate that a DNA sequence duplicated by HoRReR during S phase is replicated semi-conservatively, but that both the leading and lagging strands are synthesised by DNA polymerase delta.
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7
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Anand RP, Tsaponina O, Greenwell PW, Lee CS, Du W, Petes TD, Haber JE. Chromosome rearrangements via template switching between diverged repeated sequences. Genes Dev 2014; 28:2394-406. [PMID: 25367035 PMCID: PMC4215184 DOI: 10.1101/gad.250258.114] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Anand et al. examined break-induced replication (BIR) and template switching between highly diverged sequences in S. cerevisiae, induced during repair of a site-specific double-strand break (DSB). Template switches between highly divergent sequences appear to be mechanistically distinct from the initial strand invasions that establish BIR. BIR traversing repeated DNA sequences frequently results in complex translocations analogous to those seen in mammalian cells. These results suggest that template switching among repeated genes is a potent driver of genome instability and evolution. Recent high-resolution genome analyses of cancer and other diseases have revealed the occurrence of microhomology-mediated chromosome rearrangements and copy number changes. Although some of these rearrangements appear to involve nonhomologous end-joining, many must have involved mechanisms requiring new DNA synthesis. Models such as microhomology-mediated break-induced replication (MM-BIR) have been invoked to explain these rearrangements. We examined BIR and template switching between highly diverged sequences in Saccharomyces cerevisiae, induced during repair of a site-specific double-strand break (DSB). Our data show that such template switches are robust mechanisms that give rise to complex rearrangements. Template switches between highly divergent sequences appear to be mechanistically distinct from the initial strand invasions that establish BIR. In particular, such jumps are less constrained by sequence divergence and exhibit a different pattern of microhomology junctions. BIR traversing repeated DNA sequences frequently results in complex translocations analogous to those seen in mammalian cells. These results suggest that template switching among repeated genes is a potent driver of genome instability and evolution.
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Affiliation(s)
- Ranjith P Anand
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02254, USA
| | - Olga Tsaponina
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02254, USA
| | - Patricia W Greenwell
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - Cheng-Sheng Lee
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02254, USA
| | - Wei Du
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02254, USA
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, 27710, USA
| | - James E Haber
- Rosenstiel Basic Medical Sciences Research Center, Department of Biology, Brandeis University, Waltham, Massachusetts 02254, USA;
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8
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Chen L, Zhou W, Zhang C, Lupski JR, Jin L, Zhang F. CNV instability associated with DNA replication dynamics: evidence for replicative mechanisms in CNV mutagenesis. Hum Mol Genet 2014; 24:1574-83. [PMID: 25398944 DOI: 10.1093/hmg/ddu572] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Copy number variation (CNV) in the human genome is of vital importance to human health and evolution of our species. However, much of the molecular basis of CNV mutagenesis remains to be elucidated. Considering the DNA replication model of 'fork stalling and template switching' for CNV formation, we hypothesized that replication fork progression could be important for CNV mutagenesis. However, molecular assays of replication fork progression at the genome level are technically challenging. Instead, we conducted an estimation of DNA replication dynamics, as the statistic R, using the readily available data of replication timing. Small R-values can reflect 'slowed' replication, which could result from less fork initiation, reduced fork speed or fork barriers. We generated genome-wide profiles of R in the genomes of human, mouse and Drosophila. Intriguingly, the CNV breakpoints in all three genomes showed significantly biased distributions toward the genomic regions with small R-values, suggesting potential replication stress-induced CNV instability. Notably, among the human CNVs with distinct breakpoint junction characteristics, the homology-mediated and VNTR-mediated CNVs contribute the most to the correlation between CNV instability and the statistic R, consistent with the recent findings in the C. elegans and yeast genomes of repeat-induced DNA replication error and consequent CNV formation. The statistic R may reflect both replication stress and the effect of local genome architecture on fork progression. Our concordant observations suggest an important role for DNA replicative mechanisms in CNV mutagenesis and genome instability.
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Affiliation(s)
- Lu Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and
| | - Weichen Zhou
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and
| | - Cheng Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and
| | - James R Lupski
- Department of Molecular and Human Genetics and Department of Pediatrics, Baylor College of Medicine, Houston TX 77030, USA Texas Children's Hospital, Houston, TX 77030, USA
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,
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9
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Peng Z, Zhou W, Fu W, Du R, Jin L, Zhang F. Correlation between frequency of non-allelic homologous recombination and homology properties: evidence from homology-mediated CNV mutations in the human genome. Hum Mol Genet 2014; 24:1225-33. [PMID: 25324539 DOI: 10.1093/hmg/ddu533] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Non-allelic homologous recombination (NAHR) is one of the key mechanisms of DNA rearrangement. NAHR occurring between direct homologous repeats can generate genomic copy number variation (CNV) and make significant contributions to both genome evolution and human diseases such as cancer. Intriguingly, previous observations on the rare CNVs at certain genomic disorder loci suggested that NAHR frequency could be dependent on homology properties. However, such a correlation remains unclear at the other NAHR-mediated CNV loci, especially the common CNVs in human populations. Different from the rare CNVs associated with genomic disorders, it is challenging to identify de novo NAHR events at common CNV loci. Therefore, our previously proposed statistic M was employed in estimating relative mutation rate for the NAHR-mediated CNVs in human populations. By utilizing generalized regression neural network and principal component analysis in studying 4330 CNVs ascertained in 3 HapMap populations, we identified the CNVs mediated by NAHR between paired segmental duplications (SDs) and further revealed the correlations between SD properties and NAHR probability. SD length and inter-SD distance were shown to make major contributions to the occurrence of NAHR, whereas chromosomal position and sequence similarity of paired SDs are also involved in NAHR. An integrated effect of SD properties on NAHR frequency was revealed for the common CNVs in human populations. These observations can be well explained by ectopic synapsis in NAHR together with our proposed model of chromosomal compression/extension/looping (CCEL) for homology mis-pairing. Our findings showed the important roles of SDs in NAHR and human genomic evolution.
