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Vervoort L, Dierckxsens N, Santos MS, Meynants S, Souche E, Cools R, Heung T, Devriendt K, Peeters H, McDonald-McGinn DM, Swillen A, Breckpot J, Emanuel BS, Van Esch H, Bassett AS, Vermeesch JR. Multiple paralogues and recombination mechanisms drive the high incidence of 22q11.2 Deletion Syndrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.585046. [PMID: 38562770 PMCID: PMC10983858 DOI: 10.1101/2024.03.14.585046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The 22q11.2 deletion syndrome (22q11.2DS) is the most common microdeletion disorder. Why the incidence of 22q11.2DS is much greater than that of other genomic disorders remains unknown. Short read sequencing cannot resolve the complex segmental duplicon structure to provide direct confirmation of the hypothesis that the rearrangements are caused by non-allelic homologous recombination between the low copy repeats on chromosome 22 (LCR22s). To enable haplotype-specific assembly and rearrangement mapping in LCR22 regions, we combined fiber-FISH optical mapping with whole genome (ultra-)long read sequencing or rearrangement-specific long-range PCR on 24 duos (22q11.2DS patient and parent-of-origin) comprising several different LCR22-mediated rearrangements. Unexpectedly, we demonstrate that not only different paralogous segmental duplicon but also palindromic AT-rich repeats (PATRR) are driving 22q11.2 rearrangements. In addition, we show the existence of two different inversion polymorphisms preceding rearrangement, and somatic mosaicism. The existence of different recombination sites and mechanisms in paralogues and PATRRs which are copy number expanding in the human population are a likely explanation for the high 22q11.2DS incidence.
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Correll-Tash S, Lilley B, Salmons Iv H, Mlynarski E, Franconi CP, McNamara M, Woodbury C, Easley CA, Emanuel BS. Double strand breaks (DSBs) as indicators of genomic instability in PATRR-mediated translocations. Hum Mol Genet 2020; 29:3872-3881. [PMID: 33258468 DOI: 10.1093/hmg/ddaa251] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/05/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Genomic instability contributes to a variety of potentially damaging conditions, including DNA-based rearrangements. Breakage in the form of double strand breaks (DSBs) increases the likelihood of DNA damage, mutations and translocations. Certain human DNA regions are known to be involved in recurrent translocations, such as the palindrome-mediated rearrangements that have been identified at the breakpoints of several recurrent constitutional translocations: t(11;22)(q23;q11), t(17;22)(q11;q11) and t(8;22) (q24;q11). These breakpoints occur at the center of palindromic AT-rich repeats (PATRRs), which suggests that the structure of the DNA may play a contributory role, potentially through the formation of secondary cruciform structures. The current study analyzed the DSB propensity of these PATRR regions in both lymphoblastoid (mitotic) and spermatogenic cells (meiotic). Initial results found an increased association of sister chromatid exchanges (SCEs) at PATRR regions in experiments that used SCEs to assay DSBs, combining SCE staining with fluorescence in situ hybridization (FISH). Additional experiments used chromatin immunoprecipitation (ChIP) with antibodies for either markers of DSBs or proteins involved in DSB repair along with quantitative polymerase chain reaction to quantify the frequency of DSBs occurring at PATRR regions. The results indicate an increased rate of DSBs at PATRR regions. Additional ChIP experiments with the cruciform binding 2D3 antibody indicate an increased rate of cruciform structures at PATRR regions in both mitotic and meiotic samples. Overall, these experiments demonstrate an elevated rate of DSBs at PATRR regions, an indication that the structure of PATRR containing DNA may lead to increased breakage in multiple cellular environments.
