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Wang L, Dong B, Xie Y, Kang H, Wu Y. The molecular mechanisms of recombinant chromosome 18 with parental pericentric inversions and a review of the literature. J Hum Genet 2023; 68:625-634. [PMID: 37161033 DOI: 10.1038/s10038-023-01157-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/07/2023] [Accepted: 04/26/2023] [Indexed: 05/11/2023]
Abstract
Chromosomal rearrangements mostly result from non-allelic homologous recombination mediated by low-copy repeats (LCRs) or segmental duplications (SDs). Recent studies on recombinant chromosome 18 (rec (18)) have focused on diagnoses and clinical phenotypes. We diagnosed two cases of prenatal rec (18) and identified precise breakpoint intervals using karyotype and chromosomal microarray analyses. We analyzed the distribution characteristics of breakpoint repetitive elements to infer rearrangement mechanisms and reviewed relevant literature to identify genetic trends. Among the 12 families with 25 pregnancies analyzed, 68% rec (18), 24% spontaneous abortions, and 8% normal births were reported. In the 17 rec (18) cases, 65% presented maternal origin and 35% were paternal. Short-arm breakpoints at p11.31 were reported in 10 cases, whereas the long-arm breakpoints were located at q21.3 (6 cases) and q12 (4 cases). Breakpoints of pericentric inversions on chromosome 18 are concentrated in p11.31, q21.3, and q12 regions. Rearrangements at 18p11.31 are non-recurrent events. ALUs, LINE1s, and MIRs were enriched at the breakpoint regions (1.85 to 3.42-fold enrichment over the entire chromosome 18), while SDs and LCRs were absent. ALU subfamilies had sequence identities of 85.94% and 83.01% between two pair breakpoints. Small repetitive elements may mediate recombination-coupled DNA repair processes, facilitating rearrangements on chromosome 18. Maternal inversion carriers are more prone to abnormal recombination in prenatal families with rec (18). Recombinant chromosomes may present preferential segregation during gamete formation.
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Affiliation(s)
- Lingxi Wang
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China.
| | - Bing Dong
- Department of Eugenics, Meishan Women and Children's Hospital, Alliance Hospital of West China Second University Hospital, Sichuan University, Meishan, 620000, China
| | - Yamei Xie
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Han Kang
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Yong Wu
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 611731, China
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2
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Liu J, Chen Z, Hu L, Song Z, Mo R, Tsang LSL, Liu Y, Huang X, Gong Z, Xiang R, Lin Z, Yang Y. Three new founder mutations in Chinese patients with Nagashima-type palmoplantar keratoderma. Br J Dermatol 2022; 187:1043-1045. [PMID: 35976164 DOI: 10.1111/bjd.21835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Juan Liu
- Department of Dermatology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Genetic Skin Disease Center, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhiming Chen
- Genetic Skin Disease Center, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Linghan Hu
- Genetic Skin Disease Center, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Zhongya Song
- Genetic Skin Disease Center, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Ran Mo
- Genetic Skin Disease Center, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Lemuel Shui-Lun Tsang
- College of Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yihe Liu
- Genetic Skin Disease Center, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Xin Huang
- Genetic Skin Disease Center, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Zhuoqing Gong
- Department of Dermatology, Peking University First Hospital, Beijing, China
| | - Ruiyu Xiang
- Genetic Skin Disease Center, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Zhimiao Lin
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Yong Yang
- Genetic Skin Disease Center, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
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López-Garrido MP, Carrascosa-Romero MC, Montero-Hernández M, Serrano-Martínez CM, Sánchez-Sánchez F. Case Report: Precision genetic diagnosis in a case of Dyggve-Melchior-Clausen syndrome reveals paternal isodisomy and heterodisomy of chromosome 18 with imprinting clinical implications. Front Genet 2022; 13:1005573. [PMID: 36468000 PMCID: PMC9716064 DOI: 10.3389/fgene.2022.1005573] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/02/2022] [Indexed: 02/19/2024] Open
Abstract
A twelve-year-old patient with a previous clinical diagnosis of spondylocostal skeletal dysplasia and moderate intellectual disability was genetically analyzed through next generation sequencing of a targeted gene panel of 179 genes associated to skeletal dysplasia and mucopolysaccharidosis in order to stablish a precision diagnosis. A homozygous nonsense [c.62C>G; p.(Ser21Ter)] mutation in DYM gene was identified in the patient. Null mutations in DYM have been associated to Dyggve-Melchior-Clausen syndrome, which is a rare autosomal-recessive disorder characterized by skeletal dysplasia and mental retardation, compatible with the patient´s phenotype. To confirm the pathogenicity of this mutation, a segregation analysis was carried out, revealing that the mutation p(Ser21Ter) was solely inherited from the father, who is a carrier of the mutation, while the mother does not carry the mutation. With the suspicion that a paternal disomy could be causing the disease, a series of microsatellite markers in chromosome 18, where the DYM gene is harbored, was analyzed in all the members of the family. Haplotype analysis provided strong evidence of paternal isodisomy and heterodisomy in that chromosome, confirming the pathological effect of this mutation. Furthermore, the patient may have a compromised expression of the ELOA3 gene due to modifications in the genomic imprinting that may potentially increase the risk of digestive cancer. All these results highlight the importance of obtaining a precision diagnosis in rare diseases.
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Affiliation(s)
- María-Pilar López-Garrido
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Facultad de Medicina de Ciudad Real, Universidad de Castilla-La Mancha (UCLM), Albacete, Spain
| | | | - Minerva Montero-Hernández
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha (UCLM), Spain
| | - Caridad-María Serrano-Martínez
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha (UCLM), Spain
| | - Francisco Sánchez-Sánchez
- Laboratorio de Genética Médica, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha (UCLM), Spain
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4
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Enjo-Barreiro JR, Ruano-Ravina A, Pérez-Ríos M, Kelsey K, Varela-Lema L, Torres-Durán M, Parente-Lamelas I, Provencio-Pulla M, Vidal-García I, Piñeiro-Lamas M, Fernández-Villar JA, Barros-Dios JM. Radon, Tobacco Exposure and Non-Small Cell Lung Cancer Risk Related to BER and NER Genetic Polymorphisms. Arch Bronconeumol 2022; 58:311-322. [PMID: 35312585 DOI: 10.1016/j.arbres.2021.07.006] [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: 04/22/2021] [Revised: 07/06/2021] [Accepted: 07/14/2021] [Indexed: 11/02/2022]
Abstract
INTRODUCTION Tobacco consumption and radon exposure are considered the first and second most common causes of lung cancer, respectively. The aim of this study was to analyze both whether selected genetic polymorphisms in loci that are in DNA repair pathways, are related to non-small-cell lung cancer (NSCLC) and whether they may modulate the association between residential radon exposure and lung cancer in both smokers and never smokers. METHODS A multicentre, hospital-based, case-control study with 826 cases and 1201 controls was designed in a radon-prone area. Genotyping was determined in whole blood and residential radon exposure was measured in participants' dwellings. RESULTS Attending to tobacco exposure, the variant in the gene NBN (rs1805794) was associated with lung cancer in never smokers (OR 2.72; 95%1.44-5.2) and heavy smokers (OR 3.04; 95%CI 1.21-7.69). The polymorphism with the highest lung cancer association was OGG1 (rs125701), showing an OR of 8.04 (95%CI 1.64-58.29) for its homozygous variant genotype in heavy smokers. Attending to indoor radon exposure (>200Bq/m3), rs1452584, for its homozygous variant genotype, showed the highest association (OR 3.04 (95%CI 1.15-8.48). CONCLUSION The genes analyzed seem to have no association with the fully adjusted model, but they might modulate lung cancer association when different categories of tobacco consumption are considered (i.e. heavy smokers). This association may similarly be elevated for those individuals having high indoor radon exposures, though at a minor extent.
