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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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Ait Saada A, Guo W, Costa AB, Yang J, Wang J, Lobachev K. Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions. Nucleic Acids Res 2023; 51:3722-3734. [PMID: 36919609 PMCID: PMC10164571 DOI: 10.1093/nar/gkad153] [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: 11/11/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
DNA inverted repeats (IRs) are widespread across many eukaryotic genomes. Their ability to form stable hairpin/cruciform secondary structures is causative in triggering chromosome instability leading to several human diseases. Distance and sequence divergence between IRs are inversely correlated with their ability to induce gross chromosomal rearrangements (GCRs) because of a lesser probability of secondary structure formation and chromosomal breakage. In this study, we demonstrate that structural parameters that normally constrain the instability of IRs are overcome when the repeats interact in single-stranded DNA (ssDNA). We established a system in budding yeast whereby >73 kb of ssDNA can be formed in cdc13-707fs mutants. We found that in ssDNA, 12 bp or 30 kb spaced Alu-IRs show similarly high levels of GCRs, while heterology only beyond 25% suppresses IR-induced instability. Mechanistically, rearrangements arise after cis-interaction of IRs leading to a DNA fold-back and the formation of a dicentric chromosome, which requires Rad52/Rad59 for IR annealing as well as Rad1-Rad10, Slx4, Msh2/Msh3 and Saw1 proteins for nonhomologous tail removal. Importantly, using structural characteristics rendering IRs permissive to DNA fold-back in yeast, we found that ssDNA regions mapped in cancer genomes contain a substantial number of potentially interacting and unstable IRs.
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Affiliation(s)
- Anissia Ait Saada
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Wenying Guo
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alex B Costa
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jiaxin Yang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Kirill S Lobachev
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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3
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Abbaspour S, Isazadeh A, Heidari M, Heidari M, Hajazimian S, Soleyman-Nejad M, Taskhiri MH, Bolhassani M, Ebrahimi AH, Keshavarz P, Shiri Z, Heidari M. Prevalence of Chromosomal Abnormalities in Iranian Patients with Infertility. ARCHIVES OF IRANIAN MEDICINE 2023; 26:110-116. [PMID: 37543931 PMCID: PMC10685900 DOI: 10.34172/aim.2023.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/13/2022] [Indexed: 08/08/2023]
Abstract
BACKGROUND The numerical and structural abnormalities of chromosomes are the most common cause of infertility. Here, we evaluated the prevalence and types of chromosomal abnormalities in Iranian infertile patients. METHODS We enrolled 1750 couples of reproductive age with infertility, who referred to infertility clinics in Tehran during 2014- 2019, in order to perform chromosomal analysis. Peripheral blood samples were obtained from all couples and chromosomal abnormalities were evaluated by G-banded metaphase karyotyping. In some cases, the detected abnormalities were confirmed using fluorescence in-situ hybridization (FISH). RESULTS We detected various chromosomal abnormalities in 114/3500 (3.257%) patients with infertility. The prevalence of chromosomal abnormalities was 44/114 (38.596%) among infertile females and 70/114 (61.403%) among infertile males. Structural chromosomal abnormalities were found in 27/1750 infertile females and 35/1750 infertile males. Numerical chromosomal abnormalities were found in 17/1750 of females and 35/1750 of males. The 45, XY, rob (13;14) (p10q10) translocation and Klinefelter syndrome (47, XXY) were the most common structural and numerical chromosomal abnormalities in the Iranian infertile patients, respectively. CONCLUSION In general, we found a high prevalence of chromosomal abnormalities in Iranian patients with reproductive problems. Our study highlights the importance of cytogenetic studies in infertile patients before starting infertility treatments approaches.
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Affiliation(s)
- Saima Abbaspour
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Alireza Isazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Masoud Heidari
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Saba Hajazimian
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | | | | | - Parvaneh Keshavarz
- Cellular and Molecular Research Center, Faculty of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Zahra Shiri
- Ariagene Medical Genetics Laboratory, Qom, Iran
| | - Mansour Heidari
- Ariagene Medical Genetics Laboratory, Qom, Iran
- Department of Medical Genetics, Tehran University of Medical Sciences (TUMS), Tehran, Iran
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Zeng H, Zhou H, Lin J, Pang Q, Chen S, Lin S, Xue C, Shen Z. Palindrome-Embedded Hairpin Structure and Its Target-Catalyzed Padlock Cyclization for Label-Free MicroRNA-Initiated Rolling Circle Amplification. ACS OMEGA 2023; 8:2253-2261. [PMID: 36687024 PMCID: PMC9850459 DOI: 10.1021/acsomega.2c06532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Highly sensitive detection of microRNAs (miRNAs) is of great significance in early diagnosis of cancers. Here, we develop a palindrome-embedded hairpin structure and its target-catalyzed padlock cyclization for rolling circle amplification, named PHP-RCA for simplicity, which can be applied in label-free ultrasensitive detection of miRNA. PHP-RCA is a facile system that consists of only an oligonucleotide probe with a palindrome-embedded hairpin structure (PHP). The two ends of PHP were extended as overhangs and designed with the complementary sequences of the target. Hence, the phosphorylated PHP can be cyclized by T4 DNA ligase in the presence of the target that serves as the ligation template. This ligation has formed a palindrome-embedded dumbbell-shaped probe (PDP) that allows phi29 polymerase to perform a typical target-primed RCA on PDP by taking miRNA as a primer, resulting in the production of a lengthy tandem repeat. Benefits from the palindromic sequences and hairpin-shaped structure in padlock double-stranded structures can be infinitely produced during the RCA reaction and provide numerous binding sites for SYBR Green I, a double-stranded dye, achieving a sharp response signal for label-free target detection. We have demonstrated that the proposed system exhibits a good linear range from 0.1 fM to 5 nM with a low detection limit of 0.1 fM, and the non-target miRNA can be clearly distinguished. The advantages of high efficiency, label-free signaling, and the use of only one oligonucleotide component make the PHP-RCA suitable for ultrasensitive, economic, and convenient detection of target miRNAs. This simple and powerful system is expected to provide a promising platform for tumor diagnosis, prognosis, and therapy.
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Affiliation(s)
- Huaiwen Zeng
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Hongyin Zhou
- Key
Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang
Provincial Key Laboratory of Medical Genetics, Department of Cell
Biology and Medical Genetics, College of Laboratory Medicine and Life
Sciences, Wenzhou Medical University, Wenzhou 325000, PR China
| | - Junliang Lin
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Qi Pang
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Siqiang Chen
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Shaoqi Lin
- Yuhuan
People’s Hospital, Taizhou Zhejiang Province, Taizhou 317600, PR China
| | - Chang Xue
- Key
Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang
Provincial Key Laboratory of Medical Genetics, Department of Cell
Biology and Medical Genetics, College of Laboratory Medicine and Life
Sciences, Wenzhou Medical University, Wenzhou 325000, PR China
| | - Zhifa Shen
- Key
Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang
Provincial Key Laboratory of Medical Genetics, Department of Cell
Biology and Medical Genetics, College of Laboratory Medicine and Life
Sciences, Wenzhou Medical University, Wenzhou 325000, PR China
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Vervoort L, Vermeesch JR. The 22q11.2 Low Copy Repeats. Genes (Basel) 2022; 13:2101. [PMID: 36421776 PMCID: PMC9690962 DOI: 10.3390/genes13112101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 07/22/2023] Open
Abstract
LCR22s are among the most complex loci in the human genome and are susceptible to nonallelic homologous recombination. This can lead to a variety of genomic disorders, including deletions, duplications, and translocations, of which the 22q11.2 deletion syndrome is the most common in humans. Interrogating these phenomena is difficult due to the high complexity of the LCR22s and the inaccurate representation of the LCRs across different reference genomes. Optical mapping techniques, which provide long-range chromosomal maps, could be used to unravel the complex duplicon structure. These techniques have already uncovered the hypervariability of the LCR22-A haplotype in the human population. Although optical LCR22 mapping is a major step forward, long-read sequencing approaches will be essential to reach nucleotide resolution of the LCR22s and map the crossover sites. Accurate maps and sequences are needed to pinpoint potential predisposing alleles and, most importantly, allow for genotype-phenotype studies exploring the role of the LCR22s in health and disease. In addition, this research might provide a paradigm for the study of other rare genomic disorders.
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Bansal A, Kaushik S, Kukreti S. Non-canonical DNA structures: Diversity and disease association. Front Genet 2022; 13:959258. [PMID: 36134025 PMCID: PMC9483843 DOI: 10.3389/fgene.2022.959258] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
A complete understanding of DNA double-helical structure discovered by James Watson and Francis Crick in 1953, unveil the importance and significance of DNA. For the last seven decades, this has been a leading light in the course of the development of modern biology and biomedical science. Apart from the predominant B-form, experimental shreds of evidence have revealed the existence of a sequence-dependent structural diversity, unusual non-canonical structures like hairpin, cruciform, Z-DNA, multistranded structures such as DNA triplex, G-quadruplex, i-motif forms, etc. The diversity in the DNA structure depends on various factors such as base sequence, ions, superhelical stress, and ligands. In response to these various factors, the polymorphism of DNA regulates various genes via different processes like replication, transcription, translation, and recombination. However, altered levels of gene expression are associated with many human genetic diseases including neurological disorders and cancer. These non-B-DNA structures are expected to play a key role in determining genetic stability, DNA damage and repair etc. The present review is a modest attempt to summarize the available literature, illustrating the occurrence of non-canonical structures at the molecular level in response to the environment and interaction with ligands and proteins. This would provide an insight to understand the biological functions of these unusual DNA structures and their recognition as potential therapeutic targets for diverse genetic diseases.
