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Zhou B, Purmann C, Guo H, Shin G, Huang Y, Pattni R, Meng Q, Greer SU, Roychowdhury T, Wood RN, Ho M, zu Dohna H, Abyzov A, Hallmayer JF, Wong WH, Ji HP, Urban AE. Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints. Proc Natl Acad Sci U S A 2024; 121:e2322834121. [PMID: 39042694 PMCID: PMC11295037 DOI: 10.1073/pnas.2322834121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/15/2024] [Indexed: 07/25/2024] Open
Abstract
We developed a generally applicable method, CRISPR/Cas9-targeted long-read sequencing (CTLR-Seq), to resolve, haplotype-specifically, the large and complex regions in the human genome that had been previously impenetrable to sequencing analysis, such as large segmental duplications (SegDups) and their associated genome rearrangements. CTLR-Seq combines in vitro Cas9-mediated cutting of the genome and pulse-field gel electrophoresis to isolate intact large (i.e., up to 2,000 kb) genomic regions that encompass previously unresolvable genomic sequences. These targets are then sequenced (amplification-free) at high on-target coverage using long-read sequencing, allowing for their complete sequence assembly. We applied CTLR-Seq to the SegDup-mediated rearrangements that constitute the boundaries of, and give rise to, the 22q11.2 Deletion Syndrome (22q11DS), the most common human microdeletion disorder. We then performed de novo assembly to resolve, at base-pair resolution, the full sequence rearrangements and exact chromosomal breakpoints of 22q11.2DS (including all common subtypes). Across multiple patients, we found a high degree of variability for both the rearranged SegDup sequences and the exact chromosomal breakpoint locations, which coincide with various transposons within the 22q11.2 SegDups, suggesting that 22q11DS can be driven by transposon-mediated genome recombination. Guided by CTLR-Seq results from two 22q11DS patients, we performed three-dimensional chromosomal folding analysis for the 22q11.2 SegDups from patient-derived neurons and astrocytes and found chromosome interactions anchored within the SegDups to be both cell type-specific and patient-specific. Lastly, we demonstrated that CTLR-Seq enables cell-type specific analysis of DNA methylation patterns within the deletion haplotype of 22q11DS.
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Affiliation(s)
- Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Carolin Purmann
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Hanmin Guo
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
- Department of Statistics, Stanford University, Stanford, CA94305
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305
| | - GiWon Shin
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Yiling Huang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Qingxi Meng
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Stephanie U. Greer
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Tanmoy Roychowdhury
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN55905
| | - Raegan N. Wood
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Marcus Ho
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
| | - Heinrich zu Dohna
- Department of Biology, American University of Beirut, Beirut1107 2020, Lebanon
| | - Alexej Abyzov
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN55905
| | - Joachim F. Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
| | - Wing H. Wong
- Department of Statistics, Stanford University, Stanford, CA94305
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305
| | - Hanlee P. Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA94305
| | - Alexander E. Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA94305
- Stanford Maternal and Child Health Research Institute, Stanford University School of Medicine, Stanford, CA94305
- Department of Genetics, Stanford University School of Medicine, Stanford, CA94305
- Program on Genetics of Brain Function, Stanford Center for Genomics and Personalized Medicine, Stanford University School of Medicine, Stanford, CA94305
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Huang S, Wu H, Qi Y, Wei L, Lv X, He Y. Case Report: Balanced Reciprocal Translocation t (17; 22) (p11.2; q11.2) and 10q23.31 Microduplication in an Infertile Male Patient Suffering From Teratozoospermia. Front Genet 2022; 13:797813. [PMID: 35719406 PMCID: PMC9204271 DOI: 10.3389/fgene.2022.797813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/05/2022] [Indexed: 02/03/2023] Open
Abstract
Two chromosomal abnormalities are described in an infertile man suffering from teratozoospermia: balanced reciprocal translocation t (17; 22) (p11.2; q11.2) and a microduplication in the region 10q23.31. Twenty genes located on the breakpoints of translocation (e.g., ALKBH5, TOP3A, SPECC1L, and CDC45) are selected due to their high expression in testicular tissues and might be influenced by chromosome translocation. Four genes located on the breakpoints of microduplication including FLJ37201, KIF20B, LINC00865, and PANK1 result in an increased dosage of genes, representing an imbalance in the genome. These genes have been reported to be associated with developmental disorders/retardation and might be risk factors affecting spermatogenesis. Bioinformatics analysis is carried out on these key genes, intending to find the pathogenic process of reproduction in the context of the translocation and microduplication encountered in the male patient. The combination of the two chromosomal abnormalities carries additional risks for gametogenesis and genomic instability and is apparently harmful to male fertility. Overall, our findings could contribute to the knowledge of male infertility caused by genetic factors.