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Affiliation(s)
- José Ramón Enjo-Barreiro
- Service of Preventive Medicine, University Complex of Santiago de Compostela, Spain; Department of Preventive Medicine, Santiago de Compostela University Teaching Hospital Complex, Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública, CIBERESP), Spain
| | - Alberto Ruano-Ravina
- Department of Preventive Medicine, Santiago de Compostela University Teaching Hospital Complex, Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública, CIBERESP), Spain; Health Research Institute of Santiago de Compostela (Instituto de Investigación Sanitaria de Santiago de Compostela-IDIS), Santiago de Compostela, Spain.
| | - Mónica Pérez-Ríos
- Department of Preventive Medicine, Santiago de Compostela University Teaching Hospital Complex, Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública, CIBERESP), Spain; Health Research Institute of Santiago de Compostela (Instituto de Investigación Sanitaria de Santiago de Compostela-IDIS), Santiago de Compostela, Spain
| | - Karl Kelsey
- Department of Epidemiology, Brown School of Public Health, Brown University, Providence, Rhode Island, USA
| | - Leonor Varela-Lema
- Department of Preventive Medicine, Santiago de Compostela University Teaching Hospital Complex, Santiago de Compostela, Spain
| | | | | | | | - Iria Vidal-García
- Service of Neumology, University Hospital Complex of A Coruña, Spain
| | - María Piñeiro-Lamas
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública, CIBERESP), Spain
| | | | - Juan M Barros-Dios
- Service of Preventive Medicine, University Complex of Santiago de Compostela, Spain; Department of Preventive Medicine, Santiago de Compostela University Teaching Hospital Complex, Santiago de Compostela, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBER en Epidemiología y Salud Pública, CIBERESP), Spain
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Kitchen P, Gaston K, Jayaraman PS. Transcription Factor Chromatin Immunoprecipitation in Endothelial Cells. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2441:257-275. [PMID: 35099743 DOI: 10.1007/978-1-0716-2059-5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interactions between DNA and proteins are crucial for the regulation of gene expression. Chromatin immunoprecipitation (ChIP) is a powerful technique that allows the study of specific protein-DNA interactions in cultured cells and fresh or fixed tissue. Chromatin is isolated and sheared, and antibodies against the protein(s) of interest are used to isolate specific protein-DNA complexes. Subsequent analysis by real-time polymerase chain reaction (qPCR) or next-generation sequencing (NGS) allows identification and quantification of the co-purified DNA fragments, and NGS also gives insight into the genomic binding sites of a protein. Here we describe a cross-linking ChIP (X-ChIP) protocol, based around the example of a myc-tagged Proline-Rich Homeodomain (PRH) protein expressed in human umbilical vein endothelial cells. We also describe how to analyse specific known or suspected binding sites using quantitative PCR as well as how to analyse genome-wide binding from ChIP sequencing data.
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Affiliation(s)
- Philip Kitchen
- College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Kevin Gaston
- Biodiscovery Institute and Division of Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK
| | - Padma-Sheela Jayaraman
- Biodiscovery Institute and Division of Translational Medical Sciences, School of Medicine, University of Nottingham, Nottingham, UK.
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Hua LL, Casas C, Mikawa T. Mitotic Antipairing of Homologous Chromosomes. Results Probl Cell Differ 2022; 70:191-220. [PMID: 36348108 PMCID: PMC9731508 DOI: 10.1007/978-3-031-06573-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromosome organization is highly dynamic and plays an essential role during cell function. It was recently found that pairs of the homologous chromosomes are continuously separated at mitosis and display a haploid (1n) chromosome set, or "antipairing," organization in human cells. Here, we provide an introduction to the current knowledge of homologous antipairing in humans and its implications in human disease.
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Affiliation(s)
- Lisa L. Hua
- Department of Biology, Sonoma State University, San Francisco
| | - Christian Casas
- Department of Biology, Sonoma State University, San Francisco
| | - Takashi Mikawa
- Department of Anatomy, Cardiovascular Research Institute, University of California, San Francisco,Corresponding author:
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7
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Lloveras E, Canellas A, Plaja A, Barranco L, Fernández D, Mendez B, Piqué M, de la Iglesia C, Palau N, Costa M, Herrero M, Yeste D, Auge M, Puig L, Pérez C. Genomic Chaos (Multiple Copy Number Variations and Structural Reorganization) Detected in Two Prenatal Cases. Cytogenet Genome Res 2021; 161:236-242. [PMID: 34274931 DOI: 10.1159/000515653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 03/03/2021] [Indexed: 11/19/2022] Open
Abstract
The use of new technologies in the routine diagnosis of constitutional abnormalities, such as high-resolution chromosomal microarray and next-generation sequencing, has unmasked new mechanisms for generating structural variation of the human genome. For example, complex chromosome rearrangements can originate by a chromosome catastrophe phenomenon in which numerous genomic rearrangements are apparently acquired in a single catastrophic event. This phenomenon is named chromoanagenesis (from the Greek "chromo" for chromosome and "anagenesis" for rebirth). Herein, we report 2 cases of genomic chaos detected at prenatal diagnosis. The terms "chromothripsis" and "chromoanasynthesis" and the challenge of genetic counseling are discussed.
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Affiliation(s)
- Elisabet Lloveras
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Anna Canellas
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Alberto Plaja
- Unitat d'arrays, Departament de Genetica, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Laura Barranco
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Daniel Fernández
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Begoña Mendez
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Meritxell Piqué
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Cristina de la Iglesia
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Núria Palau
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Marta Costa
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Marta Herrero
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Diana Yeste
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Marc Auge
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Laia Puig
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
| | - Cristina Pérez
- Departament de Genètica, Laboratori Central Barcelona, SYNLAB International Group, Barcelona, Spain
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8
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Sun S, Zhan F, Jiang J, Zhang X, Yan L, Cai W, Liu H, Cao D. Karyotyping and prenatal diagnosis of 47,XX,+ 8[67]/46,XX [13] Mosaicism: case report and literature review. BMC Med Genomics 2019; 12:197. [PMID: 31864361 PMCID: PMC6925423 DOI: 10.1186/s12920-019-0639-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 11/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trisomy 8 mosaicism has a wide phenotypic variability, ranging from mild dysmorphic features to severe malformations. This report concluded a female pregnant woman with trisomy 8 mosaicism, and carefully cytogenetic diagnoses were performed to give her prenatal diagnostic information. This report also provides more knowledge about trisomy 8 mosaicism and the prenatal diagnostic for clinicians. CASE PRESENTATION In this present study, we reported one case of pregnancy woman with trisomy 8 mosaicism. Noninvasive prenatal testing prompted an abnormal Z-score, but further three dimension color ultrasound result suggested a single live fetus with no abnormality. The phenotypic of the pregnant woman was normal. Based on our results, there were no abnormal initial myeloid cells (< 10- 4), which suggested that the patient had no blood diseases. The peripheral blood karyotype of the patient was 47,XX,+ 8[67]/46,XX [13], and karyotype of amniotic fluid was 46, XX. The next generation sequencing (NGS) result suggested that the proportions of trisomy 8 in different tissues were obviously different; and 0% in amniotic fluid. Last, the chromosomes of the patient and her baby were confirmed using chromosome microarray analysis (CMA), and the results were arr[GRCh37](8) × 3,11p15.5p13(230750-33,455,733) × 2 hmz and normal. CONCLUSIONS This pregnancy woman was trisomy 8 mosaicism, but the phenotypic was normal, and also the fetus was normal. Carefully cytogenetic diagnoses should be performed for prenatal diagnose.
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Affiliation(s)
- Shaohua Sun
- Genetic Disease Laboratory, Dalian Maternal and Child Health Care Hospital, Dalian, 116033, China
| | - Fang Zhan
- Genetic Disease Laboratory, Dalian Maternal and Child Health Care Hospital, Dalian, 116033, China
| | - Jiusheng Jiang
- Genetic Disease Laboratory, Dalian Maternal and Child Health Care Hospital, Dalian, 116033, China
| | - Xuerui Zhang
- Genetic Disease Laboratory, Dalian Maternal and Child Health Care Hospital, Dalian, 116033, China
| | - Lei Yan
- Genetic Disease Laboratory, Dalian Maternal and Child Health Care Hospital, Dalian, 116033, China
| | - Weiyi Cai
- CapitalBio Technology Inc, Beijing, 101111, China
| | - Hailiang Liu
- CapitalBio Technology Inc, Beijing, 101111, China.
| | - Donghua Cao
- Genetic Disease Laboratory, Dalian Maternal and Child Health Care Hospital, Dalian, 116033, China.
