1
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Groza C, Chen X, Pacis A, Simon MM, Pramatarova A, Aracena KA, Pastinen T, Barreiro LB, Bourque G. Genome graphs detect human polymorphisms in active epigenomic state during influenza infection. CELL GENOMICS 2023; 3:100294. [PMID: 37228750 PMCID: PMC10203048 DOI: 10.1016/j.xgen.2023.100294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/26/2022] [Accepted: 03/09/2023] [Indexed: 05/27/2023]
Abstract
Genetic variants, including mobile element insertions (MEIs), are known to impact the epigenome. We hypothesized that genome graphs, which encapsulate genetic diversity, could reveal missing epigenomic signals. To test this, we sequenced the epigenome of monocyte-derived macrophages from 35 ancestrally diverse individuals before and after influenza infection, allowing us to investigate the role of MEIs in immunity. We characterized genetic variants and MEIs using linked reads and built a genome graph. Mapping epigenetic data revealed 2.3%-3% novel peaks for H3K4me1, H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq), and ATAC-seq. Additionally, the use of a genome graph modified some quantitative trait loci estimates and revealed 375 polymorphic MEIs in an active epigenomic state. Among these is an AluYh3 polymorphism whose chromatin state changed after infection and was associated with the expression of TRIM25, a gene that restricts influenza RNA synthesis. Our results demonstrate that graph genomes can reveal regulatory regions that would have been overlooked by other approaches.
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Affiliation(s)
- Cristian Groza
- Quantitative Life Sciences, McGill University, Montréal, QC, Canada
| | - Xun Chen
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Alain Pacis
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
| | - Marie-Michelle Simon
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC, Canada
| | - Albena Pramatarova
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC, Canada
| | | | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Hospital and Research Institute, Kansas City, MO, USA
| | - Luis B. Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Committee on Immunology, University of Chicago, Chicago, IL, USA
| | - Guillaume Bourque
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Canadian Centre for Computational Genomics, McGill University, Montréal, QC, Canada
- Victor Phillip Dahdaleh Institute of Genomic Medicine at McGill University, Montréal, QC, Canada
- Human Genetics, McGill University, Montréal, QC, Canada
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2
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Chen X, Bourque G, Goubert C. Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments. Methods Mol Biol 2023; 2607:63-83. [PMID: 36449158 DOI: 10.1007/978-1-0716-2883-6_4] [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] [Indexed: 06/17/2023]
Abstract
Transposable element (TE) insertions are a major source of structural variation in the human genome. Due to the repetitive nature and biological importance of TEs, many bioinformatic tools have been developed to identify and genotype TE insertion polymorphisms using high-throughput short-reads. In this chapter, we outline recently developed methods to characterize TE insertion polymorphisms in human populations. We also provide detailed protocols to tackle this question primarily using three software: MELT2, ERVcaller, and TypeREF.
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Affiliation(s)
- Xun Chen
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.
| | - Guillaume Bourque
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, Montreal, QC, Canada
- Human Genetics, McGill University, Montreal, QC, Canada
| | - Clément Goubert
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada.
- McGill Genome Centre, Montreal, QC, Canada.
- Human Genetics, McGill University, Montreal, QC, Canada.
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3
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El Hage K, Ribaudo G, Lagardère L, Ongaro A, Kahn PH, Demange L, Piquemal JP, Zagotto G, Gresh N. Targeting the Major Groove of the Palindromic d(GGCGCC) 2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators. J Chem Inf Model 2022; 62:6649-6666. [PMID: 35895094 DOI: 10.1021/acs.jcim.2c00337] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
GC-rich sequences are recurring motifs in oncogenes and retroviruses and could be targeted by noncovalent major-groove therapeutic ligands. We considered the palindromic sequence d(G1G2C3G4C5C6)2, and designed several oligopeptide derivatives of the anticancer intercalator mitoxantrone. The stability of their complexes with an 18-mer oligonucleotide encompassing this sequence in its center was validated using polarizable molecular dynamics. We report the most salient structural features of two novel compounds, having a dialkylammonium group as a side chain on both arms. The anthraquinone ring is intercalated in the central d(CpG)2 sequence with its long axis perpendicular to that of the two base pairs. On each strand, this enables each ammonium group to bind in-register to O6/N7 of the two facing G bases upstream. We subsequently designed tris-intercalating derivatives, each dialkylammonium substituted with a connector to an N9-aminoacridine intercalator extending our target range from a six- to a ten-base-pair palindromic sequence, d(C1G2G3G4C5G6C7C8C9G10)2. The structural features of the complex of the most promising derivative are reported. The present design strategy paves the way for designing intercalator-oligopeptide derivatives with even higher selectivity, targeting an increased number of DNA bases, going beyond ten.