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Affiliation(s)
- Shan Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Huiling Wu
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yunwei Qi
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Liqiang Wei
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaodan Lv
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yu He
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Vervoort L, Dierckxsens N, Pereboom Z, Capozzi O, Rocchi M, Shaikh TH, Vermeesch JR. 22q11.2 Low Copy Repeats Expanded in the Human Lineage. Front Genet 2021; 12:706641. [PMID: 34335701 PMCID: PMC8320366 DOI: 10.3389/fgene.2021.706641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Segmental duplications or low copy repeats (LCRs) constitute duplicated regions interspersed in the human genome, currently neglected in standard analyses due to their extreme complexity. Recent functional studies have indicated the potential of genes within LCRs in synaptogenesis, neuronal migration, and neocortical expansion in the human lineage. One of the regions with the highest proportion of duplicated sequence is the 22q11.2 locus, carrying eight LCRs (LCR22-A until LCR22-H), and rearrangements between them cause the 22q11.2 deletion syndrome. The LCR22-A block was recently reported to be hypervariable in the human population. It remains unknown whether this variability also exists in non-human primates, since research is strongly hampered by the presence of sequence gaps in the human and non-human primate reference genomes. To chart the LCR22 haplotypes and the associated inter- and intra-species variability, we de novo assembled the region in non-human primates by a combination of optical mapping techniques. A minimal and likely ancient haplotype is present in the chimpanzee, bonobo, and rhesus monkey without intra-species variation. In addition, the optical maps identified assembly errors and closed gaps in the orthologous chromosome 22 reference sequences. These findings indicate the LCR22 expansion to be unique to the human population, which might indicate involvement of the region in human evolution and adaptation. Those maps will enable LCR22-specific functional studies and investigate potential associations with the phenotypic variability in the 22q11.2 deletion syndrome.
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Affiliation(s)
| | | | - Zjef Pereboom
- Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
- Evolutionary Ecology Group, Department of Biology, Antwerp University, Antwerp, Belgium
| | | | | | - Tamim H. Shaikh
- Section of Genetics and Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States
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A De Novo sSMC (22) Characterized by High-Resolution Chromosome Microarray Analysis in a Chinese Boy with Cat-Eye Syndrome. Case Rep Genet 2021; 2021:8824184. [PMID: 33728075 PMCID: PMC7937470 DOI: 10.1155/2021/8824184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/18/2021] [Accepted: 02/14/2021] [Indexed: 11/17/2022] Open
Abstract
We report a 15-year-old boy with cat-eye syndrome (CES) without short stature or intellectual disorder. The boy was confirmed by cytogenetic and high-resolution chromosome microarray analysis (CMA). The G-banding karyotype confirmed the de novo of the patient. Also, the CMA result showed 1.76 Mb tetrasomy of proximal 22Q11.1 ⟶ 22Q11.21 consistent with CES {arr22q11.1q11.21 (16,888,899-18,644,241) X4}, a typical small type I CES chromosome. The patient has many of the basic characteristics of CES; however, he is taller than his peers instead of shorter. It is rarely reported in the past since short stature is a common feature of this syndrome. Furthermore, the boy has no intellectual disorder and attends a normal school since he was six-year-old. What bothered him most were recurrent respiratory infections, retromicrognathia, and heart defects.
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Rubino E, Cruciani M, Tchitchek N, Le Tortorec A, Rolland AD, Veli Ö, Vallet L, Gaggi G, Michel F, Dejucq-Rainsford N, Pellegrini S. Human Ubiquitin-Specific Peptidase 18 Is Regulated by microRNAs via the 3'Untranslated Region, A Sequence Duplicated in Long Intergenic Non-coding RNA Genes Residing in chr22q11.21. Front Genet 2021; 11:627007. [PMID: 33633774 PMCID: PMC7901961 DOI: 10.3389/fgene.2020.627007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 12/30/2020] [Indexed: 12/16/2022] Open
Abstract
Ubiquitin-specific peptidase 18 (USP18) acts as gatekeeper of type I interferon (IFN) responses by binding to the IFN receptor subunit IFNAR2 and preventing activation of the downstream JAK/STAT pathway. In any given cell type, the level of USP18 is a key determinant of the output of IFN-stimulated transcripts. How the baseline level of USP18 is finely tuned in different cell types remains ill defined. Here, we identified microRNAs (miRNAs) that efficiently target USP18 through binding to the 3’untranslated region (3’UTR). Among these, three miRNAs are particularly enriched in circulating monocytes which exhibit low baseline USP18. Intriguingly, the USP18 3’UTR sequence is duplicated in human and chimpanzee genomes. In humans, four USP18 3’UTR copies were previously found to be embedded in long intergenic non-coding (linc) RNA genes residing in chr22q11.21 and known as FAM247A-D. Here, we further characterized their sequence and measured their expression profile in human tissues. Importantly, we describe an additional lincRNA bearing USP18 3’UTR (here linc-UR-B1) that is expressed only in testis. RNA-seq data analyses from testicular cell subsets revealed a positive correlation between linc-UR-B1 and USP18 expression in spermatocytes and spermatids. Overall, our findings uncover a set of miRNAs and lincRNAs, which may be part of a network evolved to fine-tune baseline USP18, particularly in cell types where IFN responsiveness needs to be tightly controlled.