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SAKAKI Y. A Japanese history of the Human Genome Project. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2019; 95:441-458. [PMID: 31611500 PMCID: PMC6819149 DOI: 10.2183/pjab.95.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/04/2019] [Indexed: 06/10/2023]
Abstract
The Human Genome Project (HGP) is one of the most important international achievements in life sciences, to which Japanese scientists made remarkable contributions. In the early 1980s, Akiyoshi Wada pioneered the first project for the automation of DNA sequencing technology. Ken-ichi Matsubara exhibited exceptional leadership to launch the comprehensive human genome program in Japan. Hideki Kambara made a major contribution by developing a key device for high-speed DNA sequencers, which enabled scientists to construct human genome draft sequences. The RIKEN team led by Yoshiyuki Sakaki (the author) played remarkable roles in the draft sequencing and completion of chromosomes 21, 18, and 11. Additionally, the Keio University team led by Nobuyoshi Shimizu made noteworthy contributions to the completion of chromosomes 22, 21, and 8. In April 2003, the Japanese team joined the international consortium in declaring the completion of the human genome sequence. Consistent with the HGP mandate, Japan has successfully developed a wide range of ambitious genomic sciences.
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Affiliation(s)
- Yoshiyuki SAKAKI
- Emeritus Professor, The University of Tokyo, Tokyo, Japan
- Emeritus Professor, Kyushu University, Fukuoka, Japan
- Emeritus Researcher, RIKEN, Wako, Saitama, Japan
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10
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Xing K, Cui Y, Luan J, Zhou X, Shi L, Han J. Establishment of a human trisomy 18 induced pluripotent stem cell line from amniotic fluid cells. Intractable Rare Dis Res 2018; 7:94-99. [PMID: 29862150 PMCID: PMC5982630 DOI: 10.5582/irdr.218.01038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Trisomy 18 (18T) is the second most common autosomal trisomy syndrome in humans, but the detailed mechanism of its pathology remains unclear due to the lack of appropriate models of this disease. To resolve this problem, the current study reprogrammed human 18T amniotic fluid cells (AFCs) into an induced pluripotent stem cell (iPSC) line by introducing integration-free episomal vectors carrying pCXLE-hOCT3/4-shp53-F, pCXLE-hSK, pCXLE-hUL, and pCXWB-EBNA1. The pluripotency of 18T-iPSCs was subsequently validated by alkaline phosphatase staining, detection of iPSC biomarkers using real-time PCR and flow cytometry, detection of embryoid body (EB) formation, and detection of in vivo teratoma formation. Moreover, this study also investigated the transcriptomic profiles of 18T-iPSCs using RNA sequencing, and several gene clusters associated with the clinical manifestations of 18T were identified. In summary, the generated induced pluripotent stem cells line has typical pluripotency characteristics and can provide a useful tool with which to understand the development of 18T.
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Affiliation(s)
- Kaixuan Xing
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Science, Ji'nan, China
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
| | - Yazhou Cui
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
| | - Jing Luan
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
| | - Xiaoyan Zhou
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
| | - Liang Shi
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
| | - Jinxiang Han
- School of Medicine and Life Sciences, University of Jinan-Shandong Academy of Medical Science, Ji'nan, China
- Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, China
- Address correspondence to:Dr. Jinxiang Han, Key Laboratory for Rare Disease Research of Shandong Province, Key Laboratory for Biotech Drugs of the Ministry of Health, Shandong Medical Biotechnological Center, Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China. E-mail:
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11
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Qin N, Wang C, Lu Q, Ma Z, Dai J, Ma H, Jin G, Shen H, Hu Z. Systematic identification of long non-coding RNAs with cancer-testis expression patterns in 14 cancer types. Oncotarget 2017; 8:94769-94779. [PMID: 29212265 PMCID: PMC5706911 DOI: 10.18632/oncotarget.21930] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 08/08/2017] [Indexed: 12/25/2022] Open
Abstract
Cancer-testis (CT) genes are a group of genes that are potential targets of immunotherapy and candidate epi-drivers participating in the development of cancers. Previous studies mainly focused on protein-coding genes, neglecting long non-coding RNAs with the same expression patterns. In this study, we performed a systematic investigation of cancer-testis long non-coding RNAs (CT-lncRNAs) with multiple independent open-access databases.We identified 1,325 extremely highly expressed CT-lncRNAs (EECT-lncRNAs) in 14 cancer types. Functional annotation revealed that CT-lncRNAs reactivated in cancers could promote genome instability and the malignant potential of cancers. We observed a mutually exclusive pattern of EECT-lncRNA activation and mutation in known oncogenes, suggesting their potential role as drivers of cancer that complement known mut-driver genes. Additionally, we provided evidence that testis-specific regulatory elements and promoter hypo-methylation may be EECT-lncRNA activation mechanisms, and EECT-lncRNAs may regulate CT gene reactivation. Taken together, our study puts forth a new hypothesis in the research field of CT genes, whereby CT-lncRNAs/EECT-lncRNAs play important roles in the progression and maintenance of tumorigenesis, expanding candidate CT epi-driver genes from coding genes to non-coding RNAs.
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Affiliation(s)
- Na Qin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Cheng Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Bioinformatics, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211116, China
| | - Qun Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Zijian Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Juncheng Dai
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hongxia Ma
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.,Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing 211166, China
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12
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Appelboom G, Bruce S, Duren A, Piazza M, Monahan A, Christophe B, Zoller S, LoPresti M, Connolly ES. Aquaporin-4 gene variant independently associated with oedema after intracerebral haemorrhage. Neurol Res 2015; 37:657-61. [PMID: 26000774 DOI: 10.1179/1743132815y.0000000047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
INTRODUCTION Aquaporin-4 (AQP4) is the prominent water-channel protein in the brain playing a critical role in controlling cell water content. After intracerebral haemorrhage (ICH), perihematomal oedema (PHE) formation leads to a rapid increase in intracranial pressure (ICP) after the initial bleed. We sought to investigate the effect of a common genomic variant in the AQP4 gene on PHE formation after ICH. METHODS We reviewed the literature and identified a candidate polymorphism in AQP4 genes previously reported in Genome Wide Association Studies (GWAS). Between February 2009 and March 2011, 128 patients consented to genetic testing and were genotyped for single nucleotide polymorphism (SNP) on the AQP4 gene. Genomic DNA was extracted from buccal swabs using MasterAmp extraction kits (Epicentre, Madison, WI, USA). DNA extracted from buffy coats of whole blood samples was amplified via PCR. Linear regression with log-transformed ICH + PHE volume as the response variable was used to determine the association of SNP controlled for admission variables age, GCS, infratentorial location, hypertension, systolic blood pressure (SBP), blood urea nitrogen (BUN), glucose and alkaline phosphatase. RESULTS Nine of 128 patients had the minor allele for SNP rs1058427. Presence of the minor allele was significant in the model (P = 0.021), and associated with an increase of 88% in ICH + PHE volume (β = 0.632, exp(β) = 1.88) after controlling for admission variables. The only other significant variables included in the model was GCS (P < 0.001). CONCLUSION The establishment of an independent association between rs1054827 and ICH + PHE volume provides evidence implicating the AQP4 gene in haematoma and oedema formation after ICH. Further investigation is needed to characterise this link.
