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Han M, Perkins MH, Novaes LS, Xu T, Chang H. Advances in transposable elements: from mechanisms to applications in mammalian genomics. Front Genet 2023; 14:1290146. [PMID: 38098473 PMCID: PMC10719622 DOI: 10.3389/fgene.2023.1290146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
It has been 70 years since Barbara McClintock discovered transposable elements (TE), and the mechanistic studies and functional applications of transposable elements have been at the forefront of life science research. As an essential part of the genome, TEs have been discovered in most species of prokaryotes and eukaryotes, and the relative proportion of the total genetic sequence they comprise gradually increases with the expansion of the genome. In humans, TEs account for about 40% of the genome and are deeply involved in gene regulation, chromosome structure maintenance, inflammatory response, and the etiology of genetic and non-genetic diseases. In-depth functional studies of TEs in mammalian cells and the human body have led to a greater understanding of these fundamental biological processes. At the same time, as a potent mutagen and efficient genome editing tool, TEs have been transformed into biological tools critical for developing new techniques. By controlling the random insertion of TEs into the genome to change the phenotype in cells and model organisms, critical proteins of many diseases have been systematically identified. Exploiting the TE's highly efficient in vitro insertion activity has driven the development of cutting-edge sequencing technologies. Recently, a new technology combining CRISPR with TEs was reported, which provides a novel targeted insertion system to both academia and industry. We suggest that interrogating biological processes that generally depend on the actions of TEs with TEs-derived genetic tools is a very efficient strategy. For example, excessive activation of TEs is an essential factor in the occurrence of cancer in humans. As potent mutagens, TEs have also been used to unravel the key regulatory elements and mechanisms of carcinogenesis. Through this review, we aim to effectively combine the traditional views of TEs with recent research progress, systematically link the mechanistic discoveries of TEs with the technological developments of TE-based tools, and provide a comprehensive approach and understanding for researchers in different fields.
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Affiliation(s)
- Mei Han
- Guangzhou National Laboratory, Guangzhou, China
| | - Matthew H. Perkins
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Leonardo Santana Novaes
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tao Xu
- Guangzhou National Laboratory, Guangzhou, China
| | - Hao Chang
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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2
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Bhat A, Ghatage T, Bhan S, Lahane GP, Dhar A, Kumar R, Pandita RK, Bhat KM, Ramos KS, Pandita TK. Role of Transposable Elements in Genome Stability: Implications for Health and Disease. Int J Mol Sci 2022; 23:7802. [PMID: 35887150 PMCID: PMC9319628 DOI: 10.3390/ijms23147802] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/11/2022] Open
Abstract
Most living organisms have in their genome a sizable proportion of DNA sequences capable of mobilization; these sequences are commonly referred to as transposons, transposable elements (TEs), or jumping genes. Although long thought to have no biological significance, advances in DNA sequencing and analytical technologies have enabled precise characterization of TEs and confirmed their ubiquitous presence across all forms of life. These findings have ignited intense debates over their biological significance. The available evidence now supports the notion that TEs exert major influence over many biological aspects of organismal life. Transposable elements contribute significantly to the evolution of the genome by giving rise to genetic variations in both active and passive modes. Due to their intrinsic nature of mobility within the genome, TEs primarily cause gene disruption and large-scale genomic alterations including inversions, deletions, and duplications. Besides genomic instability, growing evidence also points to many physiologically important functions of TEs, such as gene regulation through cis-acting control elements and modulation of the transcriptome through epigenetic control. In this review, we discuss the latest evidence demonstrating the impact of TEs on genome stability and the underling mechanisms, including those developed to mitigate the deleterious impact of TEs on genomic stability and human health. We have also highlighted the potential therapeutic application of TEs.
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Affiliation(s)
- Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Trupti Ghatage
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Sonali Bhan
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Ganesh P. Lahane
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Arti Dhar
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Rakesh Kumar
- Department of Biotechnology, Shri Mata Vaishnav Devi University, Katra 182320, India;
| | - Raj K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Kenneth S. Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
| | - Tej K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
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3
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Agrawal N, Kumar R, Masih S, Srivastava P, Singh P, Jaiswal SK, Moirangthem A, Saxena D, Phadke SR, Mandal K. Molecular analysis of severe hemophilia B in Indian families: Identification of mutational hotspot and novel variants. Int J Lab Hematol 2021; 44:186-192. [PMID: 34590426 DOI: 10.1111/ijlh.13715] [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: 05/29/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Hemophilia B is associated with molecular heterogeneity, with more than 1200 unique variants in the F9 gene. We hereby describe the mutational spectrum of severe hemophilia B patients presenting in a tertiary-care center in India. METHOD DNA was extracted from peripheral blood samples of 35 diagnosed severe hemophilia B patients belonging to 32 families, and were subjected to Sanger sequencing. Determination of the effect of novel variants on the protein structure and correlation between genotype and phenotype was attempted using in-silico tools. RESULTS Twenty-seven different mutations were detected in 30 probands, including 20 known and 7 novel variants. Also, we found one suspected case of whole gene deletion. The serine peptidase domain harbored most of the variants (48.1%). Inhibitory antibodies were found in two patients. CONCLUSIONS This study provides a comprehensive mutational spectrum and mutation screening strategy by Sanger sequencing of F9 gene in severe hemophilia B patients, in a resource-constraint setting.