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Affiliation(s)
- Aparna Bansal
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Shikha Kaushik
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- Department of Chemistry, Rajdhani College, University of Delhi, New Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Lab, Department of Chemistry, University of Delhi, Delhi, India
- *Correspondence: Shrikant Kukreti,
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Delihas N. An ancestral genomic sequence that serves as a nucleation site for de novo gene birth. PLoS One 2022; 17:e0267864. [PMID: 35552551 PMCID: PMC9097989 DOI: 10.1371/journal.pone.0267864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/17/2022] [Indexed: 11/24/2022] Open
Abstract
The process of gene birth is of major interest with current excitement concerning de novo gene formation. We report a new and different mechanism of de novo gene birth based on the finding and the characteristics of a short non-coding sequence situated between two protein genes, termed a spacer sequence. This non-coding sequence is present in genomes of Mus musculus, the house mouse and Philippine tarsier, a primitive ancestral primate. The ancestral sequence is highly conserved during primate evolution with certain base pairs totally invariant from mouse to humans. By following the birth of the sequence of human lincRNA BCRP3 (BCR activator of RhoGEF and GTPase 3 pseudogene) during primate evolution, we find diverse genes, long non-coding RNA and protein genes (and sequences that do not appear to encode a gene) that all stem from the 3’ end of the spacer, and all begin with a similar sequence. During primate evolution, part of the BCRP3 sequence initially formed in the Old World Monkeys and developed into different primate genes before evolving into the BCRP3 gene in humans. The gene developmental process consists of the initiation of DNA synthesis at spacer 3’ ends, addition of a complex of tandem transposable elements and the addition of a segment of another gene. The findings support the concept of the spacer sequence as a starting site for DNA synthesis that leads to formation of different genes with the addition of other sequences. These data suggest a new process of de novo gene birth.
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Affiliation(s)
- Nicholas Delihas
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, United States of America
- * E-mail:
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Hao X, Wu J, Fu W, Zhang R, Zhong S, Deng Y, Zhu Y, Ye Y, Fang Q. Prenatal Diagnosis of Fetuses with Emanuel Syndrome: Results of Ultrasound Examination and Invasive Genetic Testing. Prenat Diagn 2022; 42:469-477. [PMID: 35043432 DOI: 10.1002/pd.6098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 11/12/2022]
Abstract
OBJECTIVE To investigate prenatal manifestations of Emanuel syndrome (ES) by retrospectively analyzing the results of prenatal diagnosis. METHODS Thirteen fetuses were collected from 5 hospitals, of which six were confirmed with 47,der(22)t(11;22) (ES) by karyotype and chromosomal microarray analysis (CMA). Seven were diagnosed with 46,t(11;22) balanced translocations by karyotype, including one de novo mosaic 46,XX,t(11;22). In 3/7, CMA was performed but did not identify chromosomal imbalances. The results of prenatal diagnoses were reviewed, including ultrasound examinations and genetic testing. RESULTS In ES fetuses, the derivative 22 was consistently inherited from the mother, while in the balanced translocation group, the t(11;22) chromosome was of paternal origin in 3/6 cases, All ES fetuses presented with multiple abnormalities by ultrasound examinations. Diaphragm hernia (3/6), Dandy-Walker complex (3/6), and kidney aplasia (3/6), were the most common ultrasound findings. Sonographic soft markers such as increased nuchal translucency, increased nuchal fold thickness appeared in 3 cases and all of these were associated with other anomalies. However, none of the ultrasound findings differentiated ES from other genetic syndromes during fetal period. CONCLUSIONS In this series, in fetuses with a der(22), the derivative chromosome was consistently of maternal origin. In contrast, 46,t(11;22) balanced translocations were of maternal or paternal origin. The results contribute to the literature regarding the fetal phenotype of ES. Due to the absence of specific features distinguishing ES from other genetic syndromes, confirming the diagnosis through invasive genetic testing is necessary. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Xiulan Hao
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jianzhu Wu
- Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenting Fu
- NHC Key laboratory of Male Reproduction and Genetic, Guangdong Provincial Reproductive Science Institute, Guangzhou, China
| | - Rui Zhang
- Division of Maternal-Fetal Medicine, Jinan University-affiliated Shenzhen Baoan Women's and Children's Hospital, Shenzhen, China
| | - Shilin Zhong
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yuqing Deng
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yunxiao Zhu
- Department of Ultrasonic Medicine, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yanchou Ye
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Qun Fang
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,Fetal Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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9
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Pei Z, Deng K, Lei C, Du D, Yu G, Sun X, Xu C, Zhang S. Identifying Balanced Chromosomal Translocations in Human Embryos by Oxford Nanopore Sequencing and Breakpoints Region Analysis. Front Genet 2022; 12:810900. [PMID: 35116057 PMCID: PMC8804325 DOI: 10.3389/fgene.2021.810900] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/13/2021] [Indexed: 01/02/2023] Open
Abstract
Background: Balanced chromosomal aberrations, especially balanced translocations, can cause infertility, recurrent miscarriage or having chromosomally defective offspring. Preimplantation genetic testing for structural rearrangement (PGT-SR) has been widely implemented to improve the clinical outcomes by selecting euploid embryos for transfer, whereas embryos with balanced translocation karyotype were difficult to be distinguished by routine genetic techniques from those with a normal karyotype. Method: In this present study, we developed a clinically applicable method for reciprocal translocation carriers to reduce the risk of pregnancy loss. In the preclinical phase, we identified reciprocal translocation breakpoints in blood of translocation carriers by long-read Oxford Nanopore sequencing, followed by junction-spanning polymerase chain reaction (PCR) and Sanger sequencing. In the clinical phase of embryo diagnosis, aneuploidies and unbalanced translocations were screened by comprehensive chromosomal screening (CCS) with single nucleotide polymorphism (SNP) microarray, carrier embryos were diagnosed by junction-spanning PCR and family haplotype linkage analysis of the breakpoints region. Amniocentesis and cytogenetic analysis of fetuses in the second trimester were performed after embryo transfer to conform the results diagnosed by the presented method. Results: All the accurate reciprocal translocation breakpoints were effectively identified by Nanopore sequencing and confirmed by Sanger sequencing. Twelve embryos were biopsied and detected, the results of junction-spanning PCR and haplotype linkage analysis were consistent. In total, 12 biopsied blastocysts diagnosed to be euploid, in which 6 were aneuploid or unbalanced, three blastocysts were identified to be balanced translocation carriers and three to be normal karyotypes. Two euploid embryos were subsequently transferred back to patients and late prenatal karyotype analysis of amniotic fluid cells was performed. The outcomes diagnosed by the current approach were totally consistent with the fetal karyotypes. Conclusions: In summary, these investigations in our study illustrated that chromosomal reciprocal translocations in embryos can be accurately diagnosed. Long-read Nanopore sequencing and breakpoint analysis contributes to precisely evaluate the genetic risk of disrupted genes, and provides a way of selecting embryos with normal karyotype, especially for couples those without a reference.
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Affiliation(s)
- Zhenle Pei
- Shanghai Ji Ai Genetics and IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Ke Deng
- Shanghai Ji Ai Genetics and IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Caixai Lei
- Shanghai Ji Ai Genetics and IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Danfeng Du
- Shanghai Ji Ai Genetics and IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Guoliang Yu
- Chigene (Beijing) Translational Medical Research Center Co. Ltd., Beijing, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics and IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Shanghai Ji Ai Genetics and IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- *Correspondence: Congjian Xu, ; Shuo Zhang,
| | - Shuo Zhang
- Shanghai Ji Ai Genetics and IVF Institute, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- *Correspondence: Congjian Xu, ; Shuo Zhang,
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10
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Ait Saada A, Costa AB, Sheng Z, Guo W, Haber JE, Lobachev K. Structural parameters of palindromic repeats determine the specificity of nuclease attack of secondary structures. Nucleic Acids Res 2021; 49:3932-3947. [PMID: 33772579 PMCID: PMC8053094 DOI: 10.1093/nar/gkab168] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/24/2021] [Accepted: 03/02/2021] [Indexed: 12/15/2022] Open
Abstract
Palindromic sequences are a potent source of chromosomal instability in many organisms and are implicated in the pathogenesis of human diseases. In this study, we investigate which nucleases are responsible for cleavage of the hairpin and cruciform structures and generation of double-strand breaks at inverted repeats in Saccharomyces cerevisiae. We demonstrate that the involvement of structure-specific nucleases in palindrome fragility depends on the distance between inverted repeats and their transcriptional status. The attack by the Mre11 complex is constrained to hairpins with loops <9 nucleotides. This restriction is alleviated upon RPA depletion, indicating that RPA controls the stability and/or formation of secondary structures otherwise responsible for replication fork stalling and DSB formation. Mus81-Mms4 cleavage of cruciforms occurs at divergently but not convergently transcribed or nontranscribed repeats. Our study also reveals the third pathway for fragility at perfect and quasi-palindromes, which involves cruciform resolution during the G2 phase of the cell cycle.