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Wang J, Ye L, Jin M, Wang X. Global analyses of Chromosome 17 and 18 genes of lung telocytes compared with mesenchymal stem cells, fibroblasts, alveolar type II cells, airway epithelial cells, and lymphocytes. Biol Direct 2015; 10:9. [PMID: 25888380 PMCID: PMC4355521 DOI: 10.1186/s13062-015-0042-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/10/2015] [Indexed: 12/15/2022] Open
Abstract
Background Telocytes (TCs) is an interstitial cell with extremely long and thin telopodes (Tps) with thin segments (podomers) and dilations (podoms) to interact with neighboring cells. TCs have been found in different organs, while there is still a lack of TCs-specific biomarkers to distinguish TCs from the other cells. Results We compared gene expression profiles of murine pulmonary TCs on days 5 (TC5) and days 10 (TC10) with mesenchymal stem cells (MSCs), fibroblasts (Fbs), alveolar type II cells (ATII), airway basal cells (ABCs), proximal airway cells (PACs), CD8+ T cells from bronchial lymph nodes (T-BL), and CD8+ T cells from lungs (T-LL). The chromosome 17 and 18 genes were extracted for further analysis. The TCs-specific genes and functional networks were identified and analyzed by bioinformatics tools. 16 and 10 of TCs-specific genes were up-regulated and 68 and 22 were down-regulated in chromosome 17 and 18, as compared with other cells respectively. Of them, Mapk14 and Trem2 were up-regulated to indicate the biological function of TCs in immune regulation, and up-regulated MCFD2 and down-regulated E4F1 and PDCD2 had an association with tissue homeostasis for TCs. Over-expressed Dpysl3 may promote TCs self-proliferation and cell-cell network forming. Conclusions The differential gene expression in chromosomes 17 and 18 clearly revealed that TCs were the distinctive type of interstitial cells. Our data also indicates that TCs may play a dual role in immune surveillance and immune homoeostasis to keep from immune disorder in acute and chronic pulmonary diseases. TCs also participated in proliferation, differentiation and regeneration. Reviewers This article was reviewed by Qing Kay Li and Dragos Cretoiu. Electronic supplementary material The online version of this article (doi:10.1186/s13062-015-0042-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jian Wang
- Department of Pulmonary Medicine, Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Biomedical Research Center, Fudan University Medical School, Shanghai, China.
| | - Ling Ye
- Department of Pulmonary Medicine, Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Biomedical Research Center, Fudan University Medical School, Shanghai, China.
| | - Meiling Jin
- Department of Pulmonary Medicine, Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Biomedical Research Center, Fudan University Medical School, Shanghai, China.
| | - Xiangdong Wang
- Department of Pulmonary Medicine, Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Biomedical Research Center, Fudan University Medical School, Shanghai, China.
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14
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Kehinde FI, Anderson CE, McGowan JE, Jethva RN, Wahab MA, Glick AR, Sterner MR, Pascasio JM, Punnett HH, Liu J. Co-occurrence of non-mosaic trisomy 22 and inherited balanced t(4;6)(q33;q23.3) in a liveborn female: Case report and review of the literature. Am J Med Genet A 2014; 164A:3187-93. [DOI: 10.1002/ajmg.a.36778] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/21/2014] [Indexed: 01/25/2023]
Affiliation(s)
- Folasade I. Kehinde
- Section of Neonatology; St. Christopher's Hospital for Children; Drexel University College of Medicine; Philadelphia Pennsylvania
| | - Carol E. Anderson
- Section of Medical Genetics; St. Christopher's Hospital for Children; Drexel University College of Medicine; Philadelphia Pennsylvania
| | - Jane E. McGowan
- Section of Neonatology; St. Christopher's Hospital for Children; Drexel University College of Medicine; Philadelphia Pennsylvania
| | - Reena N. Jethva
- Section of Medical Genetics; St. Christopher's Hospital for Children; Drexel University College of Medicine; Philadelphia Pennsylvania
| | - Mohammed A. Wahab
- Department of Pathology and Laboratory Medicine; St. Christopher's Hospital for Children; Drexel University College of Medicine; Philadelphia Pennsylvania
| | - Adina R. Glick
- Department of Pathology and Laboratory Medicine; St. Christopher's Hospital for Children; Drexel University College of Medicine; Philadelphia Pennsylvania
| | - Mark R. Sterner
- Department of Pathology and Laboratory Medicine; St. Christopher's Hospital for Children; Drexel University College of Medicine; Philadelphia Pennsylvania
| | - Judy M. Pascasio
- Department of Pathology and Laboratory Medicine; St. Christopher's Hospital for Children; Drexel University College of Medicine; Philadelphia Pennsylvania
| | - Hope H. Punnett
- Department of Pathology and Laboratory Medicine; St. Christopher's Hospital for Children; Drexel University College of Medicine; Philadelphia Pennsylvania
| | - Jinglan Liu
- Department of Pathology and Laboratory Medicine; St. Christopher's Hospital for Children; Drexel University College of Medicine; Philadelphia Pennsylvania
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15
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Ponomarenko E, Poverennaya E, Pyatnitskiy M, Lisitsa A, Moshkovskii S, Ilgisonis E, Chernobrovkin A, Archakov A. Comparative ranking of human chromosomes based on post-genomic data. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:604-11. [PMID: 22966780 DOI: 10.1089/omi.2012.0034] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The goal of the Human Proteome Project (HPP) is to fully characterize the 21,000 human protein-coding genes with respect to the estimated two million proteins they encode. As such, the HPP aims to create a comprehensive, detailed resource to help elucidate protein functions and to advance medical treatment. Similarly to the Human Genome Project (HGP), the HPP chose a chromosome-centric approach, assigning different chromosomes to different countries. Here we introduce a scoring method for chromosome ranking based on several characteristics, including relevance to health problems, existing published knowledge, and current transcriptome and proteome coverage. The score of each chromosome was computed as a weighted combination of indexes reflecting the aforementioned characteristics. The approach is tailored to the chromosome-centric HPP (C-HPP), and is advantageous in that it takes into account currently available information. We ranked the human chromosomes using the proposed score, and observed that Chr Y, Chr 13, and Chr 18 were top-ranked, whereas the scores of Chr 19, Chr 11, and Chr 17 were comparatively low. For Chr 18, selected for the Russian part of C-HPP, about 25% of the encoded genes were associated with diseases, including cancers and neurodegenerative and psychiatric diseases, as well as type 1 diabetes and essential hypertension. This ranking approach could easily be adapted to prioritize research for other sets of genes, such as metabolic pathways and functional categories.
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Affiliation(s)
- Elena Ponomarenko
- Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, Moscow, Russia
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16
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Frenkel S, Kirzhner V, Korol A. Organizational heterogeneity of vertebrate genomes. PLoS One 2012; 7:e32076. [PMID: 22384143 PMCID: PMC3288070 DOI: 10.1371/journal.pone.0032076] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 01/23/2012] [Indexed: 01/06/2023] Open
Abstract
Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.
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Affiliation(s)
| | | | - Abraham Korol
- Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
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17
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Livernois AM, Graves JAM, Waters PD. The origin and evolution of vertebrate sex chromosomes and dosage compensation. Heredity (Edinb) 2011; 108:50-8. [PMID: 22086077 DOI: 10.1038/hdy.2011.106] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
In mammals, birds, snakes and many lizards and fish, sex is determined genetically (either male XY heterogamy or female ZW heterogamy), whereas in alligators, and in many reptiles and turtles, the temperature at which eggs are incubated determines sex. Evidently, different sex-determining systems (and sex chromosome pairs) have evolved independently in different vertebrate lineages. Homology shared by Xs and Ys (and Zs and Ws) within species demonstrates that differentiated sex chromosomes were once homologous, and that the sex-specific non-recombining Y (or W) was progressively degraded. Consequently, genes are left in single copy in the heterogametic sex, which results in an imbalance of the dosage of genes on the sex chromosomes between the sexes, and also relative to the autosomes. Dosage compensation has evolved in diverse species to compensate for these dose differences, with the stringency of compensation apparently differing greatly between lineages, perhaps reflecting the concentration of genes on the original autosome pair that required dosage compensation. We discuss the organization and evolution of amniote sex chromosomes, and hypothesize that dosage insensitivity might predispose an autosome to evolving function as a sex chromosome.