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Affiliation(s)
- Neha Agrawal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Ravi Kumar
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Suzena Masih
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Priyanka Srivastava
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Parshw Singh
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Sushil Kumar Jaiswal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Deepti Saxena
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
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4
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Chatron N, Cassinari K, Quenez O, Baert-Desurmont S, Bardel C, Buisine MP, Calpena E, Capri Y, Corominas Galbany J, Diguet F, Edery P, Isidor B, Labalme A, Le Caignec C, Lévy J, Lecoquierre F, Lindenbaum P, Pichon O, Rollat-Farnier PA, Simonet T, Saugier-Veber P, Tabet AC, Toutain A, Wilkie AOM, Lesca G, Sanlaville D, Nicolas G, Schluth-Bolard C. Identification of mobile retrocopies during genetic testing: Consequences for routine diagnosis. Hum Mutat 2019; 40:1993-2000. [PMID: 31230393 DOI: 10.1002/humu.23845] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 05/29/2019] [Accepted: 06/17/2019] [Indexed: 12/24/2022]
Abstract
Human retrocopies, that is messenger RNA transcripts benefitting from the long interspersed element 1 machinery for retrotransposition, may have specific consequences for genomic testing. Next genetration sequencing (NGS) techniques allow the detection of such mobile elements but they may be misinterpreted as genomic duplications or be totally overlooked. We report eight observations of retrocopies detected during diagnostic NGS analyses of targeted gene panels, exome, or genome sequencing. For seven cases, while an exons-only copy number gain was called, read alignment inspection revealed a depth of coverage shift at every exon-intron junction where indels were also systematically called. Moreover, aberrant chimeric read pairs spanned entire introns or were paired with another locus for terminal exons. The 8th retrocopy was present in the reference genome and thus showed a normal NGS profile. We emphasize the existence of retrocopies and strategies to accurately detect them at a glance during genetic testing and discuss pitfalls for genetic testing.
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Affiliation(s)
- Nicolas Chatron
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
| | - Kevin Cassinari
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Olivier Quenez
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Stéphanie Baert-Desurmont
- Department of Genetics, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Claire Bardel
- Bioinformatics group of the Lyon University Hospital NGS facility, Groupement Hospitalier Est, Lyon, France.,Biostatistics and Bioinformatics Department, HCL, Lyon, France
| | - Marie-Pierre Buisine
- Department of Biochemistry and Molecular Biology, JPA Research Center, Inserm UMR-S 1172, Lille University, Lille University Hospital, Lille, France
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Yline Capri
- Genetics Department, Clinical Genetics Unit, Hôpital Universitaire Robert Debré, Paris, France
| | | | - Flavie Diguet
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
| | - Patrick Edery
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
| | | | - Audrey Labalme
- Genetics Department, Hospices Civils de Lyon, Lyon, France
| | - Cedric Le Caignec
- Genetics Department, CHU Nantes, Nantes, France.,INSERM UMR_S915, Institut du thorax, Nantes University, Nantes, France
| | - Jonathan Lévy
- Genetics Department, Cytogenetics Unit, Hôpital Universitaire Robert Debré, Paris, France
| | - François Lecoquierre
- Department of Genetics, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Pierre Lindenbaum
- INSERM, UMR_S1087, Institut du thorax, Nantes, France.,CNRS, UMR 6291, Nantes, France
| | | | - Pierre-Antoine Rollat-Farnier
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,Bioinformatics group of the Lyon University Hospital NGS facility, Groupement Hospitalier Est, Lyon, France
| | - Thomas Simonet
- Cellular Biotechnology Center, Hospices Civils de Lyon, Lyon, France.,Nerve-Muscle Interactions Team, Institut NeuroMyoGène CNRS UMR 5310-INSERM U1217-Université Claude Bernard Lyon 1, Lyon, France
| | - Pascale Saugier-Veber
- Department of Genetics, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Anne-Claude Tabet
- Genetics Department, Cytogenetics Unit, Hôpital Universitaire Robert Debré, Paris, France.,Neuroscience Department, Human Genetics and Cognitive Function Unit, Institut Pasteur, Paris, France
| | - Annick Toutain
- Genetics Department, Hôpital Bretonneau, CHU, Tours, France.,UMR 1253, iBrain, Tours University, Inserm, Tours, France
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gaetan Lesca
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
| | - Damien Sanlaville
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
| | - Gaël Nicolas
- Department of Genetics and CNR-MAJ, Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, F 76000, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - Caroline Schluth-Bolard
- Genetics Department, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, INSERM U1028, CNRS UMR5292, UCBL1, Lyon, France
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5
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Wilkes MC, Repellin CE, Sakamoto KM. Beyond mRNA: The role of non-coding RNAs in normal and aberrant hematopoiesis. Mol Genet Metab 2017; 122:28-38. [PMID: 28757239 PMCID: PMC5722683 DOI: 10.1016/j.ymgme.2017.07.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/21/2017] [Accepted: 07/21/2017] [Indexed: 02/02/2023]
Abstract
The role of non-coding Ribonucleic Acids (ncRNAs) in biology is currently an area of intense focus. Hematopoiesis requires rapidly changing regulatory molecules to guide appropriate differentiation and ncRNA are well suited for this. It is not surprising that virtually all aspects of hematopoiesis have roles for ncRNAs assigned to them and doubtlessly much more await characterization. Stem cell maintenance, lymphoid, myeloid and erythroid differentiation are all regulated by various ncRNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and various transposable elements within the genome. As our understanding of the many and complex ncRNA roles continues to grow, new discoveries are challenging the existing classification schemes. In this review we briefly overview the broad categories of ncRNAs and discuss a few examples regulating normal and aberrant hematopoiesis.