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Affiliation(s)
- Erminia Rubino
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France.,École Doctorale Physiologie, Physiopathologie et Thérapeutique, ED394, Sorbonne Université, Paris, France
| | - Melania Cruciani
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
| | - Nicolas Tchitchek
- École Doctorale Physiologie, Physiopathologie et Thérapeutique, ED394, Sorbonne Université, Paris, France.,i3 research unit, Hôpital Pitié-Salpêtrière-Sorbonne Université, Paris, France
| | - Anna Le Tortorec
- UMR_S1085, Institut de recherche en santé, environnement et travail (Irset), EHESP, Inserm, Univ Rennes, Rennes, France
| | - Antoine D Rolland
- UMR_S1085, Institut de recherche en santé, environnement et travail (Irset), EHESP, Inserm, Univ Rennes, Rennes, France
| | - Önay Veli
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
| | - Leslie Vallet
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
| | - Giulia Gaggi
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
| | - Frédérique Michel
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
| | - Nathalie Dejucq-Rainsford
- UMR_S1085, Institut de recherche en santé, environnement et travail (Irset), EHESP, Inserm, Univ Rennes, Rennes, France
| | - Sandra Pellegrini
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
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Morrow BE, McDonald-McGinn DM, Emanuel BS, Vermeesch JR, Scambler PJ. Molecular genetics of 22q11.2 deletion syndrome. Am J Med Genet A 2019; 176:2070-2081. [PMID: 30380194 DOI: 10.1002/ajmg.a.40504] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/11/2018] [Accepted: 07/17/2018] [Indexed: 02/02/2023]
Abstract
The 22q11.2 deletion syndrome (22q11.2DS) is a congenital malformation and neuropsychiatric disorder caused by meiotic chromosome rearrangements. One of the goals of this review is to summarize the current state of basic research studies of 22q11.2DS. It highlights efforts to understand the mechanisms responsible for the 22q11.2 deletion that occurs in meiosis. This mechanism involves the four sets of low copy repeats (LCR22) that are dispersed in the 22q11.2 region and the deletion is mediated by nonallelic homologous recombination events. This review also highlights selected genes mapping to the 22q11.2 region that may contribute to the typical clinical findings associated with the disorder and explain that mutations in genes on the remaining allele can uncover rare recessive conditions. Another important aspect of 22q11.2DS is the existence of phenotypic heterogeneity. While some patients are mildly affected, others have severe medical, cognitive, and/or psychiatric challenges. Variability may be due in part to the presence of genetic modifiers. This review discusses current genome-wide efforts to identify such modifiers that could shed light on molecular pathways required for normal human development, cognition or behavior.
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Affiliation(s)
- Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Beverly S Emanuel
- Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Joris R Vermeesch
- Center for Human Genetics, Katholieke Universiteit Leuven (KU Leuven), Leuven, Belgium
| | - Peter J Scambler
- Institute of Child Health, University College London, London, UK
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Guo T, Diacou A, Nomaru H, McDonald-McGinn DM, Hestand M, Demaerel W, Zhang L, Zhao Y, Ujueta F, Shan J, Montagna C, Zheng D, Crowley TB, Kushan-Wells L, Bearden CE, Kates WR, Gothelf D, Schneider M, Eliez S, Breckpot J, Swillen A, Vorstman J, Zackai E, Benavides Gonzalez F, Repetto GM, Emanuel BS, Bassett AS, Vermeesch JR, Marshall CR, Morrow BE. Deletion size analysis of 1680 22q11.2DS subjects identifies a new recombination hotspot on chromosome 22q11.2. Hum Mol Genet 2018; 27:1150-1163. [PMID: 29361080 PMCID: PMC6059186 DOI: 10.1093/hmg/ddy028] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/22/2017] [Accepted: 01/09/2018] [Indexed: 02/07/2023] Open
Abstract
Recurrent, de novo, meiotic non-allelic homologous recombination events between low copy repeats, termed LCR22s, leads to the 22q11.2 deletion syndrome (22q11.2DS; velo-cardio-facial syndrome/DiGeorge syndrome). Although most 22q11.2DS patients have a similar sized 3 million base pair (Mb), LCR22A-D deletion, some have nested LCR22A-B or LCR22A-C deletions. Our goal is to identify additional recurrent 22q11.2 deletions associated with 22q11.2DS, serving as recombination hotspots for meiotic chromosomal rearrangements. Here, using data from Affymetrix 6.0 microarrays on 1680 22q11.2DS subjects, we identified what appeared to be a nested proximal 22q11.2 deletion in 38 (2.3%) of them. Using molecular and haplotype analyses from 14 subjects and their parent(s) with available DNA, we found essentially three types of scenarios to explain this observation. In eight subjects, the proximal breakpoints occurred in a small sized 12 kb LCR distal to LCR22A, referred to LCR22A+, resulting in LCR22A+-B or LCR22A+-D deletions. Six of these eight subjects had a nested 22q11.2 deletion that occurred during meiosis in a parent carrying a benign 0.2 Mb duplication of the LCR22A-LCR22A+ region with a breakpoint in LCR22A+. Another six had a typical de novo LCR22A-D deletion on one allele and inherited the LCR22A-A+ duplication from the other parent thus appearing on microarrays to have a nested deletion. LCR22A+ maps to an evolutionary breakpoint between mice and humans and appears to serve as a local hotspot for chromosome rearrangements on 22q11.2.