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Affiliation(s)
- Krystel El Hage
- SABNP, Univ Evry, INSERM U1204, Université Paris-Saclay, 91000 Evry, France
| | - Giovanni Ribaudo
- Dipartimento di Medicina Molecolare e Traslazionale, Universita degli Studi di Brescia, 25123 Brescia, Italy
| | - Louis Lagardère
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France
| | - Alberto Ongaro
- Dipartimento di Medicina Molecolare e Traslazionale, Universita degli Studi di Brescia, 25123 Brescia, Italy
| | | | - Luc Demange
- Université Paris Cité, CiTCoM, UMR 8038 CNRS, 75006 Paris, France
| | - Jean-Philip Piquemal
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France.,The University of Texas at Austin, Department of Biomedical Engineering, Austin, Texas 78705, United States
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo, 35131 Padova, Italy
| | - Nohad Gresh
- LCT, UMR7616 CNRS, Sorbonne Université Paris, 75005 Paris, France
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4
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Borges-Monroy R, Chu C, Dias C, Choi J, Lee S, Gao Y, Shin T, Park PJ, Walsh CA, Lee EA. Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder. Mob DNA 2021; 12:28. [PMID: 34838103 PMCID: PMC8627061 DOI: 10.1186/s13100-021-00256-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/02/2021] [Indexed: 12/30/2022] Open
Abstract
Background Retrotransposons have been implicated as causes of Mendelian disease, but their role in autism spectrum disorder (ASD) has not been systematically defined, because they are only called with adequate sensitivity from whole genome sequencing (WGS) data and a large enough cohort for this analysis has only recently become available. Results We analyzed WGS data from a cohort of 2288 ASD families from the Simons Simplex Collection by establishing a scalable computational pipeline for retrotransposon insertion detection. We report 86,154 polymorphic retrotransposon insertions—including > 60% not previously reported—and 158 de novo retrotransposition events. The overall burden of de novo events was similar between ASD individuals and unaffected siblings, with 1 de novo insertion per 29, 117, and 206 births for Alu, L1, and SVA respectively, and 1 de novo insertion per 21 births total. However, ASD cases showed more de novo L1 insertions than expected in ASD genes. Additionally, we observed exonic insertions in loss-of-function intolerant genes, including a likely pathogenic exonic insertion in CSDE1, only in ASD individuals. Conclusions These findings suggest a modest, but important, impact of intronic and exonic retrotransposon insertions in ASD, show the importance of WGS for their analysis, and highlight the utility of specific bioinformatic tools for high-throughput detection of retrotransposon insertions. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-021-00256-w.
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Affiliation(s)
- Rebeca Borges-Monroy
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chong Chu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Caroline Dias
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Division of Developmental Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jaejoon Choi
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, MA, Boston, USA
| | - Soohyun Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yue Gao
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Pediatrics, Harvard Medical School, MA, Boston, USA
| | - Taehwan Shin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Pediatrics, Harvard Medical School, MA, Boston, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Department of Pediatrics, Harvard Medical School, MA, Boston, USA. .,Department of Neurology, Harvard Medical School, Boston, MA, USA. .,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA.
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children's Hospital, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Department of Pediatrics, Harvard Medical School, MA, Boston, USA.
