1
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Garrison MA, Jang Y, Bae T, Cherskov A, Emery SB, Fasching L, Jones A, Moldovan JB, Molitor C, Pochareddy S, Peters MA, Shin JH, Wang Y, Yang X, Akbarian S, Chess A, Gage FH, Gleeson JG, Kidd JM, McConnell M, Mills RE, Moran JV, Park PJ, Sestan N, Urban AE, Vaccarino FM, Walsh CA, Weinberger DR, Wheelan SJ, Abyzov A. Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. Sci Data 2023; 10:813. [PMID: 37985666 PMCID: PMC10662356 DOI: 10.1038/s41597-023-02645-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/16/2023] [Indexed: 11/22/2023] Open
Abstract
Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic of multicellular organisms that plays a crucial role in normal development and disease. To study the nature and extent of somatic mosaicism in autism spectrum disorder, bipolar disorder, focal cortical dysplasia, schizophrenia, and Tourette syndrome, a multi-institutional consortium called the Brain Somatic Mosaicism Network (BSMN) was formed through the National Institute of Mental Health (NIMH). In addition to genomic data of affected and neurotypical brains, the BSMN also developed and validated a best practices somatic single nucleotide variant calling workflow through the analysis of reference brain tissue. These resources, which include >400 terabytes of data from 1087 subjects, are now available to the research community via the NIMH Data Archive (NDA) and are described here.
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Affiliation(s)
- McKinzie A Garrison
- Program in Biochemistry, Molecular and Cellular Biology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Adriana Cherskov
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Attila Jones
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John B Moldovan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Cindy Molitor
- Sage Bionetworks, 2901 Third Ave., Suite 330, Seattle, WA, 98121, USA
| | - Sirisha Pochareddy
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Mette A Peters
- Sage Bionetworks, 2901 Third Ave., Suite 330, Seattle, WA, 98121, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Xiaoxu Yang
- Rady Children's Institute for Genomic Medicine, 7910 Frost St., Suite #300, San Diego, CA, 92123, USA
- Department of Neurosciences, University of California San Diego, La Jolla, California, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Chess
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fred H Gage
- Laboratory of Genetics LOG-G, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, 7910 Frost St., Suite #300, San Diego, CA, 92123, USA
- Department of Neurosciences, University of California San Diego, La Jolla, California, 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, Ann Arbor, Michigan, 48109, USA
| | | | - Ryan E Mills
- 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, Ann Arbor, Michigan, 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Flora M Vaccarino
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sarah J Wheelan
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- National Human Genome Research Institute, National Institutes of Health, 6700B Rockledge Dr, Bethesda, MD, 20892, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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2
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Zhu X, Zhou B, Pattni R, Gleason K, Tan C, Kalinowski A, Sloan S, Fiston-Lavier AS, Mariani J, Petrov D, Barres BA, Duncan L, Abyzov A, Vogel H, Moran JV, Vaccarino FM, Tamminga CA, Levinson DF, Urban AE. Author Correction: Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia. Nat Neurosci 2023; 26:1833. [PMID: 37648813 DOI: 10.1038/s41593-023-01438-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Affiliation(s)
- Xiaowei Zhu
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | - Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | - Kelly Gleason
- Division of Translational Research in Schizophrenia, Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chunfeng Tan
- Division of Translational Research in Schizophrenia, Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Agnieszka Kalinowski
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
| | - Steven Sloan
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Anna-Sophie Fiston-Lavier
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Montpellier, France
| | | | - Dmitri Petrov
- Department of Biology, Stanford University, Palo Alto, CA, USA
| | - Ben A Barres
- Department of Neurobiology, Stanford University, Palo Alto, CA, USA
| | - Laramie Duncan
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Hannes Vogel
- Department of Pathology, Stanford University, Palo Alto, CA, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Carol A Tamminga
- Division of Translational Research in Schizophrenia, Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Douglas F Levinson
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA.