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Affiliation(s)
- Tingwei Guo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hiroko Nomaru
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children’s Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Matthew Hestand
- Center for Human Genetics, Katholieke University Leuven (KULeuven), Leuven, Belgium
| | - Wolfram Demaerel
- Center for Human Genetics, Katholieke University Leuven (KULeuven), Leuven, Belgium
| | - Liangtian Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yingjie Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Francisco Ujueta
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jidong Shan
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Terrence B Crowley
- Division of Human Genetics, Children’s Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Leila Kushan-Wells
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles, CA, USA
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles, CA, USA
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, and Program in Neuroscience, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Doron Gothelf
- Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
- Felsenstein Medical Research Center, Sackler Faculty of Medicine, Tel Aviv University, Petah Tikva, Israel
| | - Maude Schneider
- Developmental Imaging and Psychopathology Lab, University of Geneva School of Medicine, Geneva, Switzerland
| | - Stephan Eliez
- Developmental Imaging and Psychopathology Lab, University of Geneva School of Medicine, Geneva, Switzerland
| | - Jeroen Breckpot
- Center for Human Genetics, Katholieke University Leuven (KULeuven), Leuven, Belgium
| | - Ann Swillen
- Center for Human Genetics, Katholieke University Leuven (KULeuven), Leuven, Belgium
| | - Jacob Vorstman
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elaine Zackai
- Division of Human Genetics, Children’s Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Felipe Benavides Gonzalez
- Center for Genetics and Genomics, Facultad de Medicina, Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Gabriela M Repetto
- Center for Genetics and Genomics, Facultad de Medicina, Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Beverly S Emanuel
- Division of Human Genetics, Children’s Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Anne S Bassett
- Center for Addiction and Mental Health, Toronto General Hospital and the University of Toronto, Toronto, Canada
- Department of Pediatric Laboratory Medicine and Laboratory of Medicine and Pathobiology, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Joris R Vermeesch
- Center for Human Genetics, Katholieke University Leuven (KULeuven), Leuven, Belgium
| | - Christian R Marshall
- Department of Pediatric Laboratory Medicine and Laboratory of Medicine and Pathobiology, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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An exploratory study of predisposing genetic factors for DiGeorge/velocardiofacial syndrome. Sci Rep 2017; 7:40031. [PMID: 28059126 PMCID: PMC5216377 DOI: 10.1038/srep40031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/01/2016] [Indexed: 12/13/2022] Open
Abstract
DiGeorge/velocardiofacial syndrome (DGS/VCFS) is a disorder caused by a 22q11.2 deletion mediated by non-allelic homologous recombination (NAHR) between low-copy repeats (LCRs). We have evaluated the role of LCR22 genomic architecture and PRDM9 variants as DGS/VCFS predisposing factors. We applied FISH using fosmid probes on chromatin fibers to analyze the number of tandem repeat blocks in LCR22 in two DGS/VCFS fathers-of-origin with proven 22q11.2 NAHR susceptibility. Results revealed copy number variations (CNVs) of L9 and K3 fosmids in these individuals compared to controls. The total number of L9 and K3 copies was also characterized using droplet digital PCR (ddPCR). Although we were unable to confirm variations, we detected an additional L9 amplicon corresponding to a pseudogene. Moreover, none of the eight DGS/VCFS parents-of-origin was heterozygote for the inv(22)(q11.2) haplotype. PRDM9 sequencing showed equivalent allelic distributions between DGS/VCFS parents-of-origin and controls, although a new PRDM9 allele (L50) was identified in one case. Our results support the hypothesis that LCR22s variations influences 22q11.2 NAHR events, however further studies are needed to confirm this association and clarify the contribution of pseudogenes and rare PDRM9 alleles to NAHR susceptibility.
