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Kurahashi H, Inagaki H, Ohye T, Kogo H, Tsutsumi M, Kato T, Tong M, Emanuel BS. The constitutional t(11;22): implications for a novel mechanism responsible for gross chromosomal rearrangements. Clin Genet 2011; 78:299-309. [PMID: 20507342 DOI: 10.1111/j.1399-0004.2010.01445.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The constitutional t(11;22)(q23;q11) is the most common recurrent non-Robertsonian translocation in humans. The breakpoint sequences of both chromosomes are characterized by several hundred base pairs of palindromic AT-rich repeats (PATRRs). Similar PATRRs have also been identified at the breakpoints of other nonrecurrent translocations, suggesting that PATRR-mediated chromosomal translocation represents one of the universal pathways for gross chromosomal rearrangement in the human genome. We propose that PATRRs have the potential to form cruciform structures through intrastrand-base pairing in single-stranded DNA, creating a source of genomic instability and leading to translocations. Indeed, de novo examples of the t(11;22) are detected at a high frequency in sperm from normal healthy males. This review synthesizes recent data illustrating a novel paradigm for an apparent spermatogenesis-specific translocation mechanism. This observation has important implications pertaining to the predominantly paternal origin of de novo gross chromosomal rearrangements in humans.
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Affiliation(s)
- H Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan.
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Ou Z, Stankiewicz P, Xia Z, Breman AM, Dawson B, Wiszniewska J, Szafranski P, Cooper ML, Rao M, Shao L, South ST, Coleman K, Fernhoff PM, Deray MJ, Rosengren S, Roeder ER, Enciso VB, Chinault AC, Patel A, Kang SHL, Shaw CA, Lupski JR, Cheung SW. Observation and prediction of recurrent human translocations mediated by NAHR between nonhomologous chromosomes. Genome Res 2011; 21:33-46. [PMID: 21205869 PMCID: PMC3012924 DOI: 10.1101/gr.111609.110] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 10/06/2010] [Indexed: 11/24/2022]
Abstract
Four unrelated families with the same unbalanced translocation der(4)t(4;11)(p16.2;p15.4) were analyzed. Both of the breakpoint regions in 4p16.2 and 11p15.4 were narrowed to large ∼359-kb and ∼215-kb low-copy repeat (LCR) clusters, respectively, by aCGH and SNP array analyses. DNA sequencing enabled mapping the breakpoints of one translocation to 24 bp within interchromosomal paralogous LCRs of ∼130 kb in length and 94.7% DNA sequence identity located in olfactory receptor gene clusters, indicating nonallelic homologous recombination (NAHR) as the mechanism for translocation formation. To investigate the potential involvement of interchromosomal LCRs in recurrent chromosomal translocation formation, we performed computational genome-wide analyses and identified 1143 interchromosomal LCR substrate pairs, >5 kb in size and sharing >94% sequence identity that can potentially mediate chromosomal translocations. Additional evidence for interchromosomal NAHR mediated translocation formation was provided by sequencing the breakpoints of another recurrent translocation, der(8)t(8;12)(p23.1;p13.31). The NAHR sites were mapped within 55 bp in ∼7.8-kb paralogous subunits of 95.3% sequence identity located in the ∼579-kb (chr 8) and ∼287-kb (chr 12) LCR clusters. We demonstrate that NAHR mediates recurrent constitutional translocations t(4;11) and t(8;12) and potentially many other interchromosomal translocations throughout the human genome. Furthermore, we provide a computationally determined genome-wide "recurrent translocation map."
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Affiliation(s)
- Zhishuo Ou
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhilian Xia
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amy M. Breman
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Brian Dawson
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Joanna Wiszniewska
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Przemyslaw Szafranski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - M. Lance Cooper
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mitchell Rao
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lina Shao
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sarah T. South
- Departments of Pediatrics and Pathology, University of Utah, Salt Lake City, Utah 84112, USA
| | - Karlene Coleman
- Children's Healthcare of Atlanta, Atlanta, Georgia 30033, USA
| | | | - Marcel J. Deray
- Department of Neurology, Miami Children's Hospital, Miami, Florida 33155, USA
| | | | | | | | - A. Craig Chinault
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ankita Patel
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sung-Hae L. Kang
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chad A. Shaw
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - James R. Lupski
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
- Texas Children's Hospital, Houston, Texas 77030, USA
| | - Sau W. Cheung
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Trombetta D, Mertens F, Lonoce A, D'Addabbo P, Rennstam K, Mandahl N, Storlazzi CT. Characterization of a hotspot region on chromosome 12 for amplification in ring chromosomes in atypical lipomatous tumors. Genes Chromosomes Cancer 2010; 48:993-1001. [PMID: 19691106 DOI: 10.1002/gcc.20700] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ring chromosomes are cytogenetic hallmarks of genomic amplification in several bone and soft tissue tumors, in particular atypical lipomatous tumors (ALT). In ALT, the ring chromosomes invariably contain amplified material from the central part of the long arm of chromosome 12, mainly 12q12-->15, but often also segments from other chromosomes are involved. Previous studies have shown that one of the recurrent amplicons in ALT, located in 12q13.3-14.1 and harboring the candidate target genes TSPAN31 and CDK4, often has a sharp centromeric border. To characterize this breakpoint region in more detail, 12 cases of ALT with ring chromosomes were analyzed by array comparative genomic hybridization and fluorescence in situ hybridization. In the seven cases showing a sharply delineated amplicon in 12q13.3-14.1, the breakpoint region was further investigated by real time quantitative polymerase chain reaction and Vectorette PCR. The breakpoints clustered to a 146-kb region containing 11 genes. Whereas there was no indication that the breakpoints gave rise to fusion genes, in silico analysis revealed that the breakpoint region was enriched for repeated elements that could be important for ring chromosome formation in ALT.
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Affiliation(s)
- Domenico Trombetta
- Department of Genetics and Microbiology, University of Bari, Bari, Italy.
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