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Affiliation(s)
- Sarah Correll-Tash
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Brenna Lilley
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Harold Salmons Iv
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elisabeth Mlynarski
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Colleen P Franconi
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Meghan McNamara
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carson Woodbury
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Charles A Easley
- Department of Environmental Health Sciences, College of Public Health at the University of Georgia, Athens, GA, 30602, USA
| | - Beverly S Emanuel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
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Delihas N. Formation of a Family of Long Intergenic Noncoding RNA Genes with an Embedded Translocation Breakpoint Motif in Human Chromosomal Low Copy Repeats of 22q11.2-Some Surprises and Questions. Noncoding RNA 2018; 4:ncrna4030016. [PMID: 30036931 PMCID: PMC6162681 DOI: 10.3390/ncrna4030016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/14/2018] [Accepted: 07/17/2018] [Indexed: 12/22/2022] Open
Abstract
A family of long intergenic noncoding RNA (lincRNA) genes, FAM230 is formed via gene sequence duplication, specifically in human chromosomal low copy repeats (LCR) or segmental duplications. This is the first group of lincRNA genes known to be formed by segmental duplications and is consistent with current views of evolution and the creation of new genes via DNA low copy repeats. It appears to be an efficient way to form multiple lincRNA genes. But as these genes are in a critical chromosomal region with respect to the incidence of abnormal translocations and resulting genetic abnormalities, the 22q11.2 region, and also carry a translocation breakpoint motif, several intriguing questions arise concerning the presence and function of the translocation breakpoint sequence in RNA genes situated in LCR22s.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, Stony Brook, New York, NY 11794-5222, USA.
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4
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Delihas N. A family of long intergenic non-coding RNA genes in human chromosomal region 22q11.2 carry a DNA translocation breakpoint/AT-rich sequence. PLoS One 2018; 13:e0195702. [PMID: 29668722 PMCID: PMC5906017 DOI: 10.1371/journal.pone.0195702] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/28/2018] [Indexed: 12/21/2022] Open
Abstract
FAM230C, a long intergenic non-coding RNA (lincRNA) gene in human chromosome 13 (chr13) is a member of lincRNA genes termed family with sequence similarity 230. An analysis using bioinformatics search tools and alignment programs was undertaken to determine properties of FAM230C and its related genes. Results reveal that the DNA translocation element, the Translocation Breakpoint Type A (TBTA) sequence, which consists of satellite DNA, Alu elements, and AT-rich sequences is embedded in the FAM230C gene. Eight lincRNA genes related to FAM230C also carry the TBTA sequences. These genes were formed from a large segment of the 3’ half of the FAM230C sequence duplicated in chr22, and are specifically in regions of low copy repeats (LCR22)s, in or close to the 22q.11.2 region. 22q11.2 is a chromosomal segment that undergoes a high rate of DNA translocation and is prone to genetic deletions. FAM230C-related genes present in other chromosomes do not carry the TBTA motif and were formed from the 5’ half region of the FAM230C sequence. These findings identify a high specificity in lincRNA gene formation by gene sequence duplication in different chromosomes.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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5
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Inagaki H, Kato T, Tsutsumi M, Ouchi Y, Ohye T, Kurahashi H. Palindrome-Mediated Translocations in Humans: A New Mechanistic Model for Gross Chromosomal Rearrangements. Front Genet 2016; 7:125. [PMID: 27462347 PMCID: PMC4940405 DOI: 10.3389/fgene.2016.00125] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/28/2016] [Indexed: 11/13/2022] Open
Abstract
Palindromic DNA sequences, which can form secondary structures, are widely distributed in the human genome. Although the nature of the secondary structure-single-stranded "hairpin" or double-stranded "cruciform"-has been extensively investigated in vitro, the existence of such unusual non-B DNA in vivo remains controversial. Here, we review palindrome-mediated gross chromosomal rearrangements possibly induced by non-B DNA in humans. Recent advances in next-generation sequencing have not yet overcome the difficulty of palindromic sequence analysis. However, a dozen palindromic AT-rich repeat (PATRR) sequences have been identified at the breakpoints of recurrent or non-recurrent chromosomal translocations in humans. The breakages always occur at the center of the palindrome. Analyses of polymorphisms within the palindromes indicate that the symmetry and length of the palindrome affect the frequency of the de novo occurrence of these palindrome-mediated translocations, suggesting the involvement of non-B DNA. Indeed, experiments using a plasmid-based model system showed that the formation of non-B DNA is likely the key to palindrome-mediated genomic rearrangements. Some evidence implies a new mechanism that cruciform DNAs may come close together first in nucleus and illegitimately joined. Analysis of PATRR-mediated translocations in humans will provide further understanding of gross chromosomal rearrangements in many organisms.