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Affiliation(s)
- Mark C Wilkes
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Kathleen M Sakamoto
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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6
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Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE, Devine SE. The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology. Genome Res 2017; 27:1916-1929. [PMID: 28855259 PMCID: PMC5668948 DOI: 10.1101/gr.218032.116] [Citation(s) in RCA: 211] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 08/07/2017] [Indexed: 01/22/2023]
Abstract
Mobile element insertions (MEIs) represent ∼25% of all structural variants in human genomes. Moreover, when they disrupt genes, MEIs can influence human traits and diseases. Therefore, MEIs should be fully discovered along with other forms of genetic variation in whole genome sequencing (WGS) projects involving population genetics, human diseases, and clinical genomics. Here, we describe the Mobile Element Locator Tool (MELT), which was developed as part of the 1000 Genomes Project to perform MEI discovery on a population scale. Using both Illumina WGS data and simulations, we demonstrate that MELT outperforms existing MEI discovery tools in terms of speed, scalability, specificity, and sensitivity, while also detecting a broader spectrum of MEI-associated features. Several run modes were developed to perform MEI discovery on local and cloud systems. In addition to using MELT to discover MEIs in modern humans as part of the 1000 Genomes Project, we also used it to discover MEIs in chimpanzees and ancient (Neanderthal and Denisovan) hominids. We detected diverse patterns of MEI stratification across these populations that likely were caused by (1) diverse rates of MEI production from source elements, (2) diverse patterns of MEI inheritance, and (3) the introgression of ancient MEIs into modern human genomes. Overall, our study provides the most comprehensive map of MEIs to date spanning chimpanzees, ancient hominids, and modern humans and reveals new aspects of MEI biology in these lineages. We also demonstrate that MELT is a robust platform for MEI discovery and analysis in a variety of experimental settings.
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Affiliation(s)
- Eugene J Gardner
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Vincent K Lam
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.,Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Daniel N Harris
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Nelson T Chuang
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.,Division of Gastroenterology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Emma C Scott
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - W Stephen Pittard
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA.,Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | | | - Scott E Devine
- Program in Molecular Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.,Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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7
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Rastogi P, Kumar N, Ahluwalia J, Das R, Panigrahi I. The first case report of a patient with coexisting hemophilia B and Down syndrome. Blood Res 2017; 52:75-76. [PMID: 28401110 PMCID: PMC5383597 DOI: 10.5045/br.2017.52.1.75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 08/10/2016] [Accepted: 08/29/2016] [Indexed: 11/17/2022] Open
Affiliation(s)
- Pulkit Rastogi
- Department of Hematology, Postgraduate Institute of Medical Education & Research, Sector 12, Chandigarh, India
| | - Narender Kumar
- Department of Hematology, Postgraduate Institute of Medical Education & Research, Sector 12, Chandigarh, India
| | - Jasmina Ahluwalia
- Department of Hematology, Postgraduate Institute of Medical Education & Research, Sector 12, Chandigarh, India
| | - Reena Das
- Department of Hematology, Postgraduate Institute of Medical Education & Research, Sector 12, Chandigarh, India
| | - Inusha Panigrahi
- Department of Paediatric Medicine, Postgraduate Institute of Medical Education & Research, Sector 12, Chandigarh, India
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8
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Vasilyev SA, Tolmacheva EN, Lebedev IN. Epigenetic regulation and role of LINE-1 retrotransposon in embryogenesis. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416120152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Hancks DC, Kazazian HH. Roles for retrotransposon insertions in human disease. Mob DNA 2016; 7:9. [PMID: 27158268 PMCID: PMC4859970 DOI: 10.1186/s13100-016-0065-9] [Citation(s) in RCA: 421] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022] Open
Abstract
Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a "copy-and-paste" mechanism, LINE-1 is able to retrotranspose other RNAs including Alu, SVA, and occasionally cellular RNAs. To date in humans, 124 LINE-1-mediated insertions which result in genetic diseases have been reported. Disease causing LINE-1 insertions have provided a wealth of insight and the foundation for valuable tools to study these genomic parasites. In this review, we provide an overview of LINE-1 biology followed by highlights from new reports of LINE-1-mediated genetic disease in humans.