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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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Meechan DW, Maynard TM, Tucker ES, Fernandez A, Karpinski BA, Rothblat LA, LaMantia AS. Modeling a model: Mouse genetics, 22q11.2 Deletion Syndrome, and disorders of cortical circuit development. Prog Neurobiol 2015; 130:1-28. [PMID: 25866365 DOI: 10.1016/j.pneurobio.2015.03.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/24/2015] [Accepted: 03/29/2015] [Indexed: 12/21/2022]
Abstract
Understanding the developmental etiology of autistic spectrum disorders, attention deficit/hyperactivity disorder and schizophrenia remains a major challenge for establishing new diagnostic and therapeutic approaches to these common, difficult-to-treat diseases that compromise neural circuits in the cerebral cortex. One aspect of this challenge is the breadth and overlap of ASD, ADHD, and SCZ deficits; another is the complexity of mutations associated with each, and a third is the difficulty of analyzing disrupted development in at-risk or affected human fetuses. The identification of distinct genetic syndromes that include behavioral deficits similar to those in ASD, ADHC and SCZ provides a critical starting point for meeting this challenge. We summarize clinical and behavioral impairments in children and adults with one such genetic syndrome, the 22q11.2 Deletion Syndrome, routinely called 22q11DS, caused by micro-deletions of between 1.5 and 3.0 MB on human chromosome 22. Among many syndromic features, including cardiovascular and craniofacial anomalies, 22q11DS patients have a high incidence of brain structural, functional, and behavioral deficits that reflect cerebral cortical dysfunction and fall within the spectrum that defines ASD, ADHD, and SCZ. We show that developmental pathogenesis underlying this apparent genetic "model" syndrome in patients can be defined and analyzed mechanistically using genomically accurate mouse models of the deletion that causes 22q11DS. We conclude that "modeling a model", in this case 22q11DS as a model for idiopathic ASD, ADHD and SCZ, as well as other behavioral disorders like anxiety frequently seen in 22q11DS patients, in genetically engineered mice provides a foundation for understanding the causes and improving diagnosis and therapy for these disorders of cortical circuit development.
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Affiliation(s)
- Daniel W Meechan
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Thomas M Maynard
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Eric S Tucker
- Department of Neurobiology and Anatomy, Neuroscience Graduate Program, and Center for Neuroscience, West Virginia University School of Medicine, Morgantown, West Virginia
| | - Alejandra Fernandez
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Beverly A Karpinski
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Lawrence A Rothblat
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States; Department of Psychology, The George Washington University, Washington, DC, United States
| | - Anthony-S LaMantia
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States.
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Vergés L, Molina O, Geán E, Vidal F, Blanco J. Deletions and duplications of the 22q11.2 region in spermatozoa from DiGeorge/velocardiofacial fathers. Mol Cytogenet 2014; 7:86. [PMID: 25435913 PMCID: PMC4247602 DOI: 10.1186/s13039-014-0086-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/04/2014] [Indexed: 11/12/2022] Open
Abstract
Background DiGeorge/velocardiofacial syndrome (DGS/VCFS) is the most common deletion syndrome in humans. Low copy repeats flanking the 22q11.2 region confer a substrate for non-allelic homologous recombination (NAHR) events leading to rearrangements. This study sought to identify DGS/VCFS fathers with increased susceptibility to deletions and duplications at the 22q11.2 region in spermatozoa and to assess the particular contribution of intra-chromatid and/or inter-chromatid NAHR. Semen samples from nine DGS/VCFS fathers were analyzed by triple-color FISH using a probe combination that discriminated between normal, deleted and duplicated genotypes. Microsatellite analysis were performed in the parents and the affected children to determine the parental origin of the deleted chromosome 22. Results A significant increase in 22q11.2 deletions was observed in the sperm of two out of nine DGS/VCFS fathers (odds ratio 2.03-fold, P < 0.01), and in both cases the deletion in the offspring was transmitted by the father. Patients with significant increases in sperm anomalies presented a disturbed deletion:duplication 1:1 ratio (P < 0.01). Conclusions Altogether, results support that intra-chromatid NAHR is the mechanism responsible for the higher rate of sperm deletions, which is directly related to the transmission of the deleted chromosome 22 to offspring. Accordingly, the screening of sperm anomalies in the 22q11.2 region should be taken into account in the genetic counseling of DGS/VCFS families.
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Affiliation(s)
- Laia Vergés
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain
| | - Oscar Molina
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain ; Current address: Wellcome Trust Center for Cell Biology, University of Edinburgh, Edinburgh, Scotland United Kingdom
| | - Esther Geán
- Secció de Genètica Clínica. Hospital Universitari Sant Joan de Déu, 08950-Esplugues de Llobregat, Barcelona, Spain
| | - Francesca Vidal
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain
| | - Joan Blanco
- Unitat de Biologia Cellular (Facultat de Biociències). Universitat Autònoma de Barcelona, 08193-Bellaterra, Cerdanyola del Vallès, Spain
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High-resolution fish on DNA fibers for low-copy repeats genome architecture studies. Genomics 2012; 100:380-6. [PMID: 22954586 PMCID: PMC3778886 DOI: 10.1016/j.ygeno.2012.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 08/10/2012] [Accepted: 08/22/2012] [Indexed: 11/22/2022]
Abstract
Low-copy repeats (LCRs) constitute 5% of the human genome. LCRs act as substrates for non-allelic homologous recombination (NAHR) leading to genomic structural variation. The aim of this study was to assess the potential of Fiber-FISH for LCRs direct visualization to support investigations of genome architecture within these challenging genomic regions. We describe a set of Fiber-FISH experiments designed for the study of the LCR22-2. This LCR is involved in recurrent reorganizations causing different genomic disorders. Four fosmid clones covering the entire length of the LCR22-2 and two single-copy BAC-clones, delimiting the LCR22-2 proximally and distally, were selected. The probes were hybridized in different multiple color combinations on DNA fibers from two karyotypically normal cell lines. We were able to identify three distinct structural haplotypes characterized by differences in copy-number and arrangement of the LCR22-2 genes and pseudogenes. Our results show that Multicolor Fiber-FISH is a viable methodological approach for the analysis of genome organization within complex LCR regions.