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Affiliation(s)
- Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health UniversityToyoake, Japan; Genome and Transcriptome Analysis Center, Fujita Health UniversityToyoake, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University Toyoake, Japan
| | - Makiko Tsutsumi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University Toyoake, Japan
| | - Yuya Ouchi
- Genome and Transcriptome Analysis Center, Fujita Health University Toyoake, Japan
| | - Tamae Ohye
- Department of Molecular Laboratory Medicine, Faculty of Medical Technology, School of Health Science, Fujita Health University Toyoake, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health UniversityToyoake, Japan; Genome and Transcriptome Analysis Center, Fujita Health UniversityToyoake, Japan
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Delihas N. Complexity of a small non-protein coding sequence in chromosomal region 22q11.2: presence of specialized DNA secondary structures and RNA exon/intron motifs. BMC Genomics 2015; 16:785. [PMID: 26467088 PMCID: PMC4607176 DOI: 10.1186/s12864-015-1958-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 09/28/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND DiGeorge Syndrome is a genetic abnormality involving ~3 Mb deletion in human chromosome 22, termed 22q.11.2. To better understand the non-coding regions of 22q.11.2, a small 10,000 bp non-protein-coding sequence close to the DiGeorge Critical Region 6 gene (DGCR6) was chosen for analysis and functional entities as the homologous sequence in the chimpanzee genome could be aligned and used for comparisons. METHODS The GenBank database provided genomic sequences. In silico computer programs were used to find homologous DNA sequences in human and chimpanzee genomes, generate random sequences, determine DNA sequence alignments, sequence comparisons and nucleotide repeat copies, and to predicted DNA secondary structures. RESULTS At its 5' half, the 10,000 bp sequence has three distinct sections that represent phylogenetically variable sequences. These Variable Regions contain biased mutations with a very high A + T content, multiple copies of the motif TATAATATA and sequences that fold into long A:T-base-paired stem loops. The 3' half of the 10,000 bp unit, highly conserved between human and chimpanzee, has sequences representing exons of lncRNA genes and segments of introns of protein genes. Central to the 10,000 bp unit are the multiple copies of a sequence that originates from the flanking 5' end of the translocation breakpoint Type A sequence. This breakpoint flanking sequence carries the exon and intron motifs. The breakpoint Type A sequence seems to be a major player in the proliferation of these RNA motifs, as well as the proliferation of Variable Regions in the 10,000 bp segment and other regions within 22q.11.2. CONCLUSIONS The data indicate that a non-coding region of the chromosome may be reserved for highly biased mutations that lead to formation of specialized sequences and DNA secondary structures. On the other hand, the highly conserved nucleotide sequence of the non-coding region may form storage sites for RNA motifs.
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Affiliation(s)
- Nicholas Delihas
- Department of Molecular Genetics and Microbiology, School of Medicine, Stony, Brook University, Stony Brook, NY, 11794, USA.
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Javadekar SM, Raghavan SC. Snaps and mends: DNA breaks and chromosomal translocations. FEBS J 2015; 282:2627-45. [PMID: 25913527 DOI: 10.1111/febs.13311] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/29/2015] [Accepted: 04/23/2015] [Indexed: 01/11/2023]
Abstract
Integrity in entirety is the preferred state of any organism. The temporal and spatial integrity of the genome ensures continued survival of a cell. DNA breakage is the first step towards creation of chromosomal translocations. In this review, we highlight the factors contributing towards the breakage of chromosomal DNA. It has been well-established that the structure and sequence of DNA play a critical role in selective fragility of the genome. Several non-B-DNA structures such as Z-DNA, cruciform DNA, G-quadruplexes, R loops and triplexes have been implicated in generation of genomic fragility leading to translocations. Similarly, specific sequences targeted by proteins such as Recombination Activating Genes and Activation Induced Cytidine Deaminase are involved in translocations. Processes that ensure the integrity of the genome through repair may lead to persistence of breakage and eventually translocations if their actions are anomalous. An insufficient supply of nucleotides and chromatin architecture may also play a critical role. This review focuses on a range of events with the potential to threaten the genomic integrity of a cell, leading to cancer.
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Affiliation(s)
- Saniya M Javadekar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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Mishra D, Kato T, Inagaki H, Kosho T, Wakui K, Kido Y, Sakazume S, Taniguchi-Ikeda M, Morisada N, Iijima K, Fukushima Y, Emanuel BS, Kurahashi H. Breakpoint analysis of the recurrent constitutional t(8;22)(q24.13;q11.21) translocation. Mol Cytogenet 2014; 7:55. [PMID: 25478009 PMCID: PMC4255720 DOI: 10.1186/s13039-014-0055-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 07/25/2014] [Indexed: 11/23/2022] Open
Abstract
Backgrounds The t(8;22)(q24.13;q11.2) has been identified as one of several recurrent
constitutional translocations mediated by palindromic AT-rich repeats (PATRRs).