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Affiliation(s)
- Dustin C. Hancks
- />Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Haig H. Kazazian
- />McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins School of Medicine, Baltimore, MD USA
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10
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Lannoy N, Hermans C. Principles of genetic variations and molecular diseases: applications in hemophilia A. Crit Rev Oncol Hematol 2016; 104:1-8. [PMID: 27296059 DOI: 10.1016/j.critrevonc.2016.04.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 03/07/2016] [Accepted: 04/14/2016] [Indexed: 11/24/2022] Open
Abstract
DNA structure alterations are the ultimate source of genetic variations. Without them, evolution would be impossible. While they are essential for DNA diversity, defects in DNA synthesis can lead to numerous genetic diseases. Due to increasingly innovative technologies, our knowledge of the human genome and genetic diseases has grown considerably over the last few years, allowing us to detect another class of variants affecting the chromosomal structure. DNA sequence can be altered in multiple ways: DNA sequence changes by substitution, deletion, or duplication of some nucleotides; chromosomal structure alterations by deletion, duplication, translocation, and inversion, ranging in size from kilobases to mega bases; changes in the cell's genome size. If the alteration is located within a gene and sufficiently deleterious, it can cause genetic disorders. Due to the F8 gene's high rate of new small mutations and its location at the tip of X chromosome, containing high repetitive sequences, a wide variety of genetic variants has been described as the cause of hemophilia A (HA). In addition to the F8 intron 22 repeat inversion, HA can also result from point mutations, other inversions, complex rearrangements, such as duplications or deletions, and transposon insertions causing phenotypes of variable severity characterized by complete or partial deficiency of circulating FVIII. This review aims to present the origins, mechanisms, and consequences of F8 alterations. A sound understanding of the multiple genetic mechanisms responsible for HA is essential to determine the appropriate strategy for molecular diagnosis and detected each type of genetic variant.
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Affiliation(s)
- N Lannoy
- Hemostasis and Thrombosis Unit, Hemophilia Clinic, Division of Hematology, Cliniques Universitaires Saint-Luc, Brussels, Belgium; Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, Brussels, Belgium.
| | - C Hermans
- Hemostasis and Thrombosis Unit, Hemophilia Clinic, Division of Hematology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
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11
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Abstract
Hemophilia B is an X-chromosome-linked inherited bleeding disorder primarily affecting males, but those carrier females with reduced factor IX activity (FIX:C) levels may also experience some bleeding. Genetic analysis has been undertaken for hemophilia B since the mid-1980s, through linkage analysis to track inheritance of an affected allele, and to enable determination of the familial mutation. Mutation analysis using PCR and Sanger sequencing along with dosage analysis for detection of large deletions/duplications enables mutation detection in > 97% of patients with hemophilia B. The risk of the development of inhibitory antibodies, which are reported in ~ 2% of patients with hemophilia B, can be predicted, especially in patients with large deletions, and these individuals are also at risk of anaphylaxis, and nephrotic syndrome if they receive immune tolerance induction. Inhibitors also occur in patients with nonsense mutations, occasionally in patients with small insertions/deletions or splice mutations, and rarely in patients with missense mutations (p.Gln237Lys and p.Gln241His). Hemophilia B results from several different mechanisms, and those associated with hemophilia B Leyden, ribosome readthrough of nonsense mutations and apparently 'silent' changes that do not alter amino acid coding are explored. Large databases of genetic variants in healthy individuals and patients with a range of disorders, including hemophilia B, are yielding useful information on sequence variant frequency to help establish possible variant pathogenicity, and a growing range of algorithms are available to help predict pathogenicity for previously unreported variants.
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Affiliation(s)
- A C Goodeve
- Haemostasis Research Group, Department of Cardiovascular Science, Sheffield Children's NHS Foundation Trust, University of Sheffield and Sheffield Diagnostic Genetics Service, Sheffield, UK
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12
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Ayarpadikannan S, Lee HE, Han K, Kim HS. Transposable element-driven transcript diversification and its relevance to genetic disorders. Gene 2015; 558:187-94. [PMID: 25617522 DOI: 10.1016/j.gene.2015.01.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 01/13/2015] [Accepted: 01/20/2015] [Indexed: 12/14/2022]
Abstract
The human genome project and subsequent gene annotation projects have shown that the human genome contains 22,000-25,000 functional genes. Therefore, it is believed that the diversity of protein repertoire is achieved by the alternative splicing (AS) mechanism. Transposable elements (TEs) are mobile in nature and can therefore alter their position in the genome. The insertion of TEs into a new gene region can result in AS of a particular transcript through various mechanisms, including intron retention, and alternative donor or acceptor splice sites. TE-derived AS is thought to have played a part in primate evolution and in hominid radiation. However, TE-derived AS or genetic instability may sometimes result in genetic disorders. For the past two decades, numerous studies have been performed on TEs and their role in genomes. Accumulating evidence shows that the term 'junk DNA', previously used for TEs is a misnomer. Recent research has indicated that TEs may have clinical potential. However, to explore the feasibility of using TEs in clinical practice, additional studies are required. This review summarizes the available literature on TE-derived AS, alternative promoter, and alternative polyadenylation. The review covers the effects of TEs on coding genes and their clinical implications, and provides our perspectives and directions for future research.
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Affiliation(s)
- Selvam Ayarpadikannan
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science, WCU Research Center, Dankook University, Cheonan 330-714, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea.