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Affiliation(s)
- Anissia Ait Saada
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GE 30332, USA
| | - Alex B Costa
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GE 30332, USA
| | - Ziwei Sheng
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GE 30332, USA
| | - Wenying Guo
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GE 30332, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Waltham, MA 02454-9110, USA
| | - Kirill S Lobachev
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GE 30332, USA
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11
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Roy U, Raghavan SC. Deleterious point mutations in T-cell acute lymphoblastic leukemia: Mechanistic insights into leukemogenesis. Int J Cancer 2021; 149:1210-1220. [PMID: 33634864 DOI: 10.1002/ijc.33527] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/11/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is characterized by the leukemogenic transformation of immature T cells, which accumulate an array of genetic and epigenetic lesions, leading to a sustained proliferation of abnormal T cells. Genetic alterations in the DNA repair genes, protooncogenes, transcription factors, and epigenetic modifiers have been studied in the past decade using next-generation sequencing and high-resolution copy number arrays. While other genomic lesions like chromosomal rearrangements, inversions, insertions, and gene fusions have been well studied at functional level, the mechanism of generation of driver mutations in T-ALL is the subject of current investigation. Novel oncogenic mutations in the TP53, BRCA2, PTEN, IL7R, RAS, NOTCH1, ETV6, BCL11B, WT1, DNMT3A, PRC2, PHF6, USP7, KDM6A and an array of other genes disrupt the genetic and epigenetic homeostasis in T-ALL. In this review, we have summarized the mechanistic role of deleterious driver mutations in T-ALL initiation and progression. We speculate that the formation of non-B DNA structures could be one of the primary reasons for the occurrence of different genomic lesions seen in T-ALL, which warrants further investigation. Understanding the mechanism behind the genesis of oncogenic mutations will pave the way to develop targeted therapies that can improve the overall survival and treatment outcome.
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Affiliation(s)
- Urbi Roy
- 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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12
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Svetec Miklenić M, Svetec IK. Palindromes in DNA-A Risk for Genome Stability and Implications in Cancer. Int J Mol Sci 2021; 22:2840. [PMID: 33799581 PMCID: PMC7999016 DOI: 10.3390/ijms22062840] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
A palindrome in DNA consists of two closely spaced or adjacent inverted repeats. Certain palindromes have important biological functions as parts of various cis-acting elements and protein binding sites. However, many palindromes are known as fragile sites in the genome, sites prone to chromosome breakage which can lead to various genetic rearrangements or even cell death. The ability of certain palindromes to initiate genetic recombination lies in their ability to form secondary structures in DNA which can cause replication stalling and double-strand breaks. Given their recombinogenic nature, it is not surprising that palindromes in the human genome are involved in genetic rearrangements in cancer cells as well as other known recurrent translocations and deletions associated with certain syndromes in humans. Here, we bring an overview of current understanding and knowledge on molecular mechanisms of palindrome recombinogenicity and discuss possible implications of DNA palindromes in carcinogenesis. Furthermore, we overview the data on known palindromic sequences in the human genome and efforts to estimate their number and distribution, as well as underlying mechanisms of genetic rearrangements specific palindromic sequences cause.
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Affiliation(s)
| | - Ivan Krešimir Svetec
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia;
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13
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Zell J, Rota Sperti F, Britton S, Monchaud D. DNA folds threaten genetic stability and can be leveraged for chemotherapy. RSC Chem Biol 2021; 2:47-76. [PMID: 35340894 PMCID: PMC8885165 DOI: 10.1039/d0cb00151a] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022] Open
Abstract
Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an anticancer target, and the manipulation of DDR pathways as a valuable anticancer strategy. We describe in detail the DDR signalling and repair pathways activated in response to DNA damage. We then summarise the current understanding of non-B DNA folds, such as G-quadruplexes and DNA junctions, when they are formed and why they can offer a more specific therapeutic target compared to that of canonical B-DNA. Finally, we merge these subjects to depict the new and highly promising chemotherapeutic strategy which combines enhanced-specificity DNA damaging and DDR targeting agents. This review thus highlights how chemical biology has given rise to significant scientific advances thanks to resolutely multidisciplinary research efforts combining molecular and cell biology, chemistry and biophysics. We aim to provide the non-specialist reader a gateway into this exciting field and the specialist reader with a new perspective on the latest results achieved and strategies devised.
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Affiliation(s)
- Joanna Zell
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS Toulouse France
- Équipe Labellisée la Ligue Contre le Cancer 2018 Toulouse France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
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14
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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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15
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A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes. Hum Genome Var 2020; 7:40. [PMID: 33298903 PMCID: PMC7680136 DOI: 10.1038/s41439-020-00127-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/24/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
A palindrome in DNA is like a palindrome in language, but when read backwards, it is a complement of the forward sequence; effectively, the two halves of a sequence complement each other from its midpoint like in a double strand of DNA. Palindromes are distributed throughout the human genome and play significant roles in gene expression and regulation. Palindromic mutations are linked to many human diseases, such as neuronal disorders, mental retardation, and various cancers. In this work, we computed and analyzed the palindromic sequences in the human genome and studied their conservation in personal genomes using 1000 Genomes data. We found that ~30% of the palindromes exhibit variation, some of which are caused by rare variants. The analysis of disease/trait-associated single-nucleotide polymorphisms in palindromic regions showed that disease-associated risk variants are 14 times more likely to be present in palindromic regions than in other regions. The catalog of palindromes in the reference genome and 1000 Genomes is being made available here with details on their variations in each individual genome to serve as a resource for future and retrospective whole-genome studies identifying statistically significant palindrome variations associated with diseases or traits and their roles in disease mechanisms.
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16
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Abstract
Mutation of the human genome results in three classes of genomic variation: single nucleotide variants; short insertions or deletions; and large structural variants (SVs). Some mutations occur during normal processes, such as meiotic recombination or B cell development, and others result from DNA replication or aberrant repair of breaks in sequence-specific contexts. Regardless of mechanism, mutations are subject to selection, and some hotspots can manifest in disease. Here, we discuss genomic regions prone to mutation, mechanisms contributing to mutation susceptibility, and the processes leading to their accumulation in normal and somatic genomes. With further, more accurate human genome sequencing, additional mutation hotspots, mechanistic details of their formation, and the relevance of hotspots to evolution and disease are likely to be discovered.
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17
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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] [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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18
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Svetec Miklenić M, Gatalica N, Matanović A, Žunar B, Štafa A, Lisnić B, Svetec IK. Size-dependent antirecombinogenic effect of short spacers on palindrome recombinogenicity. DNA Repair (Amst) 2020; 90:102848. [PMID: 32388488 DOI: 10.1016/j.dnarep.2020.102848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 03/21/2020] [Accepted: 03/28/2020] [Indexed: 01/01/2023]
Abstract
Palindromic sequences in DNA can instigate genetic recombination and genome instability, which can result in devastating conditions such as the Emmanuel syndrome. Palindrome recombinogenicity increases with its size and sequence similarity between palindrome arms, while quasipalindromes with long spacers are less recombinogenic. However, the minimal spacer length, which could reduce or abolish palindrome recombinogenicity in the eukaryotic genome, was never determined. Therefore, we constructed a series of palindromes containing spacers of lengths ranging from 0 (perfect palindrome) to 10 bp and tested their recombinogenicity in yeast Saccharomyces cerevisiae. We found that a 7 bp spacer significantly reduces 126 bp palindrome recombinogenicity, while a 10 bp spacer completely stabilizes palindromes up to 150 bp long. Additionally, we showed that palindrome stimulated recombination rate is not dependent on Mus81 and Yen1 endonucleases. We also compared the recombinogenicity of a perfect 126 bp palindrome and a corresponding quasipalindrome consisting of the same palindrome arms with a stabilising 10 bp spacer in sgs1Δ and rad27Δ backgrounds, since both Sgs1 helicase and Rad27 endonuclease are implicated in preventing hairpin formation at palindromic sequences during replication.
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Affiliation(s)
- Marina Svetec Miklenić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Nikolina Gatalica
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Angela Matanović
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Bojan Žunar
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Anamarija Štafa
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Berislav Lisnić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ivan Krešimir Svetec
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia.
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19
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Demaerel W, Mostovoy Y, Yilmaz F, Vervoort L, Pastor S, Hestand MS, Swillen A, Vergaelen E, Geiger EA, Coughlin CR, Chow SK, McDonald-McGinn D, Morrow B, Kwok PY, Xiao M, Emanuel BS, Shaikh TH, Vermeesch JR. The 22q11 low copy repeats are characterized by unprecedented size and structural variability. Genome Res 2020; 29:1389-1401. [PMID: 31481461 PMCID: PMC6724673 DOI: 10.1101/gr.248682.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022]
Abstract
Low copy repeats (LCRs) are recognized as a significant source of genomic instability, driving genome variability and evolution. The Chromosome 22 LCRs (LCR22s) mediate nonallelic homologous recombination (NAHR) leading to the 22q11 deletion syndrome (22q11DS). However, LCR22s are among the most complex regions in the genome, and their structure remains unresolved. The difficulty in generating accurate maps of LCR22s has also hindered localization of the deletion end points in 22q11DS patients. Using fiber FISH and Bionano optical mapping, we assembled LCR22 alleles in 187 cell lines. Our analysis uncovered an unprecedented level of variation in LCR22s, including LCR22A alleles ranging in size from 250 to 2000 kb. Further, the incidence of various LCR22 alleles varied within different populations. Additionally, the analysis of LCR22s in 22q11DS patients and their parents enabled further refinement of the rearrangement site within LCR22A and -D, which flank the 22q11 deletion. The NAHR site was localized to a 160-kb paralog shared between the LCR22A and -D in seven 22q11DS patients. Thus, we present the most comprehensive map of LCR22 variation to date. This will greatly facilitate the investigation of the role of LCR variation as a driver of 22q11 rearrangements and the phenotypic variability among 22q11DS patients.