Although the breakage on 22q11 utilizes the same PATRR as that of the more
prevalent constitutional t(11;22)(q23;q11.2), the breakpoint region on 8q24 has
not been elucidated in detail since the analysis of palindromic sequence is
technically challenging. Results In this study, the entire 8q24 breakpoint region has been resolved by next
generation sequencing. Eight polymorphic alleles were identified and compared with
the junction sequences of previous and two recently identified t(8;22) cases . All
of the breakpoints were found to be within the PATRRs on chromosomes 8 and 22
(PATRR8 and PATRR22), but the locations were different among cases at the level of
nucleotide resolution. The translocations were always found to arise on symmetric
PATRR8 alleles with breakpoints at the center of symmetry. The translocation
junction is often accompanied by symmetric deletions at the center of both PATRRs.
Rejoining occurs with minimal homology between the translocation partners.
Remarkably, comparison of der (8) to der(22) sequences shows identical breakpoint
junctions between them, which likely represent products of two independent events
on the basis of a classical model. Conclusions Our data suggest the hypothesis that interactions between the two PATRRs prior to
the translocation event might trigger illegitimate recombination resulting in the
recurrent palindrome-mediated translocation.
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Affiliation(s)
- Divya Mishra
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto 390-8621, Nagano, Japan
| | - Keiko Wakui
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto 390-8621, Nagano, Japan
| | - Yasuhiro Kido
- Department of Pediatrics, Dokkyo Medical University Koshigaya Hospital, Koshigaya 343-8555, Saitama, Japan
| | - Satoru Sakazume
- Department of Pediatrics, Dokkyo Medical University Koshigaya Hospital, Koshigaya 343-8555, Saitama, Japan
| | - Mariko Taniguchi-Ikeda
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Hyogo, Japan
| | - Naoya Morisada
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Hyogo, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe 650-0017, Hyogo, Japan
| | - Yoshimitsu Fukushima
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto 390-8621, Nagano, Japan
| | - Beverly S Emanuel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia 19104, PA, USA.,Department of Pediatrics, The Perelman School of Medicine of the University of Pennsylvania, Philadelphia 19104, PA, USA
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Aichi, Japan
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Ohye T, Inagaki H, Kato T, Tsutsumi M, Kurahashi H. Prevalence of Emanuel syndrome: theoretical frequency and surveillance result. Pediatr Int 2014; 56:462-6. [PMID: 24980921 DOI: 10.1111/ped.12437] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 04/03/2014] [Accepted: 05/12/2014] [Indexed: 02/03/2023]
Abstract
Constitutional t(11;22)(q23;q11) is the most frequent recurrent non-Robertsonian translocation in humans. Balanced carriers of t(11;22) usually manifest no clinical symptoms, and are often identified after the birth of offspring with an unbalanced form of this translocation, known as Emanuel syndrome. To determine the prevalence of the disorder, we sent surveillance questionnaires to 735 core hospitals in Japan. The observed number of Emanuel syndrome cases was 36 and that of t(11;22) balanced translocation carriers, 40. On the basis of the de novo t(11;22) translocation frequency in sperm from healthy men, we calculated the frequency of the translocations in the general population. Accordingly, the prevalence of Emanuel syndrome was estimated at 1 in 110,000. Based on this calculation, the estimated number of Emanuel syndrome cases in Japan is 1063 and of t(11;22) balanced translocation carriers, 16,604, which are much higher than the numbers calculated from the questionnaire responses. It is possible that this discordance is partly attributable to a lack of disease identification. Further efforts should be made to increase the awareness of Emanuel syndrome to ensure a better quality of life for affected patients and their families.