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Lee HE, Ayarpadikannan S, Kim HS. Role of transposable elements in genomic rearrangement, evolution, gene regulation and epigenetics in primates. Genes Genet Syst 2015; 90:245-57. [DOI: 10.1266/ggs.15-00016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hee-Eun Lee
- Department of Biological Sciences, College of Natural Sciences, Pusan National University
- Genetic Engineering Institute, Pusan National University
| | - Selvam Ayarpadikannan
- Department of Biological Sciences, College of Natural Sciences, Pusan National University
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University
- Genetic Engineering Institute, Pusan National University
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Ayarpadikannan S, Kim HS. The impact of transposable elements in genome evolution and genetic instability and their implications in various diseases. Genomics Inform 2014; 12:98-104. [PMID: 25317108 PMCID: PMC4196381 DOI: 10.5808/gi.2014.12.3.98] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 12/15/2022] Open
Abstract
Approximately 45% of the human genome is comprised of transposable elements (TEs). Results from the Human Genome Project have emphasized the biological importance of TEs. Many studies have revealed that TEs are not simply "junk" DNA, but rather, they play various roles in processes, including genome evolution, gene expression regulation, genetic instability, and cancer disposition. The effects of TE insertion in the genome varies from negligible to disease conditions. For the past two decades, many studies have shown that TEs are the causative factors of various genetic disorders and cancer. TEs are a subject of interest worldwide, not only in terms of their clinical aspects but also in basic research, such as evolutionary tracking. Although active TEs contribute to genetic instability and disease states, non-long terminal repeat transposons are well studied, and their roles in these processes have been confirmed. In this review, we will give an overview of the importance of TEs in studying genome evolution and genetic instability, and we suggest that further in-depth studies on the mechanisms related to these phenomena will be useful for both evolutionary tracking and clinical diagnostics.
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Affiliation(s)
- Selvam Ayarpadikannan
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea
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Cao DH, Liu XL, Mu K, Ma XW, Sun JL, Bai XZ, Lin CK, Jin CL. Identification and Genetic Analysis of a Factor IX Gene Intron 3 Mutation in a Hemophilia B Pedigree in China. Turk J Haematol 2014; 31:226-30. [PMID: 25330515 PMCID: PMC4287022 DOI: 10.4274/tjh.2013.0275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Objective: Hemophilia B is caused by coagulation defects in the factor IX gene located in Xq27.1 on the X chromosome. A wide range of mutations, showing extensive molecular heterogeneity, have been described in hemophilia B patients. Our study was aimed at genetic analysis and prenatal diagnosis of hemophilia B in order to further elucidate the pathogenesis of the hemophilia B pedigree in China. Materials and Methods: Polymerase chain reaction amplification and direct sequencing of all the coding regions was conducted in hemophilia B patients and carriers. Prenatal diagnosis of the proband was conducted at 20 weeks. Results: We identified the novel point mutation 10.389 A>G, located upstream of the intron 3 acceptor site in hemophilia B patients. The fetus of the proband’s cousin was identified as a carrier. Conclusion: Our identification of a novel mutation in the F9 gene associated with hemophilia B provides novel insight into the pathogenesis of this genetically inherited disorder and also represents the basis of prenatal diagnosis.
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Affiliation(s)
- Dong-Hua Cao
- China Medical University, Department of Medical Genetics, Shenyang, China. E-ma-il:
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16
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Robinson KM, Dunning Hotopp JC. Mobile elements and viral integrations prompt considerations for bacterial DNA integration as a novel carcinogen. Cancer Lett 2014; 352:137-44. [PMID: 24956175 DOI: 10.1016/j.canlet.2014.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/30/2014] [Accepted: 05/01/2014] [Indexed: 12/11/2022]
Abstract
Insertional mutagenesis has been repeatedly demonstrated in cancer genomes and has a role in oncogenesis. Mobile genetic elements can induce cancer development by random insertion into cancer related genes or by inducing translocations. L1s are typically implicated in cancers of an epithelial cell origin, while Alu elements have been implicated in leukemia as well as epithelial cell cancers. Likewise, viral infections have a significant role in cancer development predominantly through integration into the human genome and mutating or deregulating cancer related genes. Human papilloma virus is the best-known example of viral integrations contributing to carcinogenesis. However, hepatitis B virus, Epstein-Barr virus, and Merkel cell polyomavirus also integrate into the human genome and disrupt cancer related genes. Thus far, the role of microbes in cancer has primarily been attributed to mutations induced through chronic inflammation or toxins, as is the case with Helicobacter pylori and enterotoxigenic Bacteroides fragilis. We hypothesize that like mobile elements and viral DNA, bacterial and parasitic DNA may also integrate into the human somatic genome and be oncogenic. Until recently it was believed that bacterial DNA could not integrate into the human genome, but new evidence demonstrates that bacterial insertional mutagenesis may occur in cancer cells. Although this work does not show causation between bacterial insertions and cancer, it prompts more research in this area. Promising new sequencing technologies may reduce the risk of artifactual chimeric sequences, thus diminishing some of the challenges of identifying novel insertions in the somatic human genome.
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Affiliation(s)
- Kelly M Robinson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA; Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.