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Affiliation(s)
| | - Yulia Mostovoy
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, California 94158, USA
| | - Feyza Yilmaz
- Department of Integrative Biology, University of Colorado Denver, Denver, Colorado 80204, USA.,Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, Colorado 80045, USA
| | | | - Steven Pastor
- Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Matthew S Hestand
- Departement of Human Genetics, KU Leuven, Leuven, 3000 Belgium.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio 45221, USA
| | - Ann Swillen
- Departement of Human Genetics, KU Leuven, Leuven, 3000 Belgium
| | - Elfi Vergaelen
- Departement of Human Genetics, KU Leuven, Leuven, 3000 Belgium
| | - Elizabeth A Geiger
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Curtis R Coughlin
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Stephen K Chow
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, California 94158, USA
| | - Donna McDonald-McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Bernice Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, UCSF School of Medicine, San Francisco, California 94158, USA
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA
| | - Beverly S Emanuel
- Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Tamim H Shaikh
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, Colorado 80045, USA
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20
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Irony-Tur Sinai M, Salamon A, Stanleigh N, Goldberg T, Weiss A, Wang YH, Kerem B. AT-dinucleotide rich sequences drive fragile site formation. Nucleic Acids Res 2019; 47:9685-9695. [PMID: 31410468 PMCID: PMC6765107 DOI: 10.1093/nar/gkz689] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/18/2019] [Accepted: 08/04/2019] [Indexed: 12/29/2022] Open
Abstract
Common fragile sites (CFSs) are genomic regions prone to breakage under replication stress conditions recurrently rearranged in cancer. Many CFSs are enriched with AT-dinucleotide rich sequences (AT-DRSs) which have the potential to form stable secondary structures upon unwinding the double helix during DNA replication. These stable structures can potentially perturb DNA replication progression, leading to genomic instability. Using site-specific targeting system, we show that targeted integration of a 3.4 kb AT-DRS derived from the human CFS FRA16C into a chromosomally stable region within the human genome is able to drive fragile site formation under conditions of replication stress. Analysis of >1300 X chromosomes integrated with the 3.4 kb AT-DRS revealed recurrent gaps and breaks at the integration site. DNA sequences derived from the integrated AT-DRS showed in vitro a significantly increased tendency to fold into branched secondary structures, supporting the predicted mechanism of instability. Our findings clearly indicate that intrinsic DNA features, such as complexed repeated sequence motifs, predispose the human genome to chromosomal instability.
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Affiliation(s)
- Michal Irony-Tur Sinai
- Department of Genetics, The Life Sciences Institute, The Hebrew University of Jerusalem, 9190401, Israel
| | - Anita Salamon
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, 229080733, USA
| | - Noemie Stanleigh
- Department of Genetics, The Life Sciences Institute, The Hebrew University of Jerusalem, 9190401, Israel
| | - Tchelet Goldberg
- Department of Genetics, The Life Sciences Institute, The Hebrew University of Jerusalem, 9190401, Israel
| | - Aryeh Weiss
- Faculty of Engineering, Bar-Ilan University, Ramat-Gan, 52900, Israel
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, 229080733, USA
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University of Jerusalem, 9190401, Israel
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21
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Bracewell R, Chatla K, Nalley MJ, Bachtrog D. Dynamic turnover of centromeres drives karyotype evolution in Drosophila. eLife 2019; 8:e49002. [PMID: 31524597 PMCID: PMC6795482 DOI: 10.7554/elife.49002] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/12/2019] [Indexed: 12/21/2022] Open
Abstract
Centromeres are the basic unit for chromosome inheritance, but their evolutionary dynamics is poorly understood. We generate high-quality reference genomes for multiple Drosophila obscura group species to reconstruct karyotype evolution. All chromosomes in this lineage were ancestrally telocentric and the creation of metacentric chromosomes in some species was driven by de novo seeding of new centromeres at ancestrally gene-rich regions, independently of chromosomal rearrangements. The emergence of centromeres resulted in a drastic size increase due to repeat accumulation, and dozens of genes previously located in euchromatin are now embedded in pericentromeric heterochromatin. Metacentric chromosomes secondarily became telocentric in the pseudoobscura subgroup through centromere repositioning and a pericentric inversion. The former (peri)centric sequences left behind shrunk dramatically in size after their inactivation, yet contain remnants of their evolutionary past, including increased repeat-content and heterochromatic environment. Centromere movements are accompanied by rapid turnover of the major satellite DNA detected in (peri)centromeric regions.
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Affiliation(s)
- Ryan Bracewell
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Kamalakar Chatla
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Matthew J Nalley
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Doris Bachtrog
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyUnited States
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22
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Zhang S, Liang F, Lei C, Wu J, Fu J, Yang Q, Luo X, Yu G, Wang D, Zhang Y, Lu D, Sun X, Liang Y, Xu C. Long-read sequencing and haplotype linkage analysis enabled preimplantation genetic testing for patients carrying pathogenic inversions. J Med Genet 2019; 56:741-749. [PMID: 31439719 PMCID: PMC6860410 DOI: 10.1136/jmedgenet-2018-105976] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 05/31/2019] [Accepted: 06/13/2019] [Indexed: 01/04/2023]
Abstract
Background Preimplantation genetic testing (PGT) has already been applied in patients known to carry chromosomal structural variants to improve the clinical outcome of assisted reproduction. However, conventional molecular techniques are not capable of reliably distinguishing embryos that carry balanced inversion from those with a normal karyotype. We aim to evaluate the use of long-read sequencing in combination with haplotype linkage analysis to address this challenge. Methods Long-read sequencing on Oxford Nanopore platform was employed to identify the precise positions of inversion break points in four patients. Comprehensive chromosomal screening and genome-wide haplotype linkage analysis were performed based on SNP microarray. The haplotypes, including the break point regions, the whole chromosomes involved in the inversion and the corresponding homologous chromosomes, were established using informative SNPs. Results All the inversion break points were successfully identified by long-read sequencing and validated by Sanger sequencing, and on average only 13 bp differences were observed between break points inferred by long-read sequencing and Sanger sequencing. Eighteen blastocysts were biopsied and tested, in which 10 were aneuploid or unbalanced and eight were diploid with normal or balanced inversion karyotypes. Diploid embryos were transferred back to patients, the predictive results of the current methodology were consistent with fetal karyotypes of amniotic fluid or cord blood. Conclusions Nanopore long-read sequencing is a powerful method to assay chromosomal inversions and identify exact break points. Identification of inversion break points combined with haplotype linkage analysis is an efficient strategy to distinguish embryos with normal or balanced inversion karyotypes, facilitating PGT applications.
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Affiliation(s)
- Shuo Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.,Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Fan Liang
- GrandOmics Biosciences, Beijing, China
| | - Caixia Lei
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Junping Wu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Jing Fu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Qi Yang
- GrandOmics Biosciences, Beijing, China
| | - Xiao Luo
- GrandOmics Biosciences, Beijing, China
| | | | | | - Yueping Zhang
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Daru Lu
- Collaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China .,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yu Liang
- GrandOmics Biosciences, Beijing, China
| | - Congjian Xu
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China .,Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
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23
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Inheritance of imbalances in recurrent chromosomal translocation t(11;22): clarification by PGT-SR and sperm-FISH analysis. Reprod Biomed Online 2019; 39:40-48. [PMID: 31097322 DOI: 10.1016/j.rbmo.2019.02.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/19/2019] [Accepted: 02/28/2019] [Indexed: 10/27/2022]
Abstract
RESEARCH QUESTION To analyse why unbalanced viable offspring are derived mainly from the 3:1 segregation mode in t(11;22)(q23;q11.2) reciprocal translocation. DESIGN Retrospective analysis of 24 pre-implantation genetic testing for chromosomal structural re-arrangements (PGT-SR) cycles was performed on seven male and five female carriers of t(11;22) translocation. Sperm analysis was performed on each male carrier. These patients were directed to the study centre after several years of miscarriages and/or abortions, primary infertility for male carriers or birth of an affected child. RESULTS Twenty-four PGT-SR cycles were performed to exclude imbalances in both male and female carriers. The unbalanced embryos derived from the adjacent-1 segregation mode were the most represented in both male and female carriers (68.4% and 50%, respectively). These results were positively related with meiotic segregation analysis of reciprocal translocation in spermatozoa. A thorough analysis of the unbalanced embryo karyotypes determined that the expected viable +der22 karyotype resulting from 3:1 malsegregation was less represented at 5.3%. CONCLUSIONS These findings highlight the divergence that may exist between meiotic segregation and post-zygotic selection. Post-zygotic selection would be responsible for the elimination of unbalanced embryos derived from the adjacent-1 segregation mode. The combined action of several factors occurs at the beginning of post-zygotic selection. Genetic counselling must consider the risk of a birth related to the adjacent-1 segregation mode, irrespective of the sex of the translocation carrier. These results will allow deeper understanding of the PGT results of t(11;22) carriers, which often include a high number of aneuploid embryos.