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Affiliation(s)
- A M Livernois
- Evolution Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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18
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Archakov A, Aseev A, Bykov V, Grigoriev A, Govorun V, Ivanov V, Khlunov A, Lisitsa A, Mazurenko S, Makarov AA, Ponomarenko E, Sagdeev R, Skryabin K. Gene-centric view on the human proteome project: the example of the Russian roadmap for chromosome 18. Proteomics 2011; 11:1853-6. [PMID: 21563312 DOI: 10.1002/pmic.201000540] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
During the 2010 Human Proteome Organization Congress in Sydney, a gene-centric approach emerged as a feasible and tractable scaffold for assemblage of the Human Proteome Project. Bringing the gene-centric principle into practice, a roadmap for the 18th chromosome was drafted, postulating the limited sensitivity of analytical methods, as a serious bottleneck in proteomics. In the context of the sensitivity problem, we refer to the "copy number of protein molecules" as a measurable assessment of protein abundance. The roadmap is focused on the development of technology to attain the low- and ultralow -"copied" portion of the proteome. Roadmap merges the genomic, transcriptomic and proteomic levels to identify the majority of 285 proteins from 18th chromosome - master proteins. Master protein is the primary translation of the coding sequence and resembling at least one of the known isoforms, coded by the gene. The executive phase of the roadmap includes the expansion of the study of the master proteins with alternate splicing, single amino acid polymorphisms (SAPs) and post-translational modifications. In implementing the roadmap, Russian scientists are expecting to establish proteomic technologies for integrating MS and atomic force microscopy (AFM). These technologies are anticipated to unlock the value of new biomarkers at a detection limit of 10(-18) M, i.e. 1 protein copy per 1 μL of plasma. The roadmap plan is posted at www.proteome.ru/en/roadmap/ and a forum for discussion of the document is supported.
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Affiliation(s)
- Alexander Archakov
- Orekhovich Institute of Biomedical Chemistry, Russian Academy of Medical Sciences (RAMS), Moscow, Russia.
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Skandalis A, Frampton M, Seger J, Richards MH. The adaptive significance of unproductive alternative splicing in primates. RNA (NEW YORK, N.Y.) 2010; 16:2014-2022. [PMID: 20719917 PMCID: PMC2941109 DOI: 10.1261/rna.2127910] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2010] [Accepted: 07/12/2010] [Indexed: 05/29/2023]
Abstract
Alternative gene splicing is pervasive in metazoa, particularly in humans, where the majority of genes generate splice variant transcripts. Characterizing the biological significance of alternative transcripts is methodologically difficult since it is impractical to assess thousands of splice variants as to whether they actually encode proteins, whether these proteins are functional, or whether transcripts have a function independent of protein synthesis. Consequently, to elucidate the functional significance of splice variants and to investigate mechanisms underlying the fidelity of mRNA splicing, we used an indirect approach based on analyzing the evolutionary conservation of splice variants among species. Using DNA polymerase β as an indicator locus, we cloned and characterized the types and frequencies of transcripts generated in primary cell lines of five primate species. Overall, we found that in addition to the canonical DNA polymerase β transcript, there were 25 alternative transcripts generated, most containing premature terminating codons. We used a statistical method borrowed from community ecology to show that there is significant diversity and little conservation in alternative splicing patterns among species, despite high sequence similarity in the underlying genomic (exonic) sequences. However, the frequency of alternative splicing at this locus correlates well with life history parameters such as the maximal longevity of each species, indicating that the alternative splicing of unproductive splice variants may have adaptive significance, even if the specific RNA transcripts themselves have no function. These results demonstrate the validity of the phylogenetic conservation approach in elucidating the biological significance of alternative splicing.
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Affiliation(s)
- Adonis Skandalis
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada.
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20
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Mackiewicz D, Zawierta M, Waga W, Cebrat S. Genome analyses and modelling the relationships between coding density, recombination rate and chromosome length. J Theor Biol 2010; 267:186-92. [PMID: 20728453 DOI: 10.1016/j.jtbi.2010.08.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Revised: 06/29/2010] [Accepted: 08/17/2010] [Indexed: 01/23/2023]
Abstract
In the human genomes, recombination frequency between homologous chromosomes during meiosis is highly correlated with their physical length while it differs significantly when their coding density is considered. Furthermore, it has been observed that the recombination events are distributed unevenly along the chromosomes. We have found that many of such recombination properties can be predicted by computer simulations of population evolution based on the Monte Carlo methods. For example, these simulations have shown that the probability of acceptance of the recombination events by selection is higher at the ends of chromosomes and lower in their middle parts. The regions of high coding density are more prone to enter the strategy of haplotype complementation and to form clusters of genes, which are "recombination deserts". The phenomenon of switching in-between the purifying selection and haplotype complementation has a phase transition character, and many relations between the effective population size, coding density, chromosome size and recombination frequency are those of the power law type.
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Affiliation(s)
- Dorota Mackiewicz
- Department of Genomics, Biotechnology Faculty, University of Wroclaw, ul. Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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Bertagnolli MM. Interpreting the Inconsistent Data Concerning the Role of 18qLOH as a Prognostic Marker for Colorectal Cancer. CURRENT COLORECTAL CANCER REPORTS 2010. [DOI: 10.1007/s11888-010-0060-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Montefusco MC, Merlo K, Bryan CD, Surks HK, Reis SE, Mendelsohn ME, Huggins GS. Little ROCK is a ROCK1 pseudogene expressed in human smooth muscle cells. BMC Genet 2010; 11:22. [PMID: 20398283 PMCID: PMC2867973 DOI: 10.1186/1471-2156-11-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 04/14/2010] [Indexed: 01/11/2023] Open
Abstract
Background Sequencing of the human genome has identified numerous chromosome copy number additions and subtractions that include stable partial gene duplications and pseudogenes that when not properly annotated can interfere with genetic analysis. As an example of this problem, an evolutionary chromosome event in the primate ancestral chromosome 18 produced a partial duplication and inversion of rho-associated protein kinase 1 (ROCK1 -18q11.1, 33 exons) in the subtelomeric region of the p arm of chromosome 18 detectable only in humans. ROCK1 and the partial gene copy, which the gene databases also currently call ROCK1, include non-unique single nucleotide polymorphisms (SNPs). Results Here, we characterize this partial gene copy of the human ROCK1, termed Little ROCK, located at 18p11.32. Little ROCK includes five exons, four of which share 99% identity with the terminal four exons of ROCK1 and one of which is unique to Little ROCK. In human while ROCK1 is expressed in many organs, Little ROCK expression is restricted to vascular smooth muscle cell (VSMC) lines and organs rich in smooth muscle. The single nucleotide polymorphism database (dbSNP) lists multiple variants contained in the region shared by ROCK1 and Little ROCK. Using gene and cDNA sequence analysis we clarified the origins of two non-synonymous SNPs annotated in the genome to actually be fixed differences between the ROCK1 and the Little ROCK gene sequences. Two additional coding SNPs were valid polymorphisms selectively within Little ROCK. Little ROCK-Green Fluorescent fusion proteins were highly unstable and degraded by the ubiquitin-proteasome system in vitro. Conclusion In this report we have characterized Little ROCK (ROCK1P1), a human expressed pseudogene derived from partial duplication of ROCK1. The large number of pseudogenes in the human genome creates significant genetic diversity. Our findings emphasize the importance of taking into consideration pseudogenes in all candidate gene and genome-wide association studies, as well as the need for complete annotation of human pseudogenome.
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Affiliation(s)
- Maria Claudia Montefusco
- Molecular Cardiology Research Institute, Tufts Medical Center, 800 Washington Street, Boston, MA 02111, USA
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Abstract
PURPOSE Microarray technology has revolutionized the field of clinical genetics with the ability to detect very small copy number changes. However, challenges remain in linking genotype with phenotype. Our goal is to enable a clinical geneticist to align the molecular karyotype information from an individual patient with the annotated genomic content, so as to provide a clinical prognosis. METHODS We have combined data regarding copy number variations, microdeletion syndromes, and classical chromosome abnormalities, with the sparse but growing knowledge about the biological role of specific genes to create a genomic map of Chromosome 18 with clinical utility. RESULTS We have created a draft model of such a map, drawing from our long-standing interest in and data regarding the abnormalities of Chromosome 18. CONCLUSION We have taken the first step toward creating a genomic map that can be used by the clinician in counseling and directing preventive or symptomatic care of individuals with Chromosome 18 abnormalities.