- Department of Genetics, Stanford University, Palo Alto, CA, USA.
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3
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Sun C, Kathuria K, Emery SB, Kim B, Burbulis IE, Shin JH, Weinberger DR, Moran JV, Kidd JM, Mills RE, McConnell MJ. Mapping the Complex Genetic Landscape of Human Neurons. bioRxiv 2023:2023.03.07.531594. [PMID: 36945473 PMCID: PMC10028870 DOI: 10.1101/2023.03.07.531594] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
When somatic cells acquire complex karyotypes, they are removed by the immune system. Mutant somatic cells that evade immune surveillance can lead to cancer. Neurons with complex karyotypes arise during neurotypical brain development, but neurons are almost never the origin of brain cancers. Instead, somatic mutations in neurons can bring about neurodevelopmental disorders, and contribute to the polygenic landscape of neuropsychiatric and neurodegenerative disease. A subset of human neurons harbors idiosyncratic copy number variants (CNVs, "CNV neurons"), but previous analyses of CNV neurons have been limited by relatively small sample sizes. Here, we developed an allele-based validation approach, SCOVAL, to corroborate or reject read-depth based CNV calls in single human neurons. We applied this approach to 2,125 frontal cortical neurons from a neurotypical human brain. This approach identified 226 CNV neurons, as well as a class of CNV neurons with complex karyotypes containing whole or substantial losses on multiple chromosomes. Moreover, we found that CNV location appears to be nonrandom. Recurrent regions of neuronal genome rearrangement contained fewer, but longer, genes.
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Affiliation(s)
- Chen Sun
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Kunal Kathuria
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - ByungJun Kim
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Ian E. Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA 22902, USA
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Sede de la Patagonia, Puerto Montt, Chile
| | - Joo Heon Shin
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | | | - Daniel R. Weinberger
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
- Department of Psychiatry and Behavioral Sciences and Neuroscience, Johns Hopkins School of Medicine, 600 North Wolfe Street, Baltimore, MD 21287, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, 733 North Broadway, Baltimore, MD 21230, USA
| | - John V. Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Jeffrey M. Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Ryan E. Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Michael J. McConnell
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
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4
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Luqman-Fatah A, Watanabe Y, Uno K, Ishikawa F, Moran JV, Miyoshi T. Author Correction: The interferon stimulated gene-encoded protein HELZ2 inhibits human LINE-1 retrotransposition and LINE-1 RNA-mediated type I interferon induction. Nat Commun 2023; 14:493. [PMID: 36717557 PMCID: PMC9886985 DOI: 10.1038/s41467-023-36226-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- Ahmad Luqman-Fatah
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.,Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Yuzo Watanabe
- Proteomics Facility, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazuko Uno
- Division of Basic Research, Louis Pasteur Center for Medical Research, Kyoto, 606-8225, Japan
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.,Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA.,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan. .,Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan. .,Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
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5
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Luqman-Fatah A, Watanabe Y, Uno K, Ishikawa F, Moran JV, Miyoshi T. The interferon stimulated gene-encoded protein HELZ2 inhibits human LINE-1 retrotransposition and LINE-1 RNA-mediated type I interferon induction. Nat Commun 2023; 14:203. [PMID: 36639706 PMCID: PMC9839780 DOI: 10.1038/s41467-022-35757-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
Some interferon stimulated genes (ISGs) encode proteins that inhibit LINE-1 (L1) retrotransposition. Here, we use immunoprecipitation followed by liquid chromatography-tandem mass spectrometry to identify proteins that associate with the L1 ORF1-encoded protein (ORF1p) in ribonucleoprotein particles. Three ISG proteins that interact with ORF1p inhibit retrotransposition: HECT and RLD domain containing E3 ubiquitin-protein ligase 5 (HERC5); 2'-5'-oligoadenylate synthetase-like (OASL); and helicase with zinc finger 2 (HELZ2). HERC5 destabilizes ORF1p, but does not affect its cellular localization. OASL impairs ORF1p cytoplasmic foci formation. HELZ2 recognizes sequences and/or structures within the L1 5'UTR to reduce L1 RNA, ORF1p, and ORF1p cytoplasmic foci levels. Overexpression of WT or reverse transcriptase-deficient L1s lead to a modest induction of IFN-α expression, which is abrogated upon HELZ2 overexpression. Notably, IFN-α expression is enhanced upon overexpression of an ORF1p RNA binding mutant, suggesting ORF1p binding might protect L1 RNA from "triggering" IFN-α induction. Thus, ISG proteins can inhibit retrotransposition by different mechanisms.