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Vittas S, Efstathiou G, Tsakalidis C, Malamaki C, Antari V, Chatzitoliou E, Chatziioannidis I, Galli-Tsinopoulou A, Soubasi V. De novo Unbalanced 1;22 Translocation with 22q11 Deletion Syndrome. Cytogenet Genome Res 2019; 158:32-37. [PMID: 30799418 DOI: 10.1159/000497173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2018] [Indexed: 11/19/2022] Open
Abstract
This report describes a newborn girl presenting with some of the common features of DiGeorge syndrome/velocardiofacial syndrome (DGS/VCFS), including hypocalcemia, atrial septal defect, and aortic stenosis. Several genetic tests were carried out to determine the origin of the clinical phenotype. MLPA was initially performed followed by aCGH, cytogenetic analysis, and FISH. Cytogenetic analysis of the proband's parents was also done. MLPA revealed a deletion in 22q11.1q11.2 spanning from the cat eye syndrome region to the most commonly deleted region in DGS/VCFS patients. The size of the deletion as defined by aCGH was 3.2 Mb. The karyotype of the proband was 45,XX,der(1)t(1;22)(p36.3;q11.2)dn,-22, the karyotypes of the parents were normal. FISH analysis showed that the 22q11 deletion occurred in the der(1). No loss or gain of chromosomal material was evident for chromosome 1, as confirmed by MLPA, aCGH, and FISH. Unbalanced translocations resulting in DGS are relatively rare, with limited reports in the literature. To our knowledge, this is the second case involving chromosome 1 and the first one with breakpoints in 1p36 and 22q11.2. This case also emphasizes the importance of combining diagnostic methods to better understand a given genetic abnormality.
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MESH Headings
- 22q11 Deletion Syndrome/genetics
- Abnormal Karyotype
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 1/ultrastructure
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 22/ultrastructure
- Comparative Genomic Hybridization
- DiGeorge Syndrome/genetics
- Female
- Humans
- In Situ Hybridization, Fluorescence
- Infant, Newborn
- Nucleic Acid Amplification Techniques
- Sequence Deletion
- Syndrome
- Translocation, Genetic/genetics
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25
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Kaushal S, Freudenreich CH. The role of fork stalling and DNA structures in causing chromosome fragility. Genes Chromosomes Cancer 2019; 58:270-283. [PMID: 30536896 DOI: 10.1002/gcc.22721] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/13/2018] [Accepted: 12/03/2018] [Indexed: 12/19/2022] Open
Abstract
Alternative non-B form DNA structures, also called secondary structures, can form in certain DNA sequences under conditions that produce single-stranded DNA, such as during replication, transcription, and repair. Direct links between secondary structure formation, replication fork stalling, and genomic instability have been found for many repeated DNA sequences that cause disease when they expand. Common fragile sites (CFSs) are known to be AT-rich and break under replication stress, yet the molecular basis for their fragility is still being investigated. Over the past several years, new evidence has linked both the formation of secondary structures and transcription to fork stalling and fragility of CFSs. How these two events may synergize to cause fragility and the role of nuclease cleavage at secondary structures in rare and CFSs are discussed here. We also highlight evidence for a new hypothesis that secondary structures at CFSs not only initiate fragility but also inhibit healing, resulting in their characteristic appearance.
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Affiliation(s)
- Simran Kaushal
- Department of Biology, Tufts University, Medford, Massachusetts
| | - Catherine H Freudenreich
- Department of Biology, Tufts University, Medford, Massachusetts.,Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts
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26
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A Familial Case Report of a 13;22 Chromosomal Translocation with Recurrent Intracytoplasmic Sperm Injection Failure. Balkan J Med Genet 2018; 21:73-77. [PMID: 30984530 PMCID: PMC6454244 DOI: 10.2478/bjmg-2018-0017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The importance of cytogenetic analysis in a family with reproductive failure in two siblings is highlighted, where two siblings and their mother presented with a balanced translocation between chromosomes 13;22. The clinical evaluation had shown the female to be normal and the male to be oligoasthenoteratozoospermic despite repeated semen analysis. The couple was referred to our laboratory after three consecutive intracytoplasmic sperm injection (ICSI) failures at a local assisted reproductive technique (ART) center. Peripheral blood lymphocytes, obtained for karyotyping, were studied by a standard G-banding technique. Chromosomal analysis of the members of the pedigree, including the probands, showed the presence of the same translocation, t(13;22)(q21.2;q13.3), carried by three generations of the family. The sister and the mother of the proband had multiple spontaneous abortions in the first trimester. The spouses, when examined cytogenetically, were found to be normal. We propose the involvement of a balanced t(13;22)(q21.2;q13.3) chromosomal translocation in the pathogenesis of recurrent ART or spontaneous reproductive failures. Hence, it is suggested that all cases with structural chromosomal abnormalities be counseled prior to opting for ART and undergoing pre-implantation genetic diagnosis (PGD). This would prevent recurrent financial, physical and emotional stress in couples seeking ART.
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27
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Genome-wide Identification of Structure-Forming Repeats as Principal Sites of Fork Collapse upon ATR Inhibition. Mol Cell 2018; 72:222-238.e11. [PMID: 30293786 DOI: 10.1016/j.molcel.2018.08.047] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 07/11/2018] [Accepted: 08/30/2018] [Indexed: 01/22/2023]
Abstract
DNA polymerase stalling activates the ATR checkpoint kinase, which in turn suppresses fork collapse and breakage. Herein, we describe use of ATR inhibition (ATRi) as a means to identify genomic sites of problematic DNA replication in murine and human cells. Over 500 high-resolution ATR-dependent sites were ascertained using two distinct methods: replication protein A (RPA)-chromatin immunoprecipitation (ChIP) and breaks identified by TdT labeling (BrITL). The genomic feature most strongly associated with ATR dependence was repetitive DNA that exhibited high structure-forming potential. Repeats most reliant on ATR for stability included structure-forming microsatellites, inverted retroelement repeats, and quasi-palindromic AT-rich repeats. Notably, these distinct categories of repeats differed in the structures they formed and their ability to stimulate RPA accumulation and breakage, implying that the causes and character of replication fork collapse under ATR inhibition can vary in a DNA-structure-specific manner. Collectively, these studies identify key sources of endogenous replication stress that rely on ATR for stability.
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28
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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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29
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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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30
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Msaouel P, Tannir NM, Walker CL. A Model Linking Sickle Cell Hemoglobinopathies and SMARCB1 Loss in Renal Medullary Carcinoma. Clin Cancer Res 2018; 24:2044-2049. [DOI: 10.1158/1078-0432.ccr-17-3296] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 01/13/2018] [Accepted: 02/05/2018] [Indexed: 11/16/2022]
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31
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Shen ZF, Li F, Jiang YF, Chen C, Xu H, Li CC, Yang Z, Wu ZS. Palindromic Molecule Beacon-Based Cascade Amplification for Colorimetric Detection of Cancer Genes. Anal Chem 2018; 90:3335-3340. [DOI: 10.1021/acs.analchem.7b04895] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Zhi-Fa Shen
- Henan Key Laboratory of Immunology and Targeted Drugs, Research Center for Molecular Oncology and Functional Nucleic Acids, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Feng Li
- Henan Key Laboratory of Immunology and Targeted Drugs, Research Center for Molecular Oncology and Functional Nucleic Acids, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, Henan 453003, PR China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Yi-Fan Jiang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Chang Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Huo Xu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Cong-Cong Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Zhe Yang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
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32
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Historical and Clinical Perspectives on Chromosomal Translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:1-14. [PMID: 29956287 DOI: 10.1007/978-981-13-0593-1_1] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Chromosomal translocations, rearrangements involving the exchange of segments between chromosomes, were documented in humans in 1959. The first accurately reported clinical phenotype resulting from a translocation was that of Down syndrome. In a small percentage of Down syndrome cases, an extra 21q is provided by a Robertsonian translocation chromosome, either occurring de novo or inherited from a phenotypically normal parent with the translocation chromosome and a balanced genome of 45 chromosomes. Balanced translocations, including both Robertsonian and reciprocal translocations, are typically benign, but meiosis in germ cells with balanced translocations may result in meiotic arrest and subsequent infertility, or in unbalanced gametes, with attendant risks of miscarriage and unbalanced progeny. Most reciprocal translocations are unique. A few to several percent of translocations disrupt haploinsufficient genes or their regulatory regions and result in clinical phenotypes. Balanced translocations from patients with clinical phenotypes have been valuable in mapping disease genes and in illuminating cis-regulatory regions. Mapping of discordant mate pairs from long-insert, low-pass genome sequencing now permits efficient and cost-effective discovery and nucleotide-level resolution of rearrangement breakpoints, information that is absolutely necessary for interpreting the etiology of clinical phenotypes in patients with rearrangements. Pathogenic translocations and other balanced chromosomal rearrangements constitute a class of typically highly penetrant mutation that is cryptic to both clinical microarray and exome sequencing. A significant proportion of rearrangements include additional complexity that is not visible by conventional karyotype analysis. Some proportion of patients with negative findings on exome/genome sequencing and clinical microarray will be found to have etiologic balanced rearrangements only discoverable by genome sequencing with analysis pipelines optimized to recover rearrangement breakpoints.