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5
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Choe SH, Park SJ, Cho HM, Park HR, Lee JR, Kim YH, Huh JW. A single mutation in the ACTR8 gene associated with lineage-specific expression in primates. BMC Evol Biol 2020; 20:66. [PMID: 32503430 PMCID: PMC7275561 DOI: 10.1186/s12862-020-01620-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/29/2020] [Indexed: 12/17/2022] Open
Abstract
Background Alternative splicing (AS) generates various transcripts from a single gene and thus plays a significant role in transcriptomic diversity and proteomic complexity. Alu elements are primate-specific transposable elements (TEs) and can provide a donor or acceptor site for AS. In a study on TE-mediated AS, we recently identified a novel AluSz6-exonized ACTR8 transcript of the crab-eating monkey (Macaca fascicularis). In the present study, we sought to determine the molecular mechanism of AluSz6 exonization of the ACTR8 gene and investigate its evolutionary and functional consequences in the crab-eating monkey. Results We performed RT-PCR and genomic PCR to analyze AluSz6 exonization in the ACTR8 gene and the expression of the AluSz6-exonized transcript in nine primate samples, including prosimians, New world monkeys, Old world monkeys, and hominoids. AluSz6 integration was estimated to have occurred before the divergence of simians and prosimians. The Alu-exonized transcript obtained by AS was lineage-specific and expressed only in Old world monkeys and apes, and humans. This lineage-specific expression was caused by a single G duplication in AluSz6, which provides a new canonical 5′ splicing site. We further identified other alternative transcripts that were unaffected by the AluSz6 insertion. Finally, we observed that the alternative transcripts were transcribed into new isoforms with C-terminus deletion, and in silico analysis showed that these isoforms do not have a destructive function. Conclusions The single G duplication in the TE sequence is the source of TE exonization and AS, and this mutation may suffer a different fate of ACTR8 gene expression during primate evolution.
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Affiliation(s)
- Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea
| | - Hyeon-Mu Cho
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Hye-Ri Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea
| | - Ja-Rang Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup, 56216, Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, 28116, Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, 34113, Korea.
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6
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Goubert C, Thomas J, Payer LM, Kidd JM, Feusier J, Watkins WS, Burns KH, Jorde LB, Feschotte C. TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data. Nucleic Acids Res 2020; 48:e36. [PMID: 32067044 PMCID: PMC7102983 DOI: 10.1093/nar/gkaa074] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/08/2020] [Accepted: 02/11/2020] [Indexed: 12/12/2022] Open
Abstract
Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alus are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alus and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses significant problems for phasing these insertions with other variants that comprise the haplotype. To ameliorate this issue, we introduce a new pipeline - TypeTE - which genotypes Alu insertions from whole-genome sequencing data. Starting from a list of polymorphic Alus, TypeTE identifies the hallmarks (poly-A tail and target site duplication) and orientation of Alu insertions using local re-assembly to reconstruct presence and absence alleles. Genotype likelihoods are then computed after re-mapping sequencing reads to the reconstructed alleles. Using a high-quality set of PCR-based genotyping of >200 loci, we show that TypeTE improves genotype accuracy from 83% to 92% in the 1000 Genomes dataset. TypeTE can be readily adapted to other retrotransposon families and brings a valuable toolbox addition for population genomics.
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Affiliation(s)
- Clément Goubert
- Department of Molecular Biology and Genetics, 215 Tower Rd, Cornell University, Ithaca, NY 14853, USA
| | - Jainy Thomas
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Julie Feusier
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - W Scott Watkins
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, 215 Tower Rd, Cornell University, Ithaca, NY 14853, USA
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7
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Rosain J, Deswarte C, Hancioglu G, Oleaga-Quintas C, Kutlug S, Kartal I, Kuzu I, Toullec L, Tusseau M, Casanova JL, Yildiran A, Bustamante J. LINE-1-Mediated AluYa5 Insertion Underlying Complete Autosomal Recessive IFN-γR1 Deficiency. J Clin Immunol 2019; 39:739-742. [PMID: 31377971 PMCID: PMC8165577 DOI: 10.1007/s10875-019-00667-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/08/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, 24 boulevard du Montparnasse, Paris, EU, France.
- Imagine Institute, Paris University, Paris, EU, France.