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Affiliation(s)
- Ahmad Luqman-Fatah
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Yuzo Watanabe
- Proteomics Facility, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazuko Uno
- Division of Basic Research, Louis Pasteur Center for Medical Research, Kyoto, 606-8225, Japan
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
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6
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Moran JV, Wilson TE. Reverse transcriptase meets DNA, again: Possible roles for transposable elements in host DNA repair. Cell 2022; 185:3643-3645. [PMID: 36179663 DOI: 10.1016/j.cell.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 01/26/2023]
Abstract
Retrotransposons are selfish genetic elements that encode an enzyme, reverse transcriptase (RT), which converts the element-encoded RNA into DNA prior to or during genomic integration. New studies provide compelling evidence that a bacterial group II intron-like RT has adapted enzymatic activities associated with RTs to function in host DNA repair.
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Affiliation(s)
- John V Moran
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
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7
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Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol 2021; 22:92. [PMID: 33781308 PMCID: PMC8006362 DOI: 10.1186/s13059-021-02285-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells. RESULTS Here, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees. CONCLUSIONS This study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.
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Affiliation(s)
- Yifan Wang
- 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 Avenue, Ann Arbor, MI, 48109, USA
| | - Taejeong Bae
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jeremy Thorpe
- Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Maxwell A Sherman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- MIT Department of Electrical Engineering and Computer Science, Cambridge, MA, USA
| | - Attila G Jones
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sean Cho
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Present Address: Arcus Biosciences, Hayward, CA, 94545, USA
| | | | - Yanmei Dou
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Javier Ganz
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alon Galor
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Irene Lobon
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chaggai Rosenbluh
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Simone Tomasi
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Livia Tomasini
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ryan Doan
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Yeongjun Jang
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - David Juan
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B Moldovan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Rujuta Narurkar
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
| | - Matthew T Oetjens
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Shobana Sekar
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eduardo Soriano
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
- Vall d'Hebron Institut de Recerca, 08035, Barcelona, Spain
- Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain
- ICREA Academia, 08010 Barcelona, Spain
| | - Richard E Straub
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Andrew Chess
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Tomas Marquès-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel R Weinberger
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT, 06520, USA
- Department of Neuroscience, Yale University, New Haven, 06520, CT, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Tashia and John Morgridge Faculty Scholar, Stanford Child Health Research Institute, Stanford, CA, 94305, 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 Avenue, Ann Arbor, MI, 48109, USA
| | - Ryan E Mills
- 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 Avenue, Ann Arbor, MI, 48109, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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8
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Halo JV, Pendleton AL, Shen F, Doucet AJ, Derrien T, Hitte C, Kirby LE, Myers B, Sliwerska E, Emery S, Moran JV, Boyko AR, Kidd JM. Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes. Proc Natl Acad Sci U S A 2021; 118:e2016274118. [PMID: 33836575 PMCID: PMC7980453 DOI: 10.1073/pnas.2016274118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3' end of LINE-1_Cfs (i.e., LINE-1_Cf 3'-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.