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Affiliation(s)
- Zhen Peng
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Weichen Zhou
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and
| | - Wenqing Fu
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Renqian Du
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,
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10
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Xiao J, Zhang L, Wang J, Jiang Y, Jin L, Lu J, Jin L, Zhong C, Xu X, Zhang F. Rearrangement structure-independent strategy of CNV breakpoint analysis. Mol Genet Genomics 2014; 289:755-63. [PMID: 24737421 DOI: 10.1007/s00438-014-0850-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 03/28/2014] [Indexed: 12/21/2022]
Abstract
Rare copy number variations (CNVs) generated by human genomic rearrangements have been shown to play an important role in pathogenesis of human diseases and cancers. CNV breakpoint analysis can help define genomic location, genetic content and sequence structure of pathogenic CNVs. This process is vital to elucidate CNV mutational mechanism and etiology of CNV-associated disorders. However, it is technically challenging to map CNV breakpoints at base-pair level, especially in the genomic regions with sequence complexity. In this study, we developed a new method of capture and breakpoint approaching sequencing (CBAS) to efficiently obtain CNV breakpoint sequences. This strategy is independent of CNV structures and applicable to various CNV types. As was demonstrated in CNV-associated patients with neurological disorders, CBAS achieved fine mapping of breakpoint sequences for compound deletion, complex duplication, and translocation. Intriguingly, CBAS also revealed unexpected CNV complexity involving long-range DNA rearrangement. Our observations showed that CBAS is an efficient method for obtaining CNV breakpoint sequence and mapping insertional events as well. This method can facilitate the researches on CNV-associated human diseases and cancers. CBAS is also applicable to mapping the integration sites of retrovirus (such as HIV) and transgenes in model organisms.
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Affiliation(s)
- Jianqiu Xiao
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai, 200433, China
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11
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Abstract
The field of cytogenetics has focused on studying the number, structure, function and origin of chromosomal abnormalities and the evolution of chromosomes. The development of fluorescent molecules that either directly or via an intermediate molecule bind to DNA has led to the development of fluorescent in situ hybridization (FISH), a technology linking cytogenetics to molecular genetics. This technique has a wide range of applications that increased the dimension of chromosome analysis. The field of cytogenetics is particularly important for medical diagnostics and research as well as for gene ordering and mapping. Furthermore, the increased application of molecular biology techniques, such as array-based technologies, has led to improved resolution, extending the recognized range of microdeletion/microduplication syndromes and genomic disorders. In adopting these newly expanded methods, cytogeneticists have used a range of technologies to study the association between visible chromosome rearrangements and defects at the single nucleotide level. Overall, molecular cytogenetic techniques offer a remarkable number of potential applications, ranging from physical mapping to clinical and evolutionary studies, making a powerful and informative complement to other molecular and genomic approaches. This manuscript does not present a detailed history of the development of molecular cytogenetics; however, references to historical reviews and experiments have been provided whenever possible. Herein, the basic principles of molecular cytogenetics, the technologies used to identify chromosomal rearrangements and copy number changes, and the applications for cytogenetics in biomedical diagnosis and research are presented and discussed.
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Affiliation(s)
- Mariluce Riegel
- Serviço de Genética Médica, Hospital de Clínicas, Porto Alegre, RS, Brazil . ; Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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12
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Cao L, Molina J, Abad C, Carmona-Mora P, Cárdenas Oyarzo A, Young JI, Walz K. Correct developmental expression level of Rai1 in forebrain neurons is required for control of body weight, activity levels and learning and memory. Hum Mol Genet 2013; 23:1771-82. [DOI: 10.1093/hmg/ddt568] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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13
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Auffray C, Caulfield T, Khoury MJ, Lupski JR, Schwab M, Veenstra T. 2012 highlights in translational 'omics. Genome Med 2013; 5:10. [PMID: 23369291 PMCID: PMC3707050 DOI: 10.1186/gm414] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Charles Auffray
- CNRS Institute of Biological Sciences, European Institute for Systems Biology & Medicine, Claude Bernard University, Université de Lyon, France
| | - Timothy Caulfield
- Faculty of Law and School of Public Health, 461 Law Centre, University of Alberta, Edmonton, T6G 2H5, Canada
| | - Muin J Khoury
- Office of Public Health Genomics, Centers for Disease Control and Prevention, 1600 Clifton Rd, NE, MS E61, Atlanta, GA 30333, USA
| | - James R Lupski
- Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbach Str. 112, 70367 Stuttgart, Germany
- Department of Clinical Pharmacology, Institute of Experimental and Clinical Pharmacology and Toxicology, University Hospital, 72076 Tübingen, Germany
| | - Timothy Veenstra
- Laboratory of Proteomics and Analytical Technologies, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA
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