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Lin PC, Su YN, Liao YM, Chang TT, Tsai SP, Shu HL, Chiou SS. Efficient detection of factor IX mutations by denaturing high-performance liquid chromatography in Taiwanese hemophilia B patients, and the identification of two novel mutations. Kaohsiung J Med Sci 2014; 30:187-93. [PMID: 24656159 DOI: 10.1016/j.kjms.2013.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 08/19/2013] [Indexed: 10/25/2022] Open
Abstract
Hemophilia B (HB) is an X-linked recessive disorder characterized by mutations in the clotting factor IX (FIX) gene that result in FIX deficiency. Previous studies have shown a wide variation of FIX gene mutations in HB. Although the quality of life in HB has greatly improved mainly because of prophylactic replacement therapy with FIX concentrates, there exists a significant burden on affected families and the medical care system. Accurate detection of FIX gene mutations is critical for genetic counseling and disease prevention in HB. In this study, we used denaturing high-performance liquid chromatography (DHPLC), which has proved to be a highly informative and practical means of detecting mutations, for the molecular diagnosis of our patients with HB. Ten Taiwanese families affected by HB were enrolled. We used the DHPLC technique followed by direct sequencing of suspected segments to detect FIX gene mutations. In all, 11 FIX gene mutations (8 point mutations, 2 small deletions/insertions, and 1 large deletion), including two novel mutations (exon6 c.687-695, del 9 mer and c.460-461, ins T) were found. According to the HB pedigrees, 25% and 75% of our patients were defined as familial and sporadic HB cases, respectively. We show that DHPLC is a highly sensitive and cost-effective method for FIX gene analysis and can be used as a convenient system for disease prevention.
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Affiliation(s)
- Pei-Chin Lin
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Ning Su
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan; Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Mei Liao
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tai-Tsung Chang
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shih-Pien Tsai
- Department of Nursing, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hsiu-Lan Shu
- Department of Nursing, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shyh-Shin Chiou
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Pediatrics, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
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18
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Jung YD, Ahn K, Kim YJ, Bae JH, Lee JR, Kim HS. Retroelements: molecular features and implications for disease. Genes Genet Syst 2013; 88:31-43. [PMID: 23676708 DOI: 10.1266/ggs.88.31] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Eukaryotic genomes comprise numerous retroelements that have a major impact on the structure and regulation of gene function. Retroelements are regulated by epigenetic controls, and they generate multiple miRNAs that are involved in the induction and progression of genomic instability. Elucidation of the biological roles of retroelements deserves continuous investigation to better understand their evolutionary features and implications for disease.
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Affiliation(s)
- Yi-Deun Jung
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
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19
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Retroelements in human disease. Gene 2013; 518:231-41. [PMID: 23333607 DOI: 10.1016/j.gene.2013.01.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 12/28/2012] [Accepted: 01/02/2013] [Indexed: 12/16/2022]
Abstract
Retroelements are an abundant class of noncoding DNAs present in about half of the human genome. Among them, L1, Alu and SVA are currently active. They "jump" by retrotransposition, shuffle genomic regions by 5' and 3' transduction, and promote or inhibit gene transcription by providing alternative promoters or generating antisense and/or regulatory noncoding RNAs. Recent data also suggest that retroelement insertions into exons and introns of genes induce different types of genetic disease, including cancer. Retroelements interfere with the expression of genes by inducing alternative splicing via exon skipping and exonization using cryptic splice sites, and by providing polyadenylation signals. Here we summarize our current understanding of the molecular mechanisms of retroelement-induced mutagenesis which causes fifty different types of human disease. We categorize these mutagenic effects according to eleven different mechanisms and show that most of them may be explained either by traditional exon definition or transcriptional interference, a previously unrecognized molecular mechanism. In summary, this review gives an overview of retroelement insertions in genes that cause significant changes in their transcription and cotranscriptional splicing and show a remarkable level of complexity.
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20
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Arias JF, Koyama T, Kinomoto M, Tokunaga K. Retroelements versus APOBEC3 family members: No great escape from the magnificent seven. Front Microbiol 2012; 3:275. [PMID: 22912627 PMCID: PMC3418512 DOI: 10.3389/fmicb.2012.00275] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 07/13/2012] [Indexed: 12/28/2022] Open
Abstract
Retroelements comprise a large and successful family of transposable genetic elements that, through intensive infiltration, have shaped the genomes of humans and other mammals over millions of years. In fact, retrotransposons now account for approximately 45% of the human genome. Because of their genomic mobility called retrotransposition, some retroelements can cause genetic diseases; such retrotransposition events occur not only in germ cells but also in somatic cells, posing a threat to genomic stability throughout all cellular populations. In response, mammals have developed intrinsic immunity mechanisms that provide resistance against the deleterious effects of retrotransposition. Among these, seven members of the APOBEC3 (A3) family of cytidine deaminases serve as highly active, intrinsic, antiretroviral host factors. Certain A3 proteins effectively counteract infections of retroviruses such as HIV-1, as well as those of other virus families, while also blocking the transposition of retroelements. Based on their preferential expression in the germ cells, in which retrotransposons may be active, it is likely that A3 proteins were acquired through mammalian evolution primarily to inhibit retrotransposition and thereby maintain genomic stability in these cells. This review summarizes the recent advances in our understanding of the interplay between the retroelements currently active in the human genome and the anti-retroelement A3 proteins.