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Affiliation(s)
- Julia V Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Feichen Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Aurélien J Doucet
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
- Université Côte d'Azur, CNRS, INSERM, Institut de Recherche sur le Cancer et le Vieillissement de Nice, F-06100 Nice, France
| | - Thomas Derrien
- Université de Rennes 1, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, F-35000 Rennes, France
| | - Christophe Hitte
- Université de Rennes 1, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, F-35000 Rennes, France
| | - Laura E Kirby
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Bridget Myers
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Elzbieta Sliwerska
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Sarah Emery
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - John V Moran
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109;
- Department Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
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9
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Zhu X, Zhou B, Pattni R, Gleason K, Tan C, Kalinowski A, Sloan S, Fiston-Lavier AS, Mariani J, Petrov D, Barres BA, Duncan L, Abyzov A, Vogel H, Moran JV, Vaccarino FM, Tamminga CA, Levinson DF, Urban AE. Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia. Nat Neurosci 2021; 24:186-196. [PMID: 33432196 PMCID: PMC8806165 DOI: 10.1038/s41593-020-00767-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Abstract
Retrotransposons can cause somatic genome variation in the human nervous system, which is hypothesized to have relevance to brain development and neuropsychiatric disease. However, the detection of individual somatic mobile element insertions presents a difficult signal-to-noise problem. Using a machine-learning method (RetroSom) and deep whole-genome sequencing, we analyzed L1 and Alu retrotransposition in sorted neurons and glia from human brains. We characterized two brain-specific L1 insertions in neurons and glia from a donor with schizophrenia. There was anatomical distribution of the L1 insertions in neurons and glia across both hemispheres, indicating retrotransposition occurred during early embryogenesis. Both insertions were within the introns of genes (CNNM2 and FRMD4A) inside genomic loci associated with neuropsychiatric disorders. Proof-of-principle experiments revealed these L1 insertions significantly reduced gene expression. These results demonstrate that RetroSom has broad applications for studies of brain development and may provide insight into the possible pathological effects of somatic retrotransposition.
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Affiliation(s)
- Xiaowei Zhu
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | - Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | - Kelly Gleason
- Division of Translational Research in Schizophrenia, Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chunfeng Tan
- Division of Translational Research in Schizophrenia, Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Agnieszka Kalinowski
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
| | - Steven Sloan
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Anna-Sophie Fiston-Lavier
- Institut des Sciences de l'Evolution de Montpellier (UMR 5554, CNRS-UM-IRD-EPHE), Université de Montpellier, Montpellier, France
| | | | - Dmitri Petrov
- Department of Biology, Stanford University, Palo Alto, CA, USA
| | - Ben A Barres
- Department of Neurobiology, Stanford University, Palo Alto, CA, USA
| | - Laramie Duncan
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Hannes Vogel
- Department of Pathology, Stanford University, Palo Alto, CA, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT, USA
- Department of Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Carol A Tamminga
- Division of Translational Research in Schizophrenia, Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Douglas F Levinson
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA.
- Department of Genetics, Stanford University, Palo Alto, CA, USA.
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10
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Zhou W, Emery SB, Flasch DA, Wang Y, Kwan KY, Kidd JM, Moran JV, Mills RE. Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. Nucleic Acids Res 2020; 48:1146-1163. [PMID: 31853540 PMCID: PMC7026601 DOI: 10.1093/nar/gkz1173] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/14/2019] [Accepted: 12/05/2019] [Indexed: 11/13/2022] Open
Abstract
Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; however, they have limitations in detecting insertions in complex repetitive genomic regions. Here, we developed a computational tool (PALMER) and used it to identify 203 non-reference L1Hs insertions in the NA12878 benchmark genome. Using PacBio long-read sequencing data, we identified L1Hs insertions that were absent in previous short-read studies (90/203). Approximately 81% (73/90) of the L1Hs insertions reside within endogenous LINE-1 sequences in the reference assembly and the analysis of unique breakpoint junction sequences revealed 63% (57/90) of these L1Hs insertions could be genotyped in 1000 Genomes Project sequences. Moreover, we observed that amplification biases encountered in single-cell WGS experiments led to a wide variation in L1Hs insertion detection rates between four individual NA12878 cells; under-amplification limited detection to 32% (65/203) of insertions, whereas over-amplification increased false positive calls. In sum, these data indicate that L1Hs insertions are often missed using standard short-read sequencing approaches and long-read sequencing approaches can significantly improve the detection of L1Hs insertions present in individual genomes.