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Affiliation(s)
- Tamae Ohye
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi, Japan
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Kato T, Franconi CP, Sheridan MB, Hacker AM, Inagakai H, Glover TW, Arlt MF, Drabkin HA, Gemmill RM, Kurahashi H, Emanuel BS. Analysis of the t(3;8) of hereditary renal cell carcinoma: a palindrome-mediated translocation. Cancer Genet 2014; 207:133-40. [PMID: 24813807 DOI: 10.1016/j.cancergen.2014.03.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/07/2014] [Accepted: 03/10/2014] [Indexed: 12/01/2022]
Abstract
It has emerged that palindrome-mediated genomic instability generates DNA-based rearrangements. The presence of palindromic AT-rich repeats (PATRRs) at the translocation breakpoints suggested a palindrome-mediated mechanism in the generation of several recurrent constitutional rearrangements: the t(11;22), t(17;22), and t(8;22). To date, all reported PATRR-mediated translocations include the PATRR on chromosome 22 (PATRR22) as a translocation partner. Here, the constitutional rearrangement, t(3;8)(p14.2;q24.1), segregating with renal cell carcinoma in two families, is examined. The chromosome 8 breakpoint lies in PATRR8 in the first intron of the RNF139 (TRC8) gene, whereas the chromosome 3 breakpoint is located in an AT-rich palindromic sequence in intron 3 of the FHIT gene (PATRR3). Thus, the t(3;8) is the first PATRR-mediated, recurrent, constitutional translocation that does not involve PATRR22. Furthermore, we detect de novo translocations similar to the t(11;22) and t(8;22), involving PATRR3 in normal sperm. The breakpoint on chromosome 3 is in proximity to FRA3B, the most common fragile site in the human genome and a site of frequent deletions in tumor cells. However, the lack of involvement of PATRR3 sequence in numerous FRA3B-related deletions suggests that there are several different DNA sequence-based etiologies responsible for chromosome 3p14.2 genomic rearrangements.
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Affiliation(s)
- Takema Kato
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Colleen P Franconi
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Molly B Sheridan
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - April M Hacker
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hidehito Inagakai
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, Japan
| | - Thomas W Glover
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Harry A Drabkin
- Division of Hematology-Oncology, Medical University of South Carolina, Charleston, SC, USA
| | - Robert M Gemmill
- Division of Hematology-Oncology, Medical University of South Carolina, Charleston, SC, USA
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, Japan
| | - Beverly S Emanuel
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
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MacArthur JAL, Spector TD, Lindsay SJ, Mangino M, Gill R, Small KS, Hurles ME. The rate of nonallelic homologous recombination in males is highly variable, correlated between monozygotic twins and independent of age. PLoS Genet 2014; 10:e1004195. [PMID: 24603440 PMCID: PMC3945173 DOI: 10.1371/journal.pgen.1004195] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 01/06/2014] [Indexed: 01/23/2023] Open
Abstract
Nonallelic homologous recombination (NAHR) between highly similar duplicated sequences generates chromosomal deletions, duplications and inversions, which can cause diverse genetic disorders. Little is known about interindividual variation in NAHR rates and the factors that influence this. We estimated the rate of deletion at the CMT1A-REP NAHR hotspot in sperm DNA from 34 male donors, including 16 monozygotic (MZ) co-twins (8 twin pairs) aged 24 to 67 years old. The average NAHR rate was 3.5×10−5 with a seven-fold variation across individuals. Despite good statistical power to detect even a subtle correlation, we observed no relationship between age of unrelated individuals and the rate of NAHR in their sperm, likely reflecting the meiotic-specific origin of these events. We then estimated the heritability of deletion rate by calculating the intraclass correlation (ICC) within MZ co-twins, revealing a significant correlation between MZ co-twins (ICC = 0.784, p = 0.0039), with MZ co-twins being significantly more correlated than unrelated pairs. We showed that this heritability cannot be explained by variation in PRDM9, a known regulator of NAHR, or variation within the NAHR hotspot itself. We also did not detect any correlation between Body Mass Index (BMI), smoking status or alcohol intake and rate of NAHR. Our results suggest that other, as yet unidentified, genetic or environmental factors play a significant role in the regulation of NAHR and are responsible for the extensive variation in the population for the probability of fathering a child with a genomic disorder resulting from a pathogenic deletion. Many genetic disorders are caused by deletions of specific regions of DNA in sperm or egg cells that go on to produce a child. This can occur through ectopic homologous recombination between highly similar segments of DNA at different positions within the genome. Little is known about the differences in rates of deletion between individuals or the factors that influence this. We analysed the rate of deletion at one such section of DNA in sperm DNA from 34 male donors, including 16 monozygotic co-twins. We observed a seven-fold variation in deletion rate across individuals. Deletion rate is significantly correlated between monozygote co-twins, indicating that deletion rate is heritable. This heritability cannot be explained by age, any known genetic regulator of deletion rate, Body Mass Index, smoking status or alcohol intake. Our results suggest that other, as yet unidentified, genetic or environmental factors play a significant role in the regulation of deletion. These factors are responsible for the extensive variation in the population for the probability of fathering a child with a genomic disorder resulting from a pathogenic deletion.