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Affiliation(s)
- Juan F Arias
- Department of Pathology, National Institute of Infectious Diseases Tokyo, Japan
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21
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Ghosh K. Coagulation disorders seen through the window of molecular biology. INDIAN JOURNAL OF HUMAN GENETICS 2011; 13:81-7. [PMID: 21957353 PMCID: PMC3168142 DOI: 10.4103/0971-6866.38980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Coagulation disorders have been traditionally worked up by their clinical phenotypes and coagulation factor assays which are dependent on APTT- and PT-based techniques. Development of chromogenic substrates in the late seventies and early eighties allowed coagulation factors to be measured like enzymes. There was still a major lacuna in the understanding of the biology of different coagulation disorders. Modern molecular biology - which developed as an unique synthesis of biochemistry, immunology, cell biology, and genetics - allowed us to have a more comprehensive understanding of the pathobiology of many of these coagulation disorders. This overview presents several examples which show how we have enriched our understanding about the varied clinical phenotypes of different coagulation disorders.
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Affiliation(s)
- Kanjaksha Ghosh
- Institute of Immunohematology, 13 Floor, KEM Hospital Campus, Parel, Mumbai - 400 012, India
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22
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Freeman P, Macfarlane C, Collier P, Jeffreys AJ, Badge RM. L1 hybridization enrichment: a method for directly accessing de novo L1 insertions in the human germline. Hum Mutat 2011; 32:978-88. [PMID: 21560187 PMCID: PMC3412225 DOI: 10.1002/humu.21533] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 04/25/2011] [Indexed: 11/14/2022]
Abstract
Long interspersed nuclear element 1 (L1) retrotransposons are the only autonomously mobile human transposable elements. L1 retrotransposition has shaped our genome via insertional mutagenesis, sequence transduction, pseudogene formation, and ectopic recombination. However, L1 germline retrotransposition dynamics are poorly understood because de novo insertions occur very rarely: the frequency of disease-causing retrotransposon insertions suggests that one insertion event occurs in roughly 18–180 gametes. The method described here recovers full-length L1 insertions by using hybridization enrichment to capture L1 sequences from multiplex PCR-amplified DNA. Enrichment is achieved by hybridizing L1-specific biotinylated oligonucleotides to complementary molecules, followed by capture on streptavidin-coated paramagnetic beads. We show that multiplex, long-range PCR can amplify single molecules containing full-length L1 insertions for recovery by hybridization enrichment. We screened 600 µg of sperm DNA from one donor, but no bone fide de novo L1 insertions were found, suggesting a L1 retrotransposition frequency of <1 insertion in 400 haploid genomes. This lies below the lower bound of previous estimates, and indicates that L1 insertion, at least into the loci studied, is very rare in the male germline. It is a paradox that L1 replication is ongoing in the face of such apparently low activity. Hum Mutat 32:1–11, 2011. © 2011 Wiley-Liss, Inc.
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Affiliation(s)
- Peter Freeman
- Department of Genetics, University of Leicester, University Road, Leicester, United Kingdom
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23
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Chen JM, Férec C, Cooper DN. LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease: mutation detection bias and multiple mechanisms of target gene disruption. J Biomed Biotechnol 2010; 2006:56182. [PMID: 16877817 PMCID: PMC1510945 DOI: 10.1155/jbb/2006/56182] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
LINE-1 (L1) elements are the most abundant autonomous non-LTR retrotransposons in the human genome. Having recently performed a meta-analysis of L1 endonuclease-mediated retrotranspositional events causing human genetic disease, we have extended this study by focusing on two key issues, namely, mutation detection bias and the multiplicity of mechanisms of target gene disruption. Our analysis suggests that whereas an ascertainment bias may have generally militated against the detection of autosomal L1-mediated insertions, autosomal L1 direct insertions could have been disproportionately overlooked owing to their unusually large size. Our analysis has also indicated that the mechanisms underlying the functional disruption of target genes by L1-mediated retrotranspositional events are likely to be dependent on several different factors such as the type of insertion (L1 direct, L1 trans-driven Alu, or SVA), the precise locations of the inserted sequences within the target gene regions, the length of the inserted sequences, and possibly also their orientation.