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Affiliation(s)
- Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Diane A Flasch
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Kenneth Y Kwan
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA.,Molecular and Behavioral Neuroscience Institute, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
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11
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Miyoshi T, Makino T, Moran JV. Poly(ADP-Ribose) Polymerase 2 Recruits Replication Protein A to Sites of LINE-1 Integration to Facilitate Retrotransposition. Mol Cell 2019; 75:1286-1298.e12. [PMID: 31473101 PMCID: PMC6754305 DOI: 10.1016/j.molcel.2019.07.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 05/23/2019] [Accepted: 07/12/2019] [Indexed: 10/26/2022]
Abstract
Long interspersed element-1 (LINE-1 or L1) retrotransposition poses a threat to genome integrity, and cells have evolved mechanisms to restrict retrotransposition. However, how cellular proteins facilitate L1 retrotransposition requires elucidation. Here, we demonstrate that single-strand DNA breaks induced by the L1 endonuclease trigger the recruitment of poly(ADP-ribose) polymerase 2 (PARP2) to L1 integration sites and that PARP2 activation leads to the subsequent recruitment of the replication protein A (RPA) complex to facilitate retrotransposition. We further demonstrate that RPA directly binds activated PARP2 through poly(ADP-ribosyl)ation and can protect single-strand L1 integration intermediates from APOBEC3-mediated cytidine deamination in vitro. Paradoxically, we provide evidence that RPA can guide APOBEC3A, and perhaps other APOBEC3 proteins, to sites of L1 integration. Thus, the interplay of L1-encoded and evolutionarily conserved cellular proteins is required for efficient retrotransposition; however, these interactions also may be exploited to restrict L1 retrotransposition in the human genome.
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Affiliation(s)
- Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Department of Stress Response, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109-5618, USA.
| | - Takeshi Makino
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan; Department of Stress Response, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109-5618, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109-5618, USA.
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12
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Flasch DA, Macia Á, Sánchez L, Ljungman M, Heras SR, García-Pérez JL, Wilson TE, Moran JV. Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication. Cell 2019; 177:837-851.e28. [PMID: 30955886 DOI: 10.1016/j.cell.2019.02.050] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 01/10/2019] [Accepted: 02/25/2019] [Indexed: 12/18/2022]
Abstract
L1 retrotransposon-derived sequences comprise approximately 17% of the human genome. Darwinian selective pressures alter L1 genomic distributions during evolution, confounding the ability to determine initial L1 integration preferences. Here, we generated high-confidence datasets of greater than 88,000 engineered L1 insertions in human cell lines that act as proxies for cells that accommodate retrotransposition in vivo. Comparing these insertions to a null model, in which L1 endonuclease activity is the sole determinant dictating L1 integration preferences, demonstrated that L1 insertions are not significantly enriched in genes, transcribed regions, or open chromatin. By comparison, we provide compelling evidence that the L1 endonuclease disproportionately cleaves predominant lagging strand DNA replication templates, while lagging strand 3'-hydroxyl groups may prime endonuclease-independent L1 retrotransposition in a Fanconi anemia cell line. Thus, acquisition of an endonuclease domain, in conjunction with the ability to integrate into replicating DNA, allowed L1 to become an autonomous, interspersed retrotransposon.
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Affiliation(s)
- Diane A Flasch
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA.
| | - Ángela Macia
- Department of Genomic Medicine, GENYO: Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016, Spain
| | - Laura Sánchez
- Department of Genomic Medicine, GENYO: Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016, Spain
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Comprehensive Cancer Center, Translational Oncology Program and Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, 48109, USA; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Sara R Heras
- Department of Genomic Medicine, GENYO: Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016, Spain
| | - José L García-Pérez
- Department of Genomic Medicine, GENYO: Centre for Genomics and Oncology (Pfizer-University of Granada and Andalusian Regional Government), PTS Granada, 18016, Spain; Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Thomas E Wilson
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA.