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Affiliation(s)
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, London, United Kingdom
| | - Sarah J. Lindsay
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, London, United Kingdom
| | - Raj Gill
- Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, London, United Kingdom
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King's College London, St. Thomas' Hospital, London, United Kingdom
| | - Matthew E. Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- * E-mail:
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12
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Inagaki H, Ohye T, Kogo H, Tsutsumi M, Kato T, Tong M, Emanuel BS, Kurahashi H. Two sequential cleavage reactions on cruciform DNA structures cause palindrome-mediated chromosomal translocations. Nat Commun 2013; 4:1592. [PMID: 23481400 DOI: 10.1038/ncomms2595] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 02/11/2013] [Indexed: 11/09/2022] Open
Abstract
Gross chromosomal rearrangements (GCRs), such as translocations, deletions or inversions, are often generated by illegitimate repair between two DNA breakages at regions with nucleotide sequences that might potentially adopt a non-B DNA conformation. We previously established a plasmid-based model system that recapitulates palindrome-mediated recurrent chromosomal translocations in humans, and demonstrated that cruciform DNA conformation is required for the translocation-like rearrangements. Here we show that two sequential reactions that cleave the cruciform structures give rise to the translocation: GEN1-mediated resolution that cleaves diagonally at the four-way junction of the cruciform and Artemis-mediated opening of the subsequently formed hairpin ends. Indeed, translocation products in human sperm reveal the remnants of this two-step mechanism. These two intrinsic pathways that normally fulfil vital functions independently, Holliday-junction resolution in homologous recombination and coding joint formation in rearrangement of antigen-receptor genes, act upon the unusual DNA conformation in concert and lead to a subset of recurrent GCRs in humans.
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Affiliation(s)
- Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
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Czuchlewski DR, Farzanmehr H, Robinett S, Haines S, Reichard KK. t(9;22)(q34;q11.2) is a recurrent constitutional non-Robertsonian translocation and a rare cytogenetic mimic of chronic myeloid leukemia. Cancer Genet 2012; 204:572-6. [PMID: 22137489 DOI: 10.1016/j.cancergen.2011.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 10/14/2011] [Accepted: 10/17/2011] [Indexed: 01/26/2023]
Abstract
The diagnosis of hematologic malignancy can be greatly aided by the detection of a cytogenetic abnormality. However, care must be taken to ensure that constitutional chromosomal abnormalities are not misattributed to a putative population of malignant cells. Here we present an unusual case in which a constitutional balanced t(9;22)(q34;q11.2) cytogenetically mimicked the acquired, t(9;22)(q34;q11.2), that is characteristic of chronic myeloid leukemia. Of special note, fluorescence in situ hybridization (FISH) analysis for this constitutional translocation (9;22)(q34;q11.2) using standard probes for BCR and ABL1 resulted in an abnormal pattern that was potentially misinterpretable as a BCR-ABL1 fusion. This is the first reported FISH analysis of a constitutional t(9;22)(q34;q11.2), and overall only the second report of such an abnormality. In light of the isolated prior report, our case also suggests that the constitutional t(9;22)(q34;q11.2) is one of the very few recurrent constitutional non-Robertsonian translocations described in humans. Our case underscores the necessity of complete clinical and laboratory correlation to avoid misdiagnosis of myeloid malignancy in the setting of rare constitutional cytogenetic abnormalities.
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Cer RZ, Bruce KH, Donohue DE, Temiz NA, Mudunuri US, Yi M, Volfovsky N, Bacolla A, Luke BT, Collins, Stephens RM. Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool). CURRENT PROTOCOLS IN HUMAN GENETICS 2012; Chapter 18:Unit 18.7.1-22. [PMID: 22470144 PMCID: PMC3350812 DOI: 10.1002/0471142905.hg1807s73] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This unit describes basic protocols on using the non-B DNA Motif Search Tool (nBMST) to search for sequence motifs predicted to form alternative DNA conformations that differ from the canonical right-handed Watson-Crick double-helix, collectively known as non-B DNA, and on using the associated PolyBrowse, a GBrowse-based genomic browser. The nBMST is a Web-based resource that allows users to submit one or more DNA sequences to search for inverted repeats (cruciform DNA), mirror repeats (triplex DNA), direct/tandem repeats (slipped/hairpin structures), G4 motifs (tetraplex, G-quadruplex DNA), alternating purine-pyrimidine tracts (left-handed Z-DNA), and A-phased repeats (static bending). The nBMST is versatile, simple to use, does not require bioinformatics skills, and can be applied to any type of DNA sequences, including viral and bacterial genomes, up to an aggregate of 20 megabasepairs (Mbp).