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Broom WJ, Johnson DV, Garber M, Andersen PM, Lennon N, Landers J, Nusbaum C, Russ C, Brown RH. DNA sequence analysis of the conserved region around the SOD1 gene locus in recessively inherited ALS. Neurosci Lett 2009; 463:64-9. [DOI: 10.1016/j.neulet.2009.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2009] [Revised: 07/06/2009] [Accepted: 07/06/2009] [Indexed: 12/13/2022]
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Pidpala OV, Yatsishina AP, Lukash LL. Human mobile genetic elements: Structure, distribution and functional role. CYTOL GENET+ 2008. [DOI: 10.3103/s009545270806011x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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A satellite-like sequence, representing a "clone gap" in the human genome, was likely involved in the seeding of a novel centromere in macaque. Chromosoma 2008; 118:269-77. [PMID: 19048265 DOI: 10.1007/s00412-008-0196-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 11/06/2008] [Accepted: 11/07/2008] [Indexed: 10/21/2022]
Abstract
Although the human genome sequence is generally considered "finished", the latest assembly (NCBI Build 36.1) still presents a number of gaps. Some of them are defined as "clone gaps" because they separate neighboring contigs. Evolutionary new centromeres are centromeres that repositioned along the chromosome, without marker order variation, during evolution. We have found that one human "clone gap" at 18q21.2 corresponds to an evolutionary new centromere in Old World Monkeys (OWM). The partially sequenced gap revealed a satellite-like structure. DNA stretches of the same satellite were found in the macaque (flanking the chromosome 18 centromere) and in the marmoset (New World Monkey), which was used as an outgroup. These findings strongly suggested that the repeat was present at the time of novel centromere seeding in OWM ancestor. We have provided, therefore, the first instance of a specific sequence hypothesized to have played a role in triggering the emergence of an evolutionary new centromere.
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Agrawal A, Morley KI, Hansell NK, Pergadia ML, Montgomery GW, Statham DJ, Todd RD, Madden PAF, Heath AC, Whitfield J, Martin NG, Lynskey MT. Autosomal linkage analysis for cannabis use behaviors in Australian adults. Drug Alcohol Depend 2008; 98:185-90. [PMID: 18606503 PMCID: PMC2584346 DOI: 10.1016/j.drugalcdep.2008.05.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 04/15/2008] [Accepted: 05/18/2008] [Indexed: 11/16/2022]
Abstract
Cannabis is the most commonly used illicit drug in developed and in developing nations. Twin studies have highlighted the role of genetic influences on early stages of cannabis use, such as a lifetime history of use, early-onset use and frequent use, however, we are not aware of any genomic studies that have examined these phenotypes. Using data on 2314 families consisting of 5600 adult Australian offspring and their parents, all of whom were scanned using 1399 unique autosomal markers, we conducted autosomal linkage analyses for lifetime history of cannabis initiation, early-onset cannabis use and frequency of use, using a variance components approach in the linkage package MERLIN. Suggestive evidence for linkage was found on chromosome 18 (LOD 2.14 for frequency of use, LOD 1.97 for initiation, at 90-97 cM) and also on chromosome 19 (LOD 1.92 for early-onset at 17 cM). These LOD scores did not meet genome-wide significance. Further replication of these linkage regions in other samples will be required, although these initial results suggest further targeted efforts on chromosome 18 may yield interesting candidate genes for early stages of cannabis-related behaviors.
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Affiliation(s)
- Arpana Agrawal
- Washington University School of Medicine, Department of Psychiatry, 660 South Euclid Avenue, St. Louis, MO 63108, USA.
| | | | | | - Michele L. Pergadia
- Washington University School of Medicine, Dept. of Psychiatry, St. Louis, MO 63108
| | | | | | - Richard D. Todd
- Washington University School of Medicine, Dept. of Psychiatry, St. Louis, MO 63108
| | - Pamela A. F. Madden
- Washington University School of Medicine, Dept. of Psychiatry, St. Louis, MO 63108
| | - Andrew C. Heath
- Washington University School of Medicine, Dept. of Psychiatry, St. Louis, MO 63108
| | - John Whitfield
- Queensland Institute of Medical Research, Brisbane, Australia
| | | | - Michael T. Lynskey
- Washington University School of Medicine, Dept. of Psychiatry, St. Louis, MO 63108
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28
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Abstract
Monosomy 18p refers to a chromosomal disorder resulting from the deletion of all or part of the short arm of chromosome 18. The incidence is estimated to be about 1:50,000 live-born infants. In the commonest form of the disorder, the dysmorphic syndrome is very moderate and non-specific. The main clinical features are short stature, round face with short philtrum, palpebral ptosis and large ears with detached pinnae. Intellectual deficiency is mild to moderate. A small subset of patients, about 10–15 percent of cases, present with severe brain/facial malformations evocative of holoprosencephaly spectrum disorders. In two-thirds of the cases, the 18p- syndrome is due to a mere terminal deletion occurring de novo, in one-third the following are possible: a de novo translocation with loss of 18p, malsegregation of a parental translocation or inversion, or a ring chr18. Parental transmission of the 18p- syndrome has been reported. Cytogenetic analysis is necessary to make a definite diagnosis. Recurrence risk for siblings is low in de novo deletions and translocations, but is significant if a parental rearrangement is present. Deletion 18p can be detected prenatally by amniocentesis or chorionic villus sampling and cytogenetic testing. Differential diagnosis may include a wide number of syndromes with short stature and mild intellectual deficiency. In young children, deletion 18p syndrome may be vaguely evocative of either Turner syndrome or trisomy 21. No specific treatment exists but speech therapy and early educational programs may help to improve the performances of the children. Except for the patients with severe brain malformations, the life expectancy does not seem significantly reduced.
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Affiliation(s)
- Catherine Turleau
- Cytogénétique AP-HP et Inserm U781, Université Paris Descartes, Hôpital Necker-Enfants Malades, 75015 Paris, France.
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29
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Parker GB. On the breeding of coauthors: just call me Al. Med J Aust 2008; 187:650-1. [PMID: 18072904 DOI: 10.5694/j.1326-5377.2007.tb01459.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 10/01/2007] [Indexed: 11/17/2022]
Affiliation(s)
- Gordon B Parker
- School of Psychiatry, University of New South Wales, Black Dog Institute, Prince of Wales Hospital, Sydney, NSW, Australia.
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30
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Abstract
The rat genome project and the resources that it has generated are transforming the translation of rat biology to human medicine. The rat genome was sequenced to a high quality “draft,” the structure and location of the genes were predicted, and a global assessment was published (Gibbs RA et al., Nature 428: 493–521, 2004). Since that time, researchers have made use of the genome sequence and annotations and related resources. We take this opportunity to review the currently available rat genome resources and to discuss the progress and future plans for the rat genome.