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Trpchevska N, Dimova I, Arabadji T, Milachich T, Angelova S, Dimitrova M, Hristova-Savova M, Andreeva P, Timeva T, Shterev A. A family study of complex chromosome rearrangement involving chromosomes 1, 8, and 11 and its reproductive consequences. J Assist Reprod Genet 2017; 34:659-669. [PMID: 28236108 PMCID: PMC5427656 DOI: 10.1007/s10815-017-0893-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/09/2017] [Indexed: 10/20/2022] Open
Abstract
Complex chromosome translocations are structural chromosomal rearrangements involving three or more chromosomes and more than two breakpoints. A complex chromosome rearrangement was detected in a phenotypically normal female patient that was referred to the hospital for genetic counseling due to reproductive failure. A cytogenetic evaluation was performed, according to standard method of chromosomal analysis, using G-banding technique. The patient's karyotype showed a balanced complex chromosome rearrangement (BCCR) involving chromosomes 1, 8, and 11 with three breakpoints 1p31, 8q13, and 11q23. The karyotype designed according to ISCN (2013), is 46,XX,t(1;8;11)(p31;q13;q23) (8qter→8q13::1p31→1qter;8pter→8q13::11q23→11qter;11pter→11q23::1p31→1pter). Additionally, the proband's mother and brother were tested, resulting in the same exact translocation. In this study, we describe all possible meiotic segregations regarding this translocation, as well as the clinical phenotypes which could arise, if unbalanced products of conception survive. This is a rare case of familial complex chromosome rearrangement, giving a view for its reproductive consequences.
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Affiliation(s)
- Natalia Trpchevska
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria.
- Laboratory of Cytogenetics and Molecular Genetics, National Specialized Hospital for Active Therapy of Hematological Diseases, Plovdivsko pole str 6, 1756, Sofia, Bulgaria.
| | - Ivanka Dimova
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
- Department of Medical Genetics, Medical University Sofia, Zdrave str 2, 1431, Sofia, Bulgaria
| | - Tatyana Arabadji
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
| | - Tanya Milachich
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
| | - Svetlana Angelova
- Laboratory of Cytogenetics and Molecular Genetics, National Specialized Hospital for Active Therapy of Hematological Diseases, Plovdivsko pole str 6, 1756, Sofia, Bulgaria
| | | | | | - Petya Andreeva
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
| | - Tania Timeva
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
| | - Atanas Shterev
- SAGBAL "Dr Shterev", Hristo Blagoev Str. 25-31, 1330, Sofia, Bulgaria
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34
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Nilsson D, Pettersson M, Gustavsson P, Förster A, Hofmeister W, Wincent J, Zachariadis V, Anderlid BM, Nordgren A, Mäkitie O, Wirta V, Käller M, Vezzi F, Lupski JR, Nordenskjöld M, Lundberg ES, Carvalho CMB, Lindstrand A. Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation. Hum Mutat 2017; 38:180-192. [PMID: 27862604 PMCID: PMC5225243 DOI: 10.1002/humu.23146] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/01/2016] [Indexed: 11/07/2022]
Abstract
Most balanced translocations are thought to result mechanistically from nonhomologous end joining or, in rare cases of recurrent events, by nonallelic homologous recombination. Here, we use low-coverage mate pair whole-genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers. Finally, seven candidate disease genes were disrupted in five carriers with neurocognitive disabilities (SVOPL, SUSD1, TOX, NCALD, SLC4A10) and one XX-male carrier with Tourette syndrome (LYPD6, GPC5). Breakpoint junction analyses revealed microhomology and small templated insertions in a substantive fraction of the analyzed translocations (17.4%; n = 4); an observation that was substantiated by reanalysis of 37 previously published translocation junctions. Microhomology associated with templated insertions is a characteristic seen in the breakpoint junctions of rearrangements mediated by error-prone replication-based repair mechanisms. Our data implicate that a mechanism involving template switching might contribute to the formation of at least 15% of the interchromosomal translocation events.
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Affiliation(s)
- Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Alisa Förster
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Vasilios Zachariadis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Children's Hospital, Helsinki University Central Hospital and University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Institute of Genetics, 00290 Helsinki, Finland
| | - Valtteri Wirta
- SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, 171 71 Stockholm, Sweden
| | - Max Käller
- SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, 171 71 Stockholm, Sweden
| | - Francesco Vezzi
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, 171 21 Stockholm, Sweden
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston TX, USA
- Texas Children’s Hospital, 77030 Houston TX, USA
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Elisabeth Syk Lundberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Claudia M. B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston TX, USA
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
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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] [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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Nikolova EN, Zhou H, Gottardo FL, Alvey HS, Kimsey IJ, Al-Hashimi HM. A historical account of Hoogsteen base-pairs in duplex DNA. Biopolymers 2016; 99:955-68. [PMID: 23818176 DOI: 10.1002/bip.22334] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 06/17/2013] [Indexed: 11/05/2022]
Abstract
In 1957, a unique pattern of hydrogen bonding between N3 and O4 on uracil and N7 and N6 on adenine was proposed to explain how poly(rU) strands can associate with poly(rA)-poly(rU) duplexes to form triplexes. Two years later, Karst Hoogsteen visualized such a noncanonical A-T base-pair through X-ray analysis of co-crystals containing 9-methyladenine and 1-methylthymine. Subsequent X-ray analyses of guanine and cytosine derivatives yielded the expected Watson-Crick base-pairing, but those of adenine and thymine (or uridine) did not yield Watson-Crick base-pairs, instead favoring "Hoogsteen" base-pairing. More than two decades ensued without experimental "proof" for A-T Watson-Crick base-pairs, while Hoogsteen base-pairs continued to surface in AT-rich sequences, closing base-pairs of apical loops, in structures of DNA bound to antibiotics and proteins, damaged and chemically modified DNA, and in polymerases that replicate DNA via Hoogsteen pairing. Recently, NMR studies have shown that base-pairs in duplex DNA exist as a dynamic equilibrium between Watson-Crick and Hoogsteen forms. There is now little doubt that Hoogsteen base-pairs exist in significant abundance in genomic DNA, where they can expand the structural and functional versatility of duplex DNA beyond that which can be achieved based only on Watson-Crick base-pairing. Here, we provide a historical account of the discovery and characterization of Hoogsteen base-pairs, hoping that this will inform future studies exploring the occurrence and functional importance of these alternative base-pairs.
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Affiliation(s)
- Evgenia N Nikolova
- Department of Chemistry & Biophysics, The University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109-1055; Integrative Structural & Computational Biology Department, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037
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Bacolla A, Tainer JA, Vasquez KM, Cooper DN. Translocation and deletion breakpoints in cancer genomes are associated with potential non-B DNA-forming sequences. Nucleic Acids Res 2016; 44:5673-88. [PMID: 27084947 PMCID: PMC4937311 DOI: 10.1093/nar/gkw261] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/30/2016] [Indexed: 12/13/2022] Open
Abstract
Gross chromosomal rearrangements (including translocations, deletions, insertions and duplications) are a hallmark of cancer genomes and often create oncogenic fusion genes. An obligate step in the generation of such gross rearrangements is the formation of DNA double-strand breaks (DSBs). Since the genomic distribution of rearrangement breakpoints is non-random, intrinsic cellular factors may predispose certain genomic regions to breakage. Notably, certain DNA sequences with the potential to fold into secondary structures [potential non-B DNA structures (PONDS); e.g. triplexes, quadruplexes, hairpin/cruciforms, Z-DNA and single-stranded looped-out structures with implications in DNA replication and transcription] can stimulate the formation of DNA DSBs. Here, we tested the postulate that these DNA sequences might be found at, or in close proximity to, rearrangement breakpoints. By analyzing the distribution of PONDS-forming sequences within ±500 bases of 19 947 translocation and 46 365 sequence-characterized deletion breakpoints in cancer genomes, we find significant association between PONDS-forming repeats and cancer breakpoints. Specifically, (AT)n, (GAA)n and (GAAA)n constitute the most frequent repeats at translocation breakpoints, whereas A-tracts occur preferentially at deletion breakpoints. Translocation breakpoints near PONDS-forming repeats also recur in different individuals and patient tumor samples. Hence, PONDS-forming sequences represent an intrinsic risk factor for genomic rearrangements in cancer genomes.
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Affiliation(s)
- Albino Bacolla
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 6767 Bertner Ave., Houston, TX 77030, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
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Gollo Dantas A, Bortolai A, Moysés-Oliveira M, Takeno Herrero S, Azoubel Antunes A, Tavares Costa-Carvalho B, Ayres Meloni V, Melaragno MI. 22q11.2 Deletion Syndrome due to a Translocation t(6;22) in a Patient Conceived via in vitro Fertilization. Mol Syndromol 2015; 6:242-7. [PMID: 26997945 DOI: 10.1159/000441243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 11/19/2022] Open
Abstract
We report on a patient conceived via in vitro fertilization (IVF) with a 22q11.2 deletion due to an unusual unbalanced translocation involving chromosomes 6 and 22 in a karyotype with 45 chromosomes. Cytogenomic studies showed that the patient has a 3.3-Mb deletion of chromosome 22q and a 0.4-Mb deletion of chromosome 6p, which resulted in haploinsufficiency of the genes responsible for the 22q11.2 deletion syndrome and also of the IRF4 gene, a member of the interferon regulatory factor family of transcription factors, which is expressed in the immune system cells. The rearrangement could be due to the manipulation of the embryo or as a sporadic event unrelated to IVF. Translocation involving chromosome 22 in a karyotype with 45 chromosomes is a rare event, with no previous reports involving chromosomes 6p and 22q.