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Affiliation(s)
- RZ Cer
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick MD 21702, USA
| | - KH Bruce
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick MD 21702, USA
| | - DE Donohue
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick MD 21702, USA
| | - NA Temiz
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick MD 21702, USA
| | - US Mudunuri
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick MD 21702, USA
| | - M Yi
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick MD 21702, USA
| | - N Volfovsky
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick MD 21702, USA
| | - A Bacolla
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick MD 21702, USA
- The Dell Pediatric Research Institute, Division of Toxicology and Pharmacology, The University of Texas at Austin, Austin TX 78723, USA
| | - BT Luke
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick MD 21702, USA
| | - Collins
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick MD 21702, USA
| | - RM Stephens
- Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick MD 21702, USA
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Kato T, Kurahashi H, Emanuel BS. Chromosomal translocations and palindromic AT-rich repeats. Curr Opin Genet Dev 2012; 22:221-8. [PMID: 22402448 DOI: 10.1016/j.gde.2012.02.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/03/2012] [Accepted: 02/06/2012] [Indexed: 10/28/2022]
Abstract
Repetitive DNA sequences constitute 30% of the human genome, and are often sites of genomic rearrangement. Recently, it has been found that several constitutional translocations, especially those that involve chromosome 22, take place utilizing palindromic sequences on 22q11 and on the partner chromosome. Analysis of translocation junction fragments shows that the breakpoints of such palindrome-mediated translocations are localized at the center of palindromic AT-rich repeats (PATRRs). The presence of PATRRs at the breakpoints indicates a palindrome-mediated mechanism involved in the generation of these constitutional translocations. Identification of these PATRR-mediated translocations suggests a universal pathway for gross chromosomal rearrangement in the human genome. De novo occurrences of PATRR-mediated translocations can be detected by PCR in normal sperm samples but not somatic cells. Polymorphisms of various PATRRs influence their propensity for adopting a secondary structure, which in turn affects de novo translocation frequency. We propose that the PATRRs form an unstable secondary structure, which leads to double-strand breaks at the center of the PATRR. The double-strand breaks appear to be followed by a non-homologous end-joining repair pathway, ultimately leading to the translocations. This review considers recent findings concerning the mechanism of meiosis-specific, PATRR-mediated translocations.
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Affiliation(s)
- Takema Kato
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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DNA secondary structure is influenced by genetic variation and alters susceptibility to de novo translocation. Mol Cytogenet 2011; 4:18. [PMID: 21899780 PMCID: PMC3197554 DOI: 10.1186/1755-8166-4-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2011] [Accepted: 09/08/2011] [Indexed: 12/15/2022] Open
Abstract
Background Cumulative evidence suggests that DNA secondary structures impact DNA replication, transcription and genomic rearrangements. One of the best studied examples is the recurrent constitutional t(11;22) in humans that is mediated by potentially cruciform-forming sequences at the breakpoints, palindromic AT-rich repeats (PATRRs). We previously demonstrated that polymorphisms of PATRR sequences affect the frequency of de novo t(11;22)s in sperm samples from normal healthy males. These studies were designed to determine whether PATRR polymorphisms affect DNA secondary structure, thus leading to variation in translocation frequency. Methods We studied the potential for DNA cruciform formation for several PATRR11 polymorphic alleles using mobility shift analysis in gel electrophoresis as well as by direct visualization of the DNA by atomic force microscopy. The structural data for various alleles were compared with the frequency of de novo t(11;22)s the allele produced. Results The data indicate that the propensity for DNA cruciform structure of each polymorphic allele correlates with the frequency of de novo t(11;22)s produced (r = 0.77, P = 0.01). Conclusions Although indirect, our results strongly suggest that the PATRR adopts unstable cruciform structures during spermatogenesis that act as translocation hotspots in humans.
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