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Affiliation(s)
- K. C. Worley
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - G. M. Weinstock
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - R. A. Gibbs
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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31
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Artamonova II, Gelfand MS. Comparative Genomics and Evolution of Alternative Splicing: The Pessimists' Science. Chem Rev 2007; 107:3407-30. [PMID: 17645315 DOI: 10.1021/cr068304c] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Irena I Artamonova
- Group of Bioinformatics, Vavilov Institute of General Genetics, RAS, Gubkina 3, Moscow 119991, Russia
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32
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Küpper K, Kölbl A, Biener D, Dittrich S, von Hase J, Thormeyer T, Fiegler H, Carter NP, Speicher MR, Cremer T, Cremer M. Radial chromatin positioning is shaped by local gene density, not by gene expression. Chromosoma 2007; 116:285-306. [PMID: 17333233 PMCID: PMC2688818 DOI: 10.1007/s00412-007-0098-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2006] [Revised: 01/19/2007] [Accepted: 01/19/2007] [Indexed: 01/01/2023]
Abstract
G- and R-bands of metaphase chromosomes are characterized by profound differences in gene density, CG content, replication timing, and chromatin compaction. The preferential localization of gene-dense, transcriptionally active, and early replicating chromatin in the nuclear interior and of gene-poor, later replicating chromatin at the nuclear envelope has been demonstrated to be evolutionary-conserved in various cell types. Yet, the impact of different local chromatin features on the radial nuclear arrangement of chromatin is still not well understood. In particular, it is not known whether radial chromatin positioning is preferentially shaped by local gene density per se or by other related parameters such as replication timing or transcriptional activity. The interdependence of these distinct chromatin features on the linear deoxyribonucleic acid (DNA) sequence precludes a simple dissection of these parameters with respect to their importance for the reorganization of the linear DNA organization into the distinct radial chromatin arrangements observed in the nuclear space. To analyze this problem, we generated probe sets of pooled bacterial artificial chromosome (BAC) clones from HSA 11, 12, 18, and 19 representing R/G-band-assigned chromatin, segments with different gene density and gene loci with different expression levels. Using multicolor 3D flourescent in situ hybridization (FISH) and 3D image analysis, we determined their localization in the nucleus and their positions within or outside the corresponding chromosome territory (CT). For each BAC data on local gene density within 2- and 10-Mb windows, as well as GC (guanine and cytosine) content, replication timing and expression levels were determined. A correlation analysis of these parameters with nuclear positioning revealed regional gene density as the decisive parameter determining the radial positioning of chromatin in the nucleus in contrast to band assignment, replication timing, and transcriptional activity. We demonstrate a polarized distribution of gene-dense vs gene-poor chromatin within CTs with respect to the nuclear border. Whereas we confirm previous reports that a particular gene-dense and transcriptionally highly active region of about 2 Mb on 11p15.5 often loops out from the territory surface, gene-dense and highly expressed sequences were not generally found preferentially at the CT surface as previously suggested.
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Affiliation(s)
- Katrin Küpper
- Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany
| | - Alexandra Kölbl
- Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany
| | - Dorothee Biener
- Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany
| | - Sandra Dittrich
- Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany
| | - Johann von Hase
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| | - Tobias Thormeyer
- Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany
| | - Heike Fiegler
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Nigel P. Carter
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Michael R. Speicher
- Institute of Medical Biology and Human Genetics, Medical University of Graz, Graz, Austria
| | - Thomas Cremer
- Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany
| | - Marion Cremer
- Department of Biology II, Anthropology and Human Genetics, Ludwig Maximilians University, Munich, Germany, e-mail:
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33
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Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Ólason PĹ, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, A. Orengo C, Patthy L, Thornton JM, Tramontano A, Valencia A. The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A 2007; 104:5495-500. [PMID: 17372197 PMCID: PMC1838448 DOI: 10.1073/pnas.0700800104] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Indexed: 12/22/2022] Open
Abstract
Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological function of the expressed protein and even to create new protein functions. Alternative splicing has been suggested as one explanation for the discrepancy between the number of human genes and functional complexity. Here, we carry out a detailed study of the alternatively spliced gene products annotated in the ENCODE pilot project. We find that alternative splicing in human genes is more frequent than has commonly been suggested, and we demonstrate that many of the potential alternative gene products will have markedly different structure and function from their constitutively spliced counterparts. For the vast majority of these alternative isoforms, little evidence exists to suggest they have a role as functional proteins, and it seems unlikely that the spectrum of conventional enzymatic or structural functions can be substantially extended through alternative splicing.
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Affiliation(s)
- Michael L. Tress
- Structural Computational Biology Programme, Spanish National Cancer Research Centre, E-28029 Madrid, Spain
| | | | - Adam Frankish
- HAVANA Group, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Gabrielle A. Reeves
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Jan Jaap Wesselink
- Structural Computational Biology Programme, Spanish National Cancer Research Centre, E-28029 Madrid, Spain
| | - Corin Yeats
- Department of Biochemistry and Molecular Biology and
| | - Páll ĺsólfur Ólason
- Center for Biological Sequence Analysis, BioCentrum-DTU, DK-2800 Lyngby, Denmark
| | - Mario Albrecht
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Hedi Hegyi
- Biological Research Center, Hungarian Academy of Sciences, 1113 Budapest, Hungary
| | - Alejandro Giorgetti
- Department of Biochemical Sciences, University of Rome “La Sapienza,” 2-00185 Rome, Italy
| | - Domenico Raimondo
- Department of Biochemical Sciences, University of Rome “La Sapienza,” 2-00185 Rome, Italy
| | - Julien Lagarde
- Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica, E-8003 Barcelona, Spain
| | - Roman A. Laskowski
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Gonzalo López
- Structural Computational Biology Programme, Spanish National Cancer Research Centre, E-28029 Madrid, Spain
| | - Michael I. Sadowski
- Bioinformatics Unit, University College London, London WC1E 6BT, United Kingdom
| | - James D. Watson
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Piero Fariselli
- Department of Biology, University of Bologna, 33-40126 Bologna, Italy
| | - Ivan Rossi
- Department of Biology, University of Bologna, 33-40126 Bologna, Italy
| | - Alinda Nagy
- Biological Research Center, Hungarian Academy of Sciences, 1113 Budapest, Hungary
| | - Wang Kai
- Center for Biological Sequence Analysis, BioCentrum-DTU, DK-2800 Lyngby, Denmark
| | - Zenia Størling
- Center for Biological Sequence Analysis, BioCentrum-DTU, DK-2800 Lyngby, Denmark
| | - Massimiliano Orsini
- Center for Advanced Studies, Research and Development in Sardinia (CRS4), 09010 Pula, Italy
| | - Yassen Assenov
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | | | | | - Fidel Ramírez
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | | | - France Denoeud
- Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica, E-8003 Barcelona, Spain
| | - Phil Jones
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Samuel Kerrien
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Sandra Orchard
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Stylianos E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, Genopode building, University of Lausanne, 1015 Lausanne, Switzerland; and
| | - Ewan Birney
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Søren Brunak
- Center for Biological Sequence Analysis, BioCentrum-DTU, DK-2800 Lyngby, Denmark
| | - Rita Casadio
- Department of Biology, University of Bologna, 33-40126 Bologna, Italy
| | - Roderic Guigo
- Research Unit on Biomedical Informatics, Institut Municipal d'Investigació Mèdica, E-8003 Barcelona, Spain
- Centre de Regulació Genòmica, Universitat Pompeu Fabra, E-08003 Barcelona, Spain
| | - Jennifer Harrow
- HAVANA Group, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Henning Hermjakob
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David T. Jones
- Bioinformatics Unit, University College London, London WC1E 6BT, United Kingdom
| | - Thomas Lengauer
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | | | - László Patthy
- Biological Research Center, Hungarian Academy of Sciences, 1113 Budapest, Hungary
| | - Janet M. Thornton
- European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom
| | | | - Alfonso Valencia
- Structural Computational Biology Programme, Spanish National Cancer Research Centre, E-28029 Madrid, Spain
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34
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Zinner R, Teller K, Versteeg R, Cremer T, Cremer M. Biochemistry meets nuclear architecture: multicolor immuno-FISH for co-localization analysis of chromosome segments and differentially expressed gene loci with various histone methylations. ACTA ACUST UNITED AC 2007; 47:223-41. [PMID: 17442381 DOI: 10.1016/j.advenzreg.2007.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Roman Zinner
- Anthropology and Human Genetics, Department of Biology II, Ludwig-Maximilians-University, Grosshadernerstrasse 2, D-82152 Martinsried, Germany
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35
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Hall HE, Chan ER, Collins A, Judis L, Shirley S, Surti U, Hoffner L, Cockwell AE, Jacobs PA, Hassold TJ. The origin of trisomy 13. Am J Med Genet A 2007; 143A:2242-8. [PMID: 17853475 DOI: 10.1002/ajmg.a.31913] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Trisomy 13 is one of the most common trisomies in clinically recognized pregnancies and one of the few trisomies identified in liveborns, yet relatively little is known about the errors that lead to trisomy 13. Accordingly, we initiated studies to investigate the origin of the extra chromosome in 78 cases of trisomy 13. Our results indicate that the majority of cases (>91%) are maternal in origin and, similar to other autosomal trisomies, the extra chromosome is typically due to errors in meiosis I. Surprisingly, however, a large number of errors also occur during maternal meiosis II ( approximately 37%), distinguishing trisomy 13 from other acrocentric and most nonacrocentric chromosomes. As with other trisomies, failure to recombine is an important contributor to nondisjunction of chromosome 13.