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, EU, France.
| | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, 24 boulevard du Montparnasse, Paris, EU, France
- Imagine Institute, Paris University, Paris, EU, France
| | - Gonca Hancioglu
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, 24 boulevard du Montparnasse, Paris, EU, France
- Imagine Institute, Paris University, Paris, EU, France
| | - Seyhan Kutlug
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Ibrahim Kartal
- Department of Pediatric Hematology-Oncology, Ondokuz Mayis University, Samsun, Turkey
| | - Isinsu Kuzu
- Department of Pathology, Ankara University, Ankara, Turkey
| | - Laurie Toullec
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, EU, France
| | - Maud Tusseau
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, EU, France
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, 24 boulevard du Montparnasse, Paris, EU, France
- Imagine Institute, Paris University, Paris, EU, France
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, AP-HP, Paris, EU, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Alisan Yildiran
- Department of Pediatric Allergy and Immunology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Inserm U1163, Necker Hospital for Sick Children, 24 boulevard du Montparnasse, Paris, EU, France.
- Imagine Institute, Paris University, Paris, EU, France.
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, EU, France.
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA.
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8
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Puurand T, Kukuškina V, Pajuste FD, Remm M. AluMine: alignment-free method for the discovery of polymorphic Alu element insertions. Mob DNA 2019; 10:31. [PMID: 31360240 PMCID: PMC6639938 DOI: 10.1186/s13100-019-0174-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/12/2019] [Indexed: 01/09/2023] Open
Abstract
Background Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. Results We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. Conclusions AluMine provides tools that allow discovery of novel Alu element insertions and/or genotyping of known Alu element insertions from personal genomes within few hours.
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Affiliation(s)
- Tarmo Puurand
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Viktoria Kukuškina
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - Maido Remm
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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9
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Halo JV, Pendleton AL, Jarosz AS, Gifford RJ, Day ML, Kidd JM. Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids. Retrovirology 2019; 16:6. [PMID: 30845962 PMCID: PMC6407205 DOI: 10.1186/s12977-019-0468-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/28/2019] [Indexed: 01/20/2023] Open
Abstract
Background Vertebrate genomes contain a record of retroviruses that invaded the germlines of ancestral hosts and are passed to offspring as endogenous retroviruses (ERVs). ERVs can impact host function since they contain the necessary sequences for expression within the host. Dogs are an important system for the study of disease and evolution, yet no substantiated reports of infectious retroviruses in dogs exist. Here, we utilized Illumina whole genome sequence data to assess the origin and evolution of a recently active gammaretroviral lineage in domestic and wild canids. Results We identified numerous recently integrated loci of a canid-specific ERV-Fc sublineage within Canis, including 58 insertions that were absent from the reference assembly. Insertions were found throughout the dog genome including within and near gene models. By comparison of orthologous occupied sites, we characterized element prevalence across 332 genomes including all nine extant canid species, revealing evolutionary patterns of ERV-Fc segregation among species as well as subpopulations. Conclusions Sequence analysis revealed common disruptive mutations, suggesting a predominant form of ERV-Fc spread by trans complementation of defective proviruses. ERV-Fc activity included multiple circulating variants that infected canid ancestors from the last 20 million to within 1.6 million years, with recent bursts of germline invasion in the sublineage leading to wolves and dogs. Electronic supplementary material The online version of this article (10.1186/s12977-019-0468-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia V Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA.