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA.
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13
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Affiliation(s)
- Haig H Kazazian
- From the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (H.H.K.), and the Departments of Human Genetics and Internal Medicine, University of Michigan Medical School, Ann Arbor (J.V.M.)
| | - John V Moran
- From the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore (H.H.K.), and the Departments of Human Genetics and Internal Medicine, University of Michigan Medical School, Ann Arbor (J.V.M.)
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14
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McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science 2017; 356:356/6336/eaal1641. [PMID: 28450582 DOI: 10.1126/science.aal1641] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neuropsychiatric disorders have a complex genetic architecture. Human genetic population-based studies have identified numerous heritable sequence and structural genomic variants associated with susceptibility to neuropsychiatric disease. However, these germline variants do not fully account for disease risk. During brain development, progenitor cells undergo billions of cell divisions to generate the ~80 billion neurons in the brain. The failure to accurately repair DNA damage arising during replication, transcription, and cellular metabolism amid this dramatic cellular expansion can lead to somatic mutations. Somatic mutations that alter subsets of neuronal transcriptomes and proteomes can, in turn, affect cell proliferation and survival and lead to neurodevelopmental disorders. The long life span of individual neurons and the direct relationship between neural circuits and behavior suggest that somatic mutations in small populations of neurons can significantly affect individual neurodevelopment. The Brain Somatic Mosaicism Network has been founded to study somatic mosaicism both in neurotypical human brains and in the context of complex neuropsychiatric disorders.
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15
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Abstract
The Long INterspersed Element-1 (LINE-1 or L1) retrotransposition assay has facilitated the discovery and characterization of active (i.e., retrotransposition-competent) LINE-1 sequences from mammalian genomes. In this assay, an engineered LINE-1 containing a retrotransposition reporter cassette is transiently transfected into a cultured cell line. Expression of the reporter cassette, which occurs only after a successful round of retrotransposition, allows the detection and quantification of the LINE-1 retrotransposition efficiency. This assay has yielded insight into the mechanism of LINE-1 retrotransposition. It also has provided a greater understanding of how the cell regulates LINE-1 retrotransposition and how LINE-1 retrotransposition impacts the structure of mammalian genomes. Below, we provide a brief introduction to LINE-1 biology and then detail how the LINE-1 retrotransposition assay is performed in cultured mammalian cells.
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Affiliation(s)
- Huira C Kopera
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine St, Ann Arbor, MI, 48109, USA.
| | - Peter A Larson
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine St, Ann Arbor, MI, 48109, USA
| | - John B Moldovan
- Cellular and Molecular Biology Program, University of Michigan Medical School, 1241 E. Catherine St, Ann Arbor, MI, 48109, USA
| | - Sandra R Richardson
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine St, Ann Arbor, MI, 48109, USA
| | - Ying Liu
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine St, Ann Arbor, MI, 48109, USA. .,Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA. .,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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16
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Abstract
Long INterspersed Element-1 (LINE-1 or L1) retrotransposons encode two proteins (ORF1p and ORF2p) that are required for retrotransposition. The L1 element amplification protocol (LEAP) assays the ability of L1 ORF2p to reverse transcribe L1 RNA in vitro. Ultracentrifugation or immunoprecipitation is used to isolate L1 ribonucleoprotein particle (RNP) complexes from cultured human cells transfected with an engineered L1 expression construct. The isolated RNPs are incubated with an oligonucleotide that contains a unique sequence at its 5' end and a thymidine-rich sequence at its 3' end. The addition of dNTPs to the reaction allows L1 ORF2p bound to L1 RNA to generate L1 cDNA. The resultant L1 cDNAs then are amplified using polymerase chain reaction (PCR) and the products are visualized by gel electrophoresis. Sequencing the resultant PCR products then allows product verification. The LEAP assay has been instrumental in determining how mutations in L1 ORF1p and ORF2p affect L1 reverse transcriptase (RT) activity. Furthermore, the LEAP assay has revealed that the L1 ORF2p RT can extend a DNA primer with mismatched 3' terminal bases when it is annealed to an L1 RNA template. As the LINE-1 biology field gravitates toward studying cellular proteins that regulate LINE-1, molecular genetic and biochemical approaches such as LEAP, in conjunction with the LINE-1-cultured cell retrotransposition assay, are essential to dissect the molecular mechanism of L1 retrotransposition.