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Affiliation(s)
- Heather E Hall
- Center for Reproductive Biology and School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA
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36
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Zhang Y, Liu XS, Liu QR, Wei L. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res 2006; 34:3465-75. [PMID: 16849434 PMCID: PMC1524920 DOI: 10.1093/nar/gkl473] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We developed a fast, integrative pipeline to identify cis natural antisense transcripts (cis-NATs) at genome scale. The pipeline mapped mRNAs and ESTs in UniGene to genome sequences in GoldenPath to find overlapping transcripts and combining information from coding sequence, poly(A) signal, poly(A) tail and splicing sites to deduce transcription orientation. We identified cis-NATs in 10 eukaryotic species, including 7830 candidate sense–antisense (SA) genes in 3915 SA pairs in human. The abundance of SA genes is remarkably low in worm and does not seem to be caused by the prevalence of operons. Hundreds of SA pairs are conserved across different species, even maintaining the same overlapping patterns. The convergent SA class is prevalent in fly, worm and sea squirt, but not in human or mouse as reported previously. The percentage of SA genes among imprinted genes in human and mouse is 24–47%, a range between the two previous reports. There is significant shortage of SA genes on Chromosome X in human and mouse but not in fly or worm, supporting X-inactivation in mammals as a possible cause. SA genes are over-represented in the catalytic activities and basic metabolism functions. All candidate cis-NATs can be downloaded from .
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Affiliation(s)
| | - X. Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Harvard School of Public Health44 Binney Street, M1B22, Boston, MA 02115, USA
| | - Qing-Rong Liu
- Molecular Neurobiology Branch, National Institute on Drug Abuse-Intramural Research Program (NIDA-IRP), NIH, Department of Health and Human Services (DHHS)Box 5180, Baltimore, MD 21224, USA
| | - Liping Wei
- To whom correspondence should be addressed. Tel: +86 10 6276 4970; Fax: +86 10 6275 2438;
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37
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Zody MC, Garber M, Adams DJ, Sharpe T, Harrow J, Lupski JR, Nicholson C, Searle SM, Wilming L, Young SK, Abouelleil A, Allen NR, Bi W, Bloom T, Borowsky ML, Bugalter BE, Butler J, Chang JL, Chen CK, Cook A, Corum B, Cuomo CA, de Jong PJ, DeCaprio D, Dewar K, FitzGerald M, Gilbert J, Gibson R, Gnerre S, Goldstein S, Grafham DV, Grocock R, Hafez N, Hagopian DS, Hart E, Norman CH, Humphray S, Jaffe DB, Jones M, Kamal M, Khodiyar VK, LaButti K, Laird G, Lehoczky J, Liu X, Lokyitsang T, Loveland J, Lui A, Macdonald P, Major JE, Matthews L, Mauceli E, McCarroll SA, Mihalev AH, Mudge J, Nguyen C, Nicol R, O'Leary SB, Osoegawa K, Schwartz DC, Shaw-Smith C, Stankiewicz P, Steward C, Swarbreck D, Venkataraman V, Whittaker CA, Yang X, Zimmer AR, Bradley A, Hubbard T, Birren BW, Rogers J, Lander ES, Nusbaum C. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature 2006; 440:1045-9. [PMID: 16625196 PMCID: PMC2610434 DOI: 10.1038/nature04689] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Accepted: 03/01/2006] [Indexed: 11/08/2022]
Abstract
Chromosome 17 is unusual among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second highest gene density in the genome. It is also enriched in segmental duplications, ranking third in density among the autosomes. Here we report a finished sequence for human chromosome 17, as well as a structural comparison with the finished sequence for mouse chromosome 11, the first finished mouse chromosome. Comparison of the orthologous regions reveals striking differences. In contrast to the typical pattern seen in mammalian evolution, the human sequence has undergone extensive intrachromosomal rearrangement, whereas the mouse sequence has been remarkably stable. Moreover, although the human sequence has a high density of segmental duplication, the mouse sequence has a very low density. Notably, these segmental duplications correspond closely to the sites of structural rearrangement, demonstrating a link between duplication and rearrangement. Examination of the main classes of duplicated segments provides insight into the dynamics underlying expansion of chromosome-specific, low-copy repeats in the human genome.
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Affiliation(s)
- Michael C Zody
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Massachusetts 02142, USA
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38
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Zody MC, Garber M, Sharpe T, Young SK, Rowen L, O'Neill K, Whittaker CA, Kamal M, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Kodira CD, Madan A, Qin S, Yang X, Abbasi N, Abouelleil A, Arachchi HM, Baradarani L, Birditt B, Bloom S, Bloom T, Borowsky ML, Burke J, Butler J, Cook A, DeArellano K, DeCaprio D, Dorris L, Dors M, Eichler EE, Engels R, Fahey J, Fleetwood P, Friedman C, Gearin G, Hall JL, Hensley G, Johnson E, Jones C, Kamat A, Kaur A, Locke DP, Madan A, Munson G, Jaffe DB, Lui A, Macdonald P, Mauceli E, Naylor JW, Nesbitt R, Nicol R, O'Leary SB, Ratcliffe A, Rounsley S, She X, Sneddon KMB, Stewart S, Sougnez C, Stone SM, Topham K, Vincent D, Wang S, Zimmer AR, Birren BW, Hood L, Lander ES, Nusbaum C. Analysis of the DNA sequence and duplication history of human chromosome 15. Nature 2006; 440:671-5. [PMID: 16572171 DOI: 10.1038/nature04601] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Accepted: 01/26/2006] [Indexed: 11/09/2022]
Abstract
Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.
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Affiliation(s)
- Michael C Zody
- Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA.
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39
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Nusbaum C, Mikkelsen TS, Zody MC, Asakawa S, Taudien S, Garber M, Kodira CD, Schueler MG, Shimizu A, Whittaker CA, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Yang X, Allen NR, Anderson S, Asakawa T, Blechschmidt K, Bloom T, Borowsky ML, Butler J, Cook A, Corum B, DeArellano K, DeCaprio D, Dooley KT, Dorris L, Engels R, Glöckner G, Hafez N, Hagopian DS, Hall JL, Ishikawa SK, Jaffe DB, Kamat A, Kudoh J, Lehmann R, Lokitsang T, Macdonald P, Major JE, Matthews CD, Mauceli E, Menzel U, Mihalev AH, Minoshima S, Murayama Y, Naylor JW, Nicol R, Nguyen C, O'Leary SB, O'Neill K, Parker SCJ, Polley A, Raymond CK, Reichwald K, Rodriguez J, Sasaki T, Schilhabel M, Siddiqui R, Smith CL, Sneddon TP, Talamas JA, Tenzin P, Topham K, Venkataraman V, Wen G, Yamazaki S, Young SK, Zeng Q, Zimmer AR, Rosenthal A, Birren BW, Platzer M, Shimizu N, Lander ES. DNA sequence and analysis of human chromosome 8. Nature 2006; 439:331-5. [PMID: 16421571 DOI: 10.1038/nature04406] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Accepted: 10/06/2005] [Indexed: 11/09/2022]
Abstract
The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.
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Affiliation(s)
- Chad Nusbaum
- Broad Institute of MIT and Harvard, 320 Charles St, Cambridge, Massachusetts 02141, USA.
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