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Abigail S Jarosz
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Robert J Gifford
- Centre for Virus Research, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Malika L Day
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, 43403, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Ave., Ann Arbor, MI, 48109, USA
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10
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Spliced integrated retrotransposed element (SpIRE) formation in the human genome. PLoS Biol 2018; 16:e2003067. [PMID: 29505568 PMCID: PMC5860796 DOI: 10.1371/journal.pbio.2003067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 03/20/2018] [Accepted: 02/14/2018] [Indexed: 12/20/2022] Open
Abstract
Human Long interspersed element-1 (L1) retrotransposons contain an internal RNA polymerase II promoter within their 5′ untranslated region (UTR) and encode two proteins, (ORF1p and ORF2p) required for their mobilization (i.e., retrotransposition). The evolutionary success of L1 relies on the continuous retrotransposition of full-length L1 mRNAs. Previous studies identified functional splice donor (SD), splice acceptor (SA), and polyadenylation sequences in L1 mRNA and provided evidence that a small number of spliced L1 mRNAs retrotransposed in the human genome. Here, we demonstrate that the retrotransposition of intra-5′UTR or 5′UTR/ORF1 spliced L1 mRNAs leads to the generation of spliced integrated retrotransposed elements (SpIREs). We identified a new intra-5′UTR SpIRE that is ten times more abundant than previously identified SpIREs. Functional analyses demonstrated that both intra-5′UTR and 5′UTR/ORF1 SpIREs lack Cis-acting transcription factor binding sites and exhibit reduced promoter activity. The 5′UTR/ORF1 SpIREs also produce nonfunctional ORF1p variants. Finally, we demonstrate that sequence changes within the L1 5′UTR over evolutionary time, which permitted L1 to evade the repressive effects of a host protein, can lead to the generation of new L1 splicing events, which, upon retrotransposition, generates a new SpIRE subfamily. We conclude that splicing inhibits L1 retrotransposition, SpIREs generally represent evolutionary “dead-ends” in the L1 retrotransposition process, mutations within the L1 5′UTR alter L1 splicing dynamics, and that retrotransposition of the resultant spliced transcripts can generate interindividual genomic variation. Long interspersed element-1 (L1) sequences comprise about 17% of the human genome reference sequence. The average human genome contains about 100 active L1s that mobilize throughout the genome by a “copy and paste” process termed retrotransposition. Active L1s encode two proteins (ORF1p and ORF2p). ORF1p and ORF2p preferentially bind to their encoding RNA, forming a ribonucleoprotein particle (RNP). During retrotransposition, the L1 RNP translocates to the nucleus, where the ORF2p endonuclease makes a single-strand nick in target site DNA that exposes a 3′ hydroxyl group in genomic DNA. The 3′ hydroxyl group then is used as a primer by the ORF2p reverse transcriptase to copy the L1 RNA into cDNA, leading to the integration of an L1 copy at a new genomic location. The evolutionary success of L1 requires the faithful retrotransposition of full-length L1 mRNAs; thus, it was surprising to find that a small number of L1 retrotransposition events are derived from spliced L1 mRNAs. By using genetic, biochemical, and computational approaches, we demonstrate that spliced L1 mRNAs can undergo an initial round of retrotransposition, leading to the generation of spliced integrated retrotransposed elements (SpIREs). SpIREs represent about 2% of previously annotated full-length primate-specific L1s in the human genome reference sequence. However, because splicing leads to intra-L1 deletions that remove critical sequences required for L1 expression, SpIREs generally cannot undergo subsequent rounds of retrotransposition and can be considered “dead on arrival” insertions. Our data further highlight how genetic conflict between L1 and its host has influenced L1 expression, L1 retrotransposition, and L1 splicing dynamics over evolutionary time.
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Viotti M, Victor AR, Zouves CG, Barnes FL. Is mitochondrial DNA quantitation in blastocyst trophectoderm cells predictive of developmental competence and outcome in clinical IVF? J Assist Reprod Genet 2017; 34:1581-1585. [PMID: 29080967 DOI: 10.1007/s10815-017-1072-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/16/2017] [Indexed: 11/25/2022] Open
Abstract
Behind every successful IVF embryo transfer, there is a great game of chance. Methods seeking to tilt the balance and increase the likelihood of implantation have been proposed and implemented with varying results, including embryo morphology, FISH-PGS, comprehensive chromosomal screening (CCS), morphokinetics, endometrial receptivity testing. It has been suggested that mitochondrial DNA (mtDNA) copy number could serve as a biomarker for embryo viability, but this concept was recently challenged. The world of IVF is left with unanswered questions: Why are there discrepancies in the reports? Should mtDNA copy number be considered to rank embryos for transfer? And in a broader sense, how well must a technique be validated before its implementation in the IVF clinic? Here, we explore these questions attempting to piece together the published data and suggest future directions to help unravel the subject matter.