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Tzetis M, Stefanaki K, Syrmou A, Kosma K, Leze E, Giannikou K, Oikonomakis V, Sofocleous C, Choulakis M, Kolialexi A, Makrythanasis P, Kitsiou-Tzeli S. An unusual case of Cat-Eye syndrome phenotype and extragonadal mature teratoma: review of the literature. ACTA ACUST UNITED AC 2012; 94:561-6. [PMID: 22730277 DOI: 10.1002/bdra.23038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 04/30/2012] [Accepted: 05/01/2012] [Indexed: 01/05/2023]
Abstract
BACKGROUND Cat-Eye syndrome (CES) with teratoma has not been previously reported. We present the clinical and molecular findings of a 9-month-old girl with features of CES and also a palpable midline neck mass proved to be an extragonadal mature teratoma, additionally characterized by array comparative genomic hybridization (aCGH). RESULTS High resolution oligonucleotide-based aCGH confirmed that the supernumerary marker chromosome (SMC) derived from chromosome 22, as was indicated by molecular cytogenetic analysis with fluorescence in situ hybridization (FISH). Additionally, aCGH clarified the size, breakpoints, and gene content of the duplication (dup 22q11.1q11.21; size:1.6 Mb; breakpoints: 15,438,946-17,041,773; hg18). The teratoma tissue was also tested with aCGH, in which the CES duplication was not found, but the analysis revealed three aberrations: del Xp22.3 (108,864-2788,689; 2.7 Mb hg18), dup Yp11.2 (6688,491-7340,982; 0.65 Mb, hg18), and dup Yq11.2q11.23 (12,570,853-27,177,133; 14.61 Mb, hg18). These results indicated 46 XY (male) karyotype of the teratoma tissue, making this the second report of mature extragonadal teratoma in a female neonate, probably deriving from an included dizygotic twin of opposite sex (fetus in fetu). CONCLUSIONS Our findings extend the phenotypic spectrum of CES syndrome, a disorder with clinical variability, pointing out specific dosage-sensitive genes that might contribute to specific phenotypic features.
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Affiliation(s)
- Maria Tzetis
- Department of Medical Genetics, Medical School, University of Athens, Greece
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Guo X, Freyer L, Morrow B, Zheng D. Characterization of the past and current duplication activities in the human 22q11.2 region. BMC Genomics 2011; 12:71. [PMID: 21269513 PMCID: PMC3040729 DOI: 10.1186/1471-2164-12-71] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 01/26/2011] [Indexed: 12/02/2022] Open
Abstract
Background Segmental duplications (SDs) on 22q11.2 (LCR22), serve as substrates for meiotic non-allelic homologous recombination (NAHR) events resulting in several clinically significant genomic disorders. Results To understand the duplication activity leading to the complicated SD structure of this region, we have applied the A-Bruijn graph algorithm to decompose the 22q11.2 SDs to 523 fundamental duplication sequences, termed subunits. Cross-species syntenic analysis of primate genomes demonstrates that many of these LCR22 subunits emerged very recently, especially those implicated in human genomic disorders. Some subunits have expanded more actively than others, and young Alu SINEs, are associated much more frequently with duplicated sequences that have undergone active expansion, confirming their role in mediating recombination events. Many copy number variations (CNVs) exist on 22q11.2, some flanked by SDs. Interestingly, two chromosome breakpoints for 13 CNVs (mean length 65 kb) are located in paralogous subunits, providing direct evidence that SD subunits could contribute to CNV formation. Sequence analysis of PACs or BACs identified extra CNVs, specifically, 10 insertions and 18 deletions within 22q11.2; four were more than 10 kb in size and most contained young AluYs at their breakpoints. Conclusions Our study indicates that AluYs are implicated in the past and current duplication events, and moreover suggests that DNA rearrangements in 22q11.2 genomic disorders perhaps do not occur randomly but involve both actively expanded duplication subunits and Alu elements.