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Affiliation(s)
- Jian-Min Chen
- INSERM U613, Génétique
Moléculaire et Génétique Épidémiologique,
29220 Brest, France
- Faculté de Médecine de Brest
et des Sciences de la Santé, Université de Bretagne Occidentale, 29238
Brest, France
- Etablissement Français du Sang-Bretagne,
35000 Rennes, France
- *Jian-Min Chen:
| | - Claude Férec
- INSERM U613, Génétique
Moléculaire et Génétique Épidémiologique,
29220 Brest, France
- Faculté de Médecine de Brest
et des Sciences de la Santé, Université de Bretagne Occidentale, 29238
Brest, France
- Etablissement Français du Sang-Bretagne,
35000 Rennes, France
- Hôpital Morvan, CHRU Brest, Laboratoire de
Génétique Moléculaire et d'Histocompatibilité, 29200 Brest, France
| | - David N. Cooper
- Institute of Medical Genetics, School of Medicine,
Cardiff University, Heath Park Campus, Cardiff CF14 4XN, UK
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25
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Novel mutations in factor IX gene from western India with reference to their phenotypic and haplotypic attributes. J Pediatr Hematol Oncol 2009; 31:157-60. [PMID: 19262239 DOI: 10.1097/mph.0b013e31818b3759] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Hemophilia B (HB) is an X-linked recessively inherited bleeding disorder caused by heterogeneous mutations in the factor IX gene. STUDY DESIGN AND METHODS We screened for mutations in HB patients using a combination of multiplex polymerase chain reaction, conformation sensitive gel electrophoresis, and DNA sequencing. Phenotypic analysis was performed using 1 stage assay for factor IX: C activity and enzyme-linked immunosorbent assay for factor IX: Ag. Haplotype analysis was performed using the common polymorphic markers of the factor IX gene. RESULTS Seventeen novel mutations comprising of missense mutations, nonsense mutations, and small deletions were detected. Haplotype analysis indicated that some of the patients had a common haplotype background but had different molecular defects thereby suggesting that all the mutations arose de novo. Phenotypic data suggested that about one-fourth of the patients (23%) had antigen-activity discordance. Furthermore, it was observed that a majority of the molecular defects (71%) were located in exon H of the factor IX gene. The mutation screening strategy was thus modified wherein exon H was screened first followed by screening of other exons. CONCLUSIONS The present findings suggest that there is a wide phenotypic and genotypic heterogeneity in HB. Presence of more than 70% of mutations in exon H of the factor IX gene allows us to adopt a cost effective screening strategy in offering genetic diagnosis to the affected families.
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MUKHERJEE S, SAHA A, BISWAS P, MANDAL C, RAY K. Structural analysis of factor IX protein variants to predict functional aberration causing haemophilia B. Haemophilia 2008; 14:1076-81. [DOI: 10.1111/j.1365-2516.2008.01788.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mills RE, Bennett EA, Iskow RC, Devine SE. Which transposable elements are active in the human genome? Trends Genet 2007; 23:183-91. [PMID: 17331616 DOI: 10.1016/j.tig.2007.02.006] [Citation(s) in RCA: 327] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 01/15/2007] [Accepted: 02/12/2007] [Indexed: 01/20/2023]
Abstract
Although a large proportion (44%) of the human genome is occupied by transposons and transposon-like repetitive elements, only a small proportion (<0.05%) of these elements remain active today. Recent evidence indicates that approximately 35-40 subfamilies of Alu, L1 and SVA elements (and possibly HERV-K elements) remain actively mobile in the human genome. These active transposons are of great interest because they continue to produce genetic diversity in human populations and also cause human diseases by integrating into genes. In this review, we examine these active human transposons and explore mechanistic factors that influence their mobilization.
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Affiliation(s)
- Ryan E Mills
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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28
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The Indian Genome Variation database (IGVdb): a project overview. Hum Genet 2005; 118:1-11. [PMID: 16133172 DOI: 10.1007/s00439-005-0009-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Accepted: 05/26/2005] [Indexed: 12/15/2022]
Abstract
Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning languages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacogenomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse population. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from Indian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A comprehensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Biotechnology (DBT), India. This paper reveals the structure of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, identification of the Indian subpopulations, collection of samples and discovery and validation of genetic markers, data analysis and monitoring as well as the project's data release policy.
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Chen JM, Stenson PD, Cooper DN, Férec C. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet 2005; 117:411-27. [PMID: 15983781 DOI: 10.1007/s00439-005-1321-0] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Accepted: 04/04/2005] [Indexed: 10/25/2022]
Abstract
Diverse long interspersed element-1 (LINE-1 or L1)-dependent mutational mechanisms have been extensively studied with respect to L1 and Alu elements engineered for retrotransposition in cultured cells and/or in genome-wide analyses. To what extent the in vitro studies can be held to accurately reflect in vivo events in the human genome, however, remains to be clarified. We have attempted to address this question by means of a systematic analysis of recent L1-mediated retrotranspositional events that have caused human genetic disease, with a view to providing a more complete picture of how L1-mediated retrotransposition impacts upon the architecture of the human genome. A total of 48 such mutations were identified, including those described as L1-mediated retrotransposons, as well as insertions reported to contain a poly(A) tail: 26 were L1 trans-driven Alu insertions, 15 were direct L1 insertions, four were L1 trans-driven SVA insertions, and three were associated with simple poly(A) insertions. The systematic study of these lesions, when combined with previous in vitro and genome-wide analyses, has strengthened several important conclusions regarding L1-mediated retrotransposition in humans: (a) approximately 25% of L1 insertions are associated with the 3' transduction of adjacent genomic sequences, (b) approximately 25% of the new L1 inserts are full-length, (c) poly(A) tail length correlates inversely with the age of the element, and (d) the length of target site duplication in vivo is rarely longer than 20 bp. Our analysis also suggests that some 10% of L1-mediated retrotranspositional events are associated with significant genomic deletions in humans. Finally, the identification of independent retrotranspositional events that have integrated at the same genomic locations provides new insight into the L1-mediated insertional process in humans.
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Affiliation(s)
- Jian-Min Chen
- INSERM U613-Génétique Moléculaire et Génétique Epidémiologique, Etablissement Français du Sang-Bretagne, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, 29220, France.
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