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Affiliation(s)
- Manuel Viotti
- Zouves Fertility Center (ZFC), 1241 E Hillsdale Blvd, Foster City, CA, 94404, USA.
| | - Andrea R Victor
- Zouves Fertility Center (ZFC), 1241 E Hillsdale Blvd, Foster City, CA, 94404, USA
| | - Christo G Zouves
- Zouves Fertility Center (ZFC), 1241 E Hillsdale Blvd, Foster City, CA, 94404, USA
| | - Frank L Barnes
- Zouves Fertility Center (ZFC), 1241 E Hillsdale Blvd, Foster City, CA, 94404, USA
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Feusier J, Witherspoon DJ, Scott Watkins W, Goubert C, Sasani TA, Jorde LB. Discovery of rare, diagnostic AluYb8/9 elements in diverse human populations. Mob DNA 2017; 8:9. [PMID: 28770012 PMCID: PMC5531096 DOI: 10.1186/s13100-017-0093-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/17/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Polymorphic human Alu elements are excellent tools for assessing population structure, and new retrotransposition events can contribute to disease. Next-generation sequencing has greatly increased the potential to discover Alu elements in human populations, and various sequencing and bioinformatics methods have been designed to tackle the problem of detecting these highly repetitive elements. However, current techniques for Alu discovery may miss rare, polymorphic Alu elements. Combining multiple discovery approaches may provide a better profile of the polymorphic Alu mobilome. AluYb8/9 elements have been a focus of our recent studies as they are young subfamilies (~2.3 million years old) that contribute ~30% of recent polymorphic Alu retrotransposition events. Here, we update our ME-Scan methods for detecting Alu elements and apply these methods to discover new insertions in a large set of individuals with diverse ancestral backgrounds. RESULTS We identified 5,288 putative Alu insertion events, including several hundred novel AluYb8/9 elements from 213 individuals from 18 diverse human populations. Hundreds of these loci were specific to continental populations, and 23 non-reference population-specific loci were validated by PCR. We provide high-quality sequence information for 68 rare AluYb8/9 elements, of which 11 have hallmarks of an active source element. Our subfamily distribution of rare AluYb8/9 elements is consistent with previous datasets, and may be representative of rare loci. We also find that while ME-Scan and low-coverage, whole-genome sequencing (WGS) detect different Alu elements in 41 1000 Genomes individuals, the two methods yield similar population structure results. CONCLUSION Current in-silico methods for Alu discovery may miss rare, polymorphic Alu elements. Therefore, using multiple techniques can provide a more accurate profile of Alu elements in individuals and populations. We improved our false-negative rate as an indicator of sample quality for future ME-Scan experiments. In conclusion, we demonstrate that ME-Scan is a good supplement for next-generation sequencing methods and is well-suited for population-level analyses.
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Affiliation(s)
- Julie Feusier
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - David J. Witherspoon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - W. Scott Watkins
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Clément Goubert
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Thomas A. Sasani
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
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Clinically Focused Molecular Investigation of 1000 Consecutive Families with Inherited Retinal Disease. Ophthalmology 2017; 124:1314-1331. [PMID: 28559085 DOI: 10.1016/j.ophtha.2017.04.008] [Citation(s) in RCA: 285] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/30/2022] Open
Abstract
PURPOSE To devise a comprehensive multiplatform genetic testing strategy for inherited retinal disease and to describe its performance in 1000 consecutive families seen by a single clinician. DESIGN Retrospective series. PARTICIPANTS One thousand consecutive families seen by a single clinician. METHODS The clinical records of all patients seen by a single retina specialist between January 2010 and June 2016 were reviewed, and all patients who met the clinical criteria for a diagnosis of inherited retinal disease were included in the study. Each patient was assigned to 1 of 62 diagnostic categories, and this clinical diagnosis was used to define the scope and order of the molecular investigations that were performed. The number of nucleotides evaluated in a given subject ranged from 2 to nearly 900 000. MAIN OUTCOME MEASURES Sensitivity and false genotype rate. RESULTS Disease-causing genotypes were identified in 760 families (76%). These genotypes were distributed across 104 different genes. More than 75% of these 104 genes have coding sequences small enough to be packaged efficiently into an adeno-associated virus. Mutations in ABCA4 were the most common cause of disease in this cohort (173 families), whereas mutations in 80 genes caused disease in 5 or fewer families (i.e., 0.5% or less). Disease-causing genotypes were identified in 576 of the families without next-generation sequencing (NGS). This included 23 families with mutations in the repetitive region of RPGR exon 15 that would have been missed by NGS. Whole-exome sequencing of the remaining 424 families revealed mutations in an additional 182 families, and whole-genome sequencing of 4 of the remaining 242 families revealed 2 additional genotypes that were invisible by the other methods. Performing the testing in a clinically focused tiered fashion would be 6.1% more sensitive and 17.7% less expensive and would have a significantly lower average false genotype rate than using whole-exome sequencing to assess more than 300 genes in all patients (7.1% vs. 128%; P < 0.001). CONCLUSIONS Genetic testing for inherited retinal disease is now more than 75% sensitive. A clinically directed tiered testing strategy can increase sensitivity and improve statistical significance without increasing cost.