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Affiliation(s)
- Xingyi Guo
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Schramm C, Draaken M, Bartels E, Boemers TM, Aretz S, Brockschmidt FF, Nöthen MM, Ludwig M, Reutter H. De novo microduplication at 22q11.21 in a patient with VACTERL association. Eur J Med Genet 2011; 54:9-13. [DOI: 10.1016/j.ejmg.2010.09.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Accepted: 09/06/2010] [Indexed: 01/27/2023]
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Molina O, Anton E, Vidal F, Blanco J. Sperm rates of 7q11.23, 15q11q13 and 22q11.2 deletions and duplications: a FISH approach. Hum Genet 2010; 129:35-44. [PMID: 20931230 DOI: 10.1007/s00439-010-0894-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 09/23/2010] [Indexed: 11/30/2022]
Abstract
Genomic disorders are human diseases caused by meiotic chromosomal rearrangements of unstable regions flanked by Low Copy Repeats (LCRs). LCRs act as substrates for Non-Allelic Homologous Recombination (NAHR) leading to deletions and duplications. The aim of this study was to assess the basal frequency of deletions and duplications of the 7q11.23, 15q11-q13 and 22q11.2 regions in spermatozoa from control donors to check differences in the susceptibility to generate anomalies and to assess the contribution of intra- and inter-chromatid NAHR events. Semen samples from ten control donors were processed by FISH. A customized combination of probes was used to discriminate among normal, deleted and duplicated sperm genotypes. A minimum of 10,000 sperm were assessed per sample and region. There were no differences in the mean frequency of deletions and duplications (del + dup) among the 7q11.23, 15q11-q13 and 22q11.2 regions (frequency ± SEM, 0.37 ± 0.02; 0.46 ± 0.07 and 0.27 ± 0.07%, respectively) (P = 0.122). Nevertheless, hierarchical cluster analysis reveals interindividual differences suggesting that particular haplotypes could be the main source of variability in NAHR rates. The mean frequency of deletions was not different from the mean frequency of duplications in the 7q11.23 (P = 0.202) and 15q11-q13 (P = 0.609) regions, indicating a predominant inter-chromatid NAHR. By contrast, in the 22q11.2 region the frequency of deletions slightly exceed duplications (P = 0.032), although at the individual level any donor showed differences. Altogether, our results support the inter-chromatid NAHR as the predominant mechanism involved in the generation of sperm deletions and duplications.
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MESH Headings
- Adult
- Chromatids/genetics
- Chromosome Aberrations
- Chromosomes, Human, Pair 15/genetics
- Chromosomes, Human, Pair 22/genetics
- Chromosomes, Human, Pair 7/genetics
- DNA Sequence, Unstable/genetics
- Gene Deletion
- Gene Duplication
- Haplotypes/genetics
- Humans
- In Situ Hybridization, Fluorescence
- Male
- Middle Aged
- Recombination, Genetic
- Segmental Duplications, Genomic/genetics
- Spermatozoa
- Tissue Donors
- Young Adult
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Affiliation(s)
- Oscar Molina
- Unitat de Biologia Cel·lular, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193, Bellaterra (Cerdanyola del Vallès), Spain
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Marques-Bonet T, Girirajan S, Eichler EE. The origins and impact of primate segmental duplications. Trends Genet 2009; 25:443-54. [PMID: 19796838 PMCID: PMC2847396 DOI: 10.1016/j.tig.2009.08.002] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Revised: 08/07/2009] [Accepted: 08/10/2009] [Indexed: 12/25/2022]
Abstract
Duplicated sequences are substrates for the emergence of new genes and are an important source of genetic instability associated with rare and common diseases. Analyses of primate genomes have shown an increase in the proportion of interspersed segmental duplications (SDs) within the genomes of humans and great apes. This contrasts with other mammalian genomes that seem to have their recently duplicated sequences organized in a tandem configuration. In this review, we focus on the mechanistic origin and impact of this difference with respect to evolution, genetic diversity and primate phenotype. Although many genomes will be sequenced in the future, resolution of this aspect of genomic architecture still requires high quality sequences and detailed analyses.
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Affiliation(s)
- Tomas Marques-Bonet
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
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Orozco LD, Cokus SJ, Ghazalpour A, Ingram-Drake L, Wang S, van Nas A, Che N, Araujo JA, Pellegrini M, Lusis AJ. Copy number variation influences gene expression and metabolic traits in mice. Hum Mol Genet 2009; 18:4118-29. [PMID: 19648292 DOI: 10.1093/hmg/ddp360] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Copy number variants (CNVs) are genomic segments which are duplicated or deleted among different individuals. CNVs have been implicated in both Mendelian and complex traits, including immune and behavioral disorders, but the study of the mechanisms by which CNVs influence gene expression and clinical phenotypes in humans is complicated by the limited access to tissues and by population heterogeneity. We now report studies of the effect of 19 CNVs on gene expression and metabolic traits in a mouse intercross between strains C57BL/6J and C3H/HeJ. We found that 83% of genes predicted to occur within CNVs were differentially expressed. The expression of most CNV genes was correlated with copy number, but we also observed evidence that gene expression was altered in genes flanking CNVs, suggesting that CNVs may contain regulatory elements for these genes. Several CNVs mapped to hotspots, genomic regions influencing expression of tens or hundreds of genes. Several metabolic traits including cholesterol, triglycerides, glucose and body weight mapped to three CNVs in the genome, in mouse chromosomes 1, 4 and 17. Predicted CNV genes, such as Itlna, Defcr-1, Trim12 and Trim34 were highly correlated with these traits. Our results suggest that CNVs have a significant impact on gene expression and that CNVs may be playing a role in the mechanisms underlying metabolic traits in mice.