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Affiliation(s)
- Anelisa Gollo Dantas
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil
| | - Adriana Bortolai
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil; Cytogenetics Division, Hospital do Servidor Público do Estado de São Paulo, São Paulo, Brazil
| | - Mariana Moysés-Oliveira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil
| | - Sylvia Takeno Herrero
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil
| | | | | | - Vera Ayres Meloni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, Brazil
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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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Weckselblatt B, Rudd MK. Human Structural Variation: Mechanisms of Chromosome Rearrangements. Trends Genet 2015; 31:587-599. [PMID: 26209074 PMCID: PMC4600437 DOI: 10.1016/j.tig.2015.05.010] [Citation(s) in RCA: 158] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 01/05/2023]
Abstract
Chromosome structural variation (SV) is a normal part of variation in the human genome, but some classes of SV can cause neurodevelopmental disorders. Analysis of the DNA sequence at SV breakpoints can reveal mutational mechanisms and risk factors for chromosome rearrangement. Large-scale SV breakpoint studies have become possible recently owing to advances in next-generation sequencing (NGS) including whole-genome sequencing (WGS). These findings have shed light on complex forms of SV such as triplications, inverted duplications, insertional translocations, and chromothripsis. Sequence-level breakpoint data resolve SV structure and determine how genes are disrupted, fused, and/or misregulated by breakpoints. Recent improvements in breakpoint sequencing have also revealed non-allelic homologous recombination (NAHR) between paralogous long interspersed nuclear element (LINE) or human endogenous retrovirus (HERV) repeats as a cause of deletions, duplications, and translocations. This review covers the genomic organization of simple and complex constitutional SVs, as well as the molecular mechanisms of their formation.
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Affiliation(s)
- Brooke Weckselblatt
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA.
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Tourasse NJ, Shtaida N, Khozin-Goldberg I, Boussiba S, Vallon O. The complete mitochondrial genome sequence of the green microalga Lobosphaera (Parietochloris) incisa reveals a new type of palindromic repetitive repeat. BMC Genomics 2015; 16:580. [PMID: 26238519 PMCID: PMC4524435 DOI: 10.1186/s12864-015-1792-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/22/2015] [Indexed: 11/10/2022] Open
Abstract
Background Lobosphaera incisa, formerly known as Myrmecia incisa and then Parietochloris incisa, is an oleaginous unicellular green alga belonging to the class Trebouxiophyceae (Chlorophyta). It is the richest known plant source of arachidonic acid, an ω-6 poly-unsaturated fatty acid valued by the pharmaceutical and baby-food industries. It is therefore an organism of high biotechnological interest, and we recently reported the sequence of its chloroplast genome. Results We now report the complete sequence of the mitochondrial genome of L. incisa from high-throughput Illumina short-read sequencing. The circular chromosome of 69,997 bp is predicted to encode a total of 64 genes, some harboring specific self-splicing group I and group II introns. Overall, the gene content is highly similar to that of the mitochondrial genomes of other Trebouxiophyceae, with 34 protein-coding, 3 rRNA, and 27 tRNA genes. Genes are distributed in two clusters located on different DNA strands, a bipartite arrangement that suggests expression from two divergent promoters yielding polycistronic primary transcripts. The L. incisa mitochondrial genome contains families of intergenic dispersed DNA repeat sequences that are not shared with other known mitochondrial genomes of Trebouxiophyceae. The most peculiar feature of the genome is a repetitive palindromic repeat, the LIMP (L. Incisa Mitochondrial Palindrome), found 19 times in the genome. It is formed by repetitions of an AACCA pentanucleotide, followed by an invariant 7-nt loop and a complementary repeat of the TGGTT motif. Analysis of the genome sequencing reads indicates that the LIMP can be a substrate for large-scale genomic rearrangements. We speculate that LIMPs can act as origins of replication. Deep sequencing of the L. incisa transcriptome also suggests that the LIMPs with long stems are sites of transcript processing. The genome also contains five copies of a related palindromic repeat, the HyLIMP, with a 10-nt motif related to that of the LIMP. Conclusions The mitochondrial genome of L. incisa encodes a unique type of repetitive palindromic repeat sequence, the LIMP, which can mediate genome rearrangements and play a role in mitochondrial gene expression. Experimental studies are needed to confirm and further characterize the functional role(s) of the LIMP.
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Affiliation(s)
- Nicolas J Tourasse
- Institut de Biologie Physico-Chimique, UMR CNRS 7141 - Université Pierre et Marie Curie, Paris, France. .,Institut de Biologie Physico-Chimique, FRC CNRS 550, Université Pierre et Marie Curie, Paris, France. .,ARNA Laboratory, INSERM UMR 869, Université Bordeaux 2, Bordeaux, France.
| | - Nastassia Shtaida
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 84990, Israel
| | - Inna Khozin-Goldberg
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 84990, Israel
| | - Sammy Boussiba
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, J. Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 84990, Israel
| | - Olivier Vallon
- Institut de Biologie Physico-Chimique, UMR CNRS 7141 - Université Pierre et Marie Curie, Paris, France
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Weckselblatt B, Hermetz KE, Rudd MK. Unbalanced translocations arise from diverse mutational mechanisms including chromothripsis. Genome Res 2015; 25:937-47. [PMID: 26070663 PMCID: PMC4484391 DOI: 10.1101/gr.191247.115] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 05/15/2015] [Indexed: 12/17/2022]
Abstract
Unbalanced translocations are a relatively common type of copy number variation and a major contributor to neurodevelopmental disorders. We analyzed the breakpoints of 57 unique unbalanced translocations to investigate the mechanisms of how they form. Fifty-one are simple unbalanced translocations between two different chromosome ends, and six rearrangements have more than three breakpoints involving two to five chromosomes. Sequencing 37 breakpoint junctions revealed that simple translocations have between 0 and 4 base pairs (bp) of microhomology (n = 26), short inserted sequences (n = 8), or paralogous repeats (n = 3) at the junctions, indicating that translocations do not arise primarily from nonallelic homologous recombination but instead form most often via nonhomologous end joining or microhomology-mediated break-induced replication. Three simple translocations fuse genes that are predicted to produce in-frame transcripts of SIRPG-WWOX, SMOC2-PROX1, and PIEZO2-MTA1, which may lead to gain of function. Three complex translocations have inversions, insertions, and multiple breakpoint junctions between only two chromosomes. Whole-genome sequencing and fluorescence in situ hybridization analysis of two de novo translocations revealed at least 18 and 33 breakpoints involving five different chromosomes. Breakpoint sequencing of one maternally inherited translocation involving four chromosomes uncovered multiple breakpoints with inversions and insertions. All of these breakpoint junctions had 0-4 bp of microhomology consistent with chromothripsis, and both de novo events occurred on paternal alleles. Together with other studies, these data suggest that germline chromothripsis arises in the paternal genome and may be transmitted maternally. Breakpoint sequencing of our large collection of chromosome rearrangements provides a comprehensive analysis of the molecular mechanisms behind translocation formation.
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Affiliation(s)
- Brooke Weckselblatt
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Karen E Hermetz
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - M Katharine Rudd
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Pylyp LY, Spinenko LO, Verhoglyad NV, Kashevarova OO, Zukin VD. Chromosomal abnormalities in patients with infertility. CYTOL GENET+ 2015. [DOI: 10.3103/s009545271503010x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Daga A, Ansari A, Rawal R, Umrania V. Characterization of chromosomal translocation breakpoint sequences in solid tumours: "an in silico analysis". Open Med Inform J 2015; 9:1-8. [PMID: 25972994 PMCID: PMC4421838 DOI: 10.2174/1874431101509010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/19/2015] [Accepted: 02/28/2015] [Indexed: 01/07/2023] Open
Abstract
Chromosomal translocations that results in formation and activation of fusion oncogenes are observed in numerous solid malignancies since years back. Expression of fusion kinases in these cancers drives the initiation & progression that ultimately leads to tumour development and thus comes out to be clinically imperative in terms of diagnosis and treatment of cancer. Nonetheless, molecular mechanisms beneath these translocations remained unexplored consequently limiting our knowledge of carcinogenesis and hence is the current field where further research is required. The issue of prime focus is the precision with which the chromosomes breaks and reunites within genome. Characterization of Genomic sequences located at Breakpoint region may direct us towards the thorough understanding of mechanism leading to chromosomal rearrangement. A unique computational multi-parametric analysis was performed for characterization of genomic sequence within and around breakpoint region. This study turns out to be novel as it reveals the occurrence of Segmental Duplications flanking the breakpoints of all translocation. Breakpoint Islands were also investigated for the presence of other intricate genomic architecture and various physico-chemical parameters. Our study particularly highlights the probable role of SDs and specific genomic features in precise chromosomal breakage. Additionally, it pinpoints the potential features that may be significant for double-strand breaks leading to chromosomal rearrangements.