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Morgan RG, Venturelli M, Gross C, Tarperi C, Schena F, Reggiani C, Naro F, Pedrinolla A, Monaco L, Richardson RS, Donato AJ. Age-Associated ALU Element Instability in White Blood Cells Is Linked to Lower Survival in Elderly Adults: A Preliminary Cohort Study. PLoS One 2017; 12:e0169628. [PMID: 28060910 PMCID: PMC5218400 DOI: 10.1371/journal.pone.0169628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/20/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND ALU element instability could contribute to gene function variance in aging, and may partly explain variation in human lifespan. OBJECTIVE To assess the role of ALU element instability in human aging and the potential efficacy of ALU element content as a marker of biological aging and survival. DESIGN Preliminary cohort study. METHODS We measured two high frequency ALU element subfamilies, ALU-J and ALU-Sx, by a single qPCR assay and compared ALU-J/Sx content in white blood cell (WBCs) and skeletal muscle cell (SMCs) biopsies from twenty-three elderly adults with sixteen healthy sex-balanced young adults; all-cause survival rates of elderly adults predicted by ALU-J/Sx content in both tissues; and cardiovascular disease (CVD)- and cancer-specific survival rates of elderly adults predicted by ALU-J/Sx content in both tissues, as planned subgroup analyses. RESULTS We found greater ALU-J/Sx content variance in WBCs from elderly adults than young adults (P < 0.001) with no difference in SMCs (P = 0.94). Elderly adults with low WBC ALU-J/Sx content had worse four-year all-cause and CVD-associated survival than those with high ALU-J/Sx content (both P = 0.03 and hazard ratios (HR) ≥ 3.40), while WBC ALU-J/Sx content had no influence on cancer-associated survival (P = 0.42 and HR = 0.74). SMC ALU-J/Sx content had no influence on all-cause, CVD- or cancer -associated survival (all P ≥ 0.26; HR ≤ 2.07). CONCLUSIONS These initial findings demonstrate that ALU element instability occurs with advanced age in WBCs, but not SMCs, and imparts greater risk of all-cause mortality that is likely driven by an increased risk for CVD and not cancer.
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Affiliation(s)
- R. Garrett Morgan
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Geriatric Research, Education, and Clinical Center, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, United States of America
| | - Massimo Venturelli
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Cole Gross
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Cantor Tarperi
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
| | - Federico Schena
- Department of Neurological and Movement Sciences, University of Verona, Verona, Italy
| | - Carlo Reggiani
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Fabio Naro
- DAHFMO-Unit of Histology and Medical Embryology, Sapienza University, Rome, Italy
| | | | - Lucia Monaco
- Department of Physiology and Pharmacology, Sapienza University of Rome, Italy
| | - Russell S. Richardson
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Geriatric Research, Education, and Clinical Center, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, United States of America
- Department of Health, Kinesiology, and Recreation, University of Utah, Salt Lake City, Utah, United States of America
| | - Anthony J. Donato
- Department of Internal Medicine, Division of Geriatrics, University of Utah School of Medicine, University of Utah, Salt Lake City, Utah, United States of America
- Geriatric Research, Education, and Clinical Center, George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, Utah, United States of America
- Department of Health, Kinesiology, and Recreation, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. Nature 2016; 538:533-536. [PMID: 27760113 PMCID: PMC5684705 DOI: 10.1038/nature20110] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 09/19/2016] [Indexed: 01/15/2023]
Abstract
The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution.