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Affiliation(s)
- Luz D Orozco
- Department of Human Genetics, UCLA, Los Angeles, CA, USA.
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Crespi B, Summers K, Dorus S. Genomic sister-disorders of neurodevelopment: an evolutionary approach. Evol Appl 2009; 2:81-100. [PMID: 25567849 PMCID: PMC3352408 DOI: 10.1111/j.1752-4571.2008.00056.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2008] [Accepted: 11/26/2008] [Indexed: 02/06/2023] Open
Abstract
Genomic sister-disorders are defined here as diseases mediated by duplications versus deletions of the same region. Such disorders can provide unique information concerning the genomic underpinnings of human neurodevelopment because effects of diametric variation in gene copy number on cognitive and behavioral phenotypes can be inferred. We describe evidence from the literature on deletions versus duplications for the regions underlying the best-known human neurogenetic sister-disorders, including Williams syndrome, Velocardiofacial syndrome, and Smith-Magenis syndrome, as well as the X-chromosomal conditions Klinefelter and Turner syndromes. These data suggest that diametric copy-number alterations can, like diametric alterations to imprinted genes, generate contrasting phenotypes associated with autistic-spectrum and psychotic-spectrum conditions. Genomically based perturbations to the development of the human social brain are thus apparently mediated to a notable degree by effects of variation in gene copy number. We also conducted the first analyses of positive selection for genes in the regions affected by these disorders. We found evidence consistent with adaptive evolution of protein-coding genes, or selective sweeps, for three of the four sets of sister-syndromes analyzed. These studies of selection facilitate identification of candidate genes for the phenotypes observed and lend a novel evolutionary dimension to the analysis of human cognitive architecture and neurogenetic disorders.
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Affiliation(s)
- Bernard Crespi
- Department of Biosciences, Simon Fraser University Burnaby, BC, Canada
| | - Kyle Summers
- Department of Biology, East Carolina University Greenville, NC, USA
| | - Steve Dorus
- Department of Biology and Biochemistry, University of Bath Bath, UK
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Perry GH, Yang F, Marques-Bonet T, Murphy C, Fitzgerald T, Lee AS, Hyland C, Stone AC, Hurles ME, Tyler-Smith C, Eichler EE, Carter NP, Lee C, Redon R. Copy number variation and evolution in humans and chimpanzees. Genome Res 2008; 18:1698-710. [PMID: 18775914 DOI: 10.1101/gr.082016.108] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Copy number variants (CNVs) underlie many aspects of human phenotypic diversity and provide the raw material for gene duplication and gene family expansion. However, our understanding of their evolutionary significance remains limited. We performed comparative genomic hybridization on a single human microarray platform to identify CNVs among the genomes of 30 humans and 30 chimpanzees as well as fixed copy number differences between species. We found that human and chimpanzee CNVs occur in orthologous genomic regions far more often than expected by chance and are strongly associated with the presence of highly homologous intrachromosomal segmental duplications. By adapting population genetic analyses for use with copy number data, we identified functional categories of genes that have likely evolved under purifying or positive selection for copy number changes. In particular, duplications and deletions of genes with inflammatory response and cell proliferation functions may have been fixed by positive selection and involved in the adaptive phenotypic differentiation of humans and chimpanzees.
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Affiliation(s)
- George H Perry
- School of Human Evolution & Social Change, Arizona State University, Tempe, Arizona 85287, USA
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Kehrer-Sawatzki H, Cooper DN. Molecular mechanisms of chromosomal rearrangement during primate evolution. Chromosome Res 2008; 16:41-56. [PMID: 18293104 DOI: 10.1007/s10577-007-1207-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Breakpoint analysis of the large chromosomal rearrangements which have occurred during primate evolution promises to yield new insights into the underlying mechanisms of mutagenesis. Comparison of these evolutionary breakpoints with those that are disease-associated in humans, and which occur during either meiotic or mitotic cell division, should help to identify basic mechanistic similarities as well as differences. It has recently become clear that segmental duplications (SDs) have had a very significant impact on genome plasticity during primate evolution. In comparisons of the human and chimpanzee genomes, SDs have been found in flanking regions of 70-80% of inversions and approximately 40% of deletions/duplications. A strong spatial association between primate-specific breakpoints and SDs has also become evident from comparisons of human with other mammalian genomes. The lineage-specific hyperexpansion of certain SDs observed in the genomes of human, chimpanzee, gorilla and gibbon is indicative of the intrinsic instability of some SDs in primates. However, since many primate-specific breakpoints map to regions lacking SDs, but containing interspersed high-copy repetitive sequence elements such as SINEs, LINEs, LTRs, alpha-satellites and (AT)( n ) repeats, we may infer that a range of different molecular mechanisms have probably been involved in promoting chromosomal breakage during the evolution of primate genomes.
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