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Affiliation(s)
- Aditi Daga
- Department of Microbiology, MVM Science College, Saurashtra University, Rajkot, Gujarat, India
| | - Afzal Ansari
- BIT Virtual Institute of Bioinformatics (GCRI Node), GSBTM, Gandhinagar, Gujarat, India
| | - Rakesh Rawal
- Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Valentina Umrania
- Department of Microbiology, MVM Science College, Saurashtra University, Rajkot, Gujarat, India
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Padeken J, Zeller P, Gasser SM. Repeat DNA in genome organization and stability. Curr Opin Genet Dev 2015; 31:12-9. [PMID: 25917896 DOI: 10.1016/j.gde.2015.03.009] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 01/03/2023]
Abstract
Eukaryotic genomes contain millions of copies of repetitive elements (RE). Although the euchromatic parts of most genomes are clearly annotated, the repetitive/heterochromatic parts are poorly defined. It is estimated that between 50 and 70% of the human genome is composed of REs. Despite this, we know surprisingly little about the physiological relevance, molecular regulation and the composition of these regions. This primarily reflects the difficulty that REs pose for PCR-based assays, and their poor map-ability in next generation sequencing experiments. Here we first summarize the nature and classification of REs and then examine how this has been used in the recent years to broaden our understanding of mechanisms that keep the repetitive regions of our genomes silent and stable.
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Affiliation(s)
- Jan Padeken
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Peter Zeller
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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Delicado A, Fernández L, de Torres ML, Nevado J, García-Santiago FA, Rodríguez R, Mansilla E, Palomares M, Santos-Simarro F, Vallespín E, Mori MÁ, Lapunzina P. Familial imbalance in 16p13.11 leads to a dosage compensation rearrangement in an unaffected carrier. BMC MEDICAL GENETICS 2014; 15:116. [PMID: 25358766 PMCID: PMC4412105 DOI: 10.1186/s12881-014-0116-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 10/03/2014] [Indexed: 11/10/2022]
Abstract
Background We and others have previously reported that familial cytogenetic studies in apparently de novo genomic imbalances may reveal complex or uncommon inheritance mechanisms. Methods A familial, combined genomic and cytogenetic approach was systematically applied to the parents of all patients with unbalanced genome copy number changes. Results Discordant array-CGH and FISH results in the mother of a child with a prenatally detected 16p13.11 interstitial microduplication disclosed a balanced uncommon rearrangement in this chromosomal region. Further dosage and haplotype familial studies revealed that both the maternal grandfather and uncle had also the same 16p duplication as the proband. Genomic compensation observed in the mother probably occurred as a consequence of interchromosomal postzygotic nonallelic homologous recombination. Conclusions We emphasize that such a dualistic strategy is essential for the full characterization of genomic rearrangements as well as for appropriate genetic counseling.
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Affiliation(s)
- Alicia Delicado
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
| | - Luis Fernández
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
| | - María Luisa de Torres
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
| | - Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
| | - Fe Amalia García-Santiago
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
| | - Roberto Rodríguez
- Servicio de Fisiopatología Fetal, Hospital Universitario La Paz, Madrid, Spain.
| | - Elena Mansilla
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
| | - María Palomares
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
| | - Elena Vallespín
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
| | - María Ángeles Mori
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Paseo de la Castellana 261, 28046, Madrid, Spain. .,CIBER de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain.
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Wang H, Li Y, Truong LN, Shi LZ, Hwang PYH, He J, Do J, Cho MJ, Li H, Negrete A, Shiloach J, Berns MW, Shen B, Chen L, Wu X. CtIP maintains stability at common fragile sites and inverted repeats by end resection-independent endonuclease activity. Mol Cell 2014; 54:1012-1021. [PMID: 24837675 PMCID: PMC4105207 DOI: 10.1016/j.molcel.2014.04.012] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/04/2013] [Accepted: 04/04/2014] [Indexed: 11/18/2022]
Abstract
Chromosomal rearrangements often occur at genomic loci with DNA secondary structures, such as common fragile sites (CFSs) and palindromic repeats. We developed assays in mammalian cells that revealed CFS-derived AT-rich sequences and inverted Alu repeats (Alu-IRs) are mitotic recombination hotspots, requiring the repair functions of carboxy-terminal binding protein (CtBP)-interacting protein (CtIP) and the Mre11/Rad50/Nbs1 complex (MRN). We also identified an endonuclease activity of CtIP that is dispensable for end resection and homologous recombination (HR) at I-SceI-generated "clean" double-strand breaks (DSBs) but is required for repair of DSBs occurring at CFS-derived AT-rich sequences. In addition, CtIP nuclease-defective mutants are impaired in Alu-IRs-induced mitotic recombination. These studies suggest that an end resection-independent CtIP function is important for processing DSB ends with secondary structures to promote HR. Furthermore, our studies uncover an important role of MRN, CtIP, and their associated nuclease activities in protecting CFSs in mammalian cells.
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Affiliation(s)
- Hailong Wang
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yongjiang Li
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Lan N Truong
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linda Z Shi
- The Institute of Engineering in Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Patty Yi-Hwa Hwang
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jing He
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Johnny Do
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael Jeffrey Cho
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hongzhi Li
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Alejandro Negrete
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Michael W Berns
- The Institute of Engineering in Medicine, University of California at San Diego, La Jolla, CA 92093, USA; Department of Biomedical Engineering, Beckman Laser Institute, University of California at Irvine, Irvine, CA 92612, USA
| | - Binghui Shen
- Department of Radiation Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
| | - Longchuan Chen
- Department of Pathology, Veterans Affairs Medical Center, Long Beach, CA 90822, USA
| | - Xiaohua Wu
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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48
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López-Carrasco A, Monfort S, Roselló M, Oltra S, Mayo S, Martínez F, Orellana C. [Chromosomal location of submicroscopic duplications in patients with neurodevelopmental disorders to identify cases with high risk of familial recurrence]. Med Clin (Barc) 2014; 142:531-7. [PMID: 23790573 DOI: 10.1016/j.medcli.2013.04.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 03/25/2013] [Accepted: 04/04/2013] [Indexed: 11/15/2022]
Abstract
BACKGROUND AND OBJECTIVE An important proportion of neurodevelopmental disorders (NDDs) results from unbalanced genomic alterations (duplication or deletion). These chromosomal rearrangements may be considered as de novo, despite they arise as a result of a balanced rearrangement not detected in a phenotypically normal parent. Therefore, if the rearrangements are inherited, the recurrence risk and the genetic counseling of these cases change radically. Fluorescence in situ hybridization (FISH) is a technique that allows detecting both balanced and unbalanced rearrangements, identifying also the location of duplicated segments. We tried to locate in the genome the duplicated segments detected in patients with NDDs in order to identify those cases due to inherited rearrangements. PATIENTS AND METHOD The study was conducted in 13 patients with NDDs and genomic duplications detected by compared genomic hybridization-array (CGH-array). Two approaches of FISH technique were taken: hybridization with painting chromosome probes and with specific probes for each duplication. RESULTS In the studied series of 13 patients with duplication, 11 patients were found to carry tandem duplications, one with an intrachromosomal insertional translocation, and another with an interchromosomal insertional translocation. Therefore, 2 of the duplications considered de novo were actually an unbalanced rearrangement inherited from a parent who is a balanced carrier. CONCLUSION The results illustrate the need to characterize by FISH technique the rearrangements that are detected by CGH-array to identify those cases with a high risk of recurrence.
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Affiliation(s)
- Amparo López-Carrasco
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Sandra Monfort
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Mónica Roselló
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Silvestre Oltra
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Sonia Mayo
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Francisco Martínez
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, España
| | - Carmen Orellana
- Unidad de Genética y Diagnóstico Prenatal, Hospital Universitario y Politécnico La Fe, Valencia, España.
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49
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Hsiao MC, Piotrowski A, Alexander J, Callens T, Fu C, Mikhail FM, Claes KBM, Messiaen L. Palindrome-mediated and replication-dependent pathogenic structural rearrangements within the NF1 gene. Hum Mutat 2014; 35:891-8. [PMID: 24760680 DOI: 10.1002/humu.22569] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 04/17/2014] [Indexed: 11/09/2022]
Abstract
Palindromic sequences can form hairpin structures or cruciform extrusions, which render them susceptible to genomic rearrangements. A 197-bp long palindromic AT-rich repeat (PATRR17) is located within intron 40 of the neurofibromatosis type 1 (NF1) gene (17q11.2). Through comprehensive NF1 analysis, we identified six unrelated patients with a rearrangement involving intron 40 (five deletions and one reciprocal translocation t(14;17)(q32;q11.2)). We hypothesized that PATRR17 may be involved in these rearrangements thereby causing NF1. Breakpoint cloning revealed that PATRR17 was indeed involved in all of the rearrangements. As microhomology was present at all breakpoint junctions of the deletions identified, and PATRR17 partner breakpoints were located within 7.1 kb upstream of PATRR17, fork stalling and template switching/microhomology-mediated break-induced replication was the most likely rearrangement mechanism. For the reciprocal translocation case, a 51 bp insertion at the translocation breakpoints mapped to a short sequence within PATRR17, proximal to the breakpoint, suggesting a multiple stalling and rereplication process, in contrast to previous studies indicating a purely replication-independent mechanism for PATRR-mediated translocations. In conclusion, we show evidence that PATRR17 is a hotspot for pathogenic intragenic deletions within the NF1 gene and suggest a novel replication-dependent mechanism for PATRR-mediated translocation.
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Affiliation(s)
- Meng-Chang Hsiao
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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50
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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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