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Affiliation(s)
- Jason T Huff
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, USA
| | - Daniel Zilberman
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Scott W Roy
- Department of Biology, San Francisco State University, San Francisco, California 94132, USA
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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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Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc Natl Acad Sci U S A 2016; 113:E2326-34. [PMID: 27001843 DOI: 10.1073/pnas.1602336113] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endogenous retroviruses (ERVs) have contributed to more than 8% of the human genome. The majority of these elements lack function due to accumulated mutations or internal recombination resulting in a solitary (solo) LTR, although members of one group of human ERVs (HERVs), HERV-K, were recently active with members that remain nearly intact, a subset of which is present as insertionally polymorphic loci that include approximately full-length (2-LTR) and solo-LTR alleles in addition to the unoccupied site. Several 2-LTR insertions have intact reading frames in some or all genes that are expressed as functional proteins. These properties reflect the activity of HERV-K and suggest the existence of additional unique loci within humans. We sought to determine the extent to which other polymorphic insertions are present in humans, using sequenced genomes from the 1000 Genomes Project and a subset of the Human Genome Diversity Project panel. We report analysis of a total of 36 nonreference polymorphic HERV-K proviruses, including 19 newly reported loci, with insertion frequencies ranging from <0.0005 to >0.75 that varied by population. Targeted screening of individual loci identified three new unfixed 2-LTR proviruses within our set, including an intact provirus present at Xq21.33 in some individuals, with the potential for retained infectivity.
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Paramasivam R, Reangasamy N, Arumugam D, Krishnan P. Association of ACE <i>DD</i> Genotype with Hypertension among the Tribal Populations of South India. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2016. [DOI: 10.56431/p-044q85] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The Renin-Angiotensin System (RAS) is an important regulator of the blood pressure (BP). The level of the vasoactive peptide Angiotensin-II, is mainly determined by the RAS enzyme, angiotensin converting enzyme-1 (ACE-1). Polymorphisms in ACE gene is reported to be associated with hypertension in various populations worldwide. We investigated the association of ACE I/D polymorphisms with hypertension among the tribal populations of South India. Samples were collected from hypertensive patients (n = 33) and healthy controls (n = 37). Genotyping was performed using Polymerase chain reaction (PCR) with allele specific primers. The DD genotype is significantly observed among the cases (OR = 1.0). Specifically, the DD genotype is more evident among the females (OR = 0 .705) than males (OR = 1.22) and is analysed to be associated with hypertension among the tribal populations of South India.
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Paramasivam R, Rengasamy N, Arumugam D, Krishnan P. Association of ACE DD Genotype with Hypertension among the Tribal Populations of South India. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2016. [DOI: 10.18052/www.scipress.com/ilns.52.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Renin-Angiotensin System (RAS) is an important regulator of the blood pressure (BP). The level of the vasoactive peptide Angiotensin-II, is mainly determined by the RAS enzyme, angiotensin converting enzyme-1 (ACE-1). Polymorphisms in ACE gene is reported to be associated with hypertension in various populations worldwide. We investigated the association of ACE I/D polymorphisms with hypertension among the tribal populations of South India. Samples were collected from hypertensive patients (n = 33) and healthy controls (n = 37). Genotyping was performed using Polymerase chain reaction (PCR) with allele specific primers. The DD genotype is significantly observed among the cases (OR = 1.0). Specifically, the DD genotype is more evident among the females (OR = 0 .705) than males (OR = 1.22) and is analysed to be associated with hypertension among the tribal populations of South India.
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