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Affiliation(s)
- Huira C Kopera
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA.
| | - Diane A Flasch
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - Mitsuhiro Nakamura
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - Tomoichiro Miyoshi
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - Aurélien J Doucet
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI, 48109, USA. .,Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA. .,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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17
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Wylie A, Jones AE, D'Brot A, Lu WJ, Kurtz P, Moran JV, Rakheja D, Chen KS, Hammer RE, Comerford SA, Amatruda JF, Abrams JM. p53 genes function to restrain mobile elements. Genes Dev 2015; 30:64-77. [PMID: 26701264 PMCID: PMC4701979 DOI: 10.1101/gad.266098.115] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/23/2015] [Indexed: 11/24/2022]
Abstract
Wylie et al. show that p53 restricts retrotransposon activity and genetically interacts with components of the piRNA pathway. In gene complementation studies, normal human p53 alleles restrained these mobile elements, but mutant p53 alleles from cancer patients could not. Consistent with these observations, they also found patterns of unrestrained retrotransposons in p53-driven mouse and human cancers. Throughout the animal kingdom, p53 genes govern stress response networks by specifying adaptive transcriptional responses. The human member of this gene family is mutated in most cancers, but precisely how p53 functions to mediate tumor suppression is not well understood. Using Drosophila and zebrafish models, we show that p53 restricts retrotransposon activity and genetically interacts with components of the piRNA (piwi-interacting RNA) pathway. Furthermore, transposon eruptions occurring in the p53− germline were incited by meiotic recombination, and transcripts produced from these mobile elements accumulated in the germ plasm. In gene complementation studies, normal human p53 alleles suppressed transposons, but mutant p53 alleles from cancer patients could not. Consistent with these observations, we also found patterns of unrestrained retrotransposons in p53-driven mouse and human cancers. Furthermore, p53 status correlated with repressive chromatin marks in the 5′ sequence of a synthetic LINE-1 element. Together, these observations indicate that ancestral functions of p53 operate through conserved mechanisms to contain retrotransposons. Since human p53 mutants are disabled for this activity, our findings raise the possibility that p53 mitigates oncogenic disease in part by restricting transposon mobility.
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Affiliation(s)
- Annika Wylie
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Amanda E Jones
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Alejandro D'Brot
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Wan-Jin Lu
- Stanford University Medical Center, Stanford, California 94305, USA
| | - Paula Kurtz
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48019, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48019, USA; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan 48019, USA
| | - Dinesh Rakheja
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Kenneth S Chen
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Robert E Hammer
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Sarah A Comerford
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - James F Amatruda
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - John M Abrams
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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18
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Abstract
Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous retrotransposon in the human genome. To investigate the interplay between the L1 retrotransposition machinery and the host cell, we used co-immunoprecipitation in conjunction with liquid chromatography and tandem mass spectrometry to identify cellular proteins that interact with the L1 first open reading frame-encoded protein, ORF1p. We identified 39 ORF1p-interacting candidate proteins including the zinc-finger antiviral protein (ZAP or ZC3HAV1). Here we show that the interaction between ZAP and ORF1p requires RNA and that ZAP overexpression in HeLa cells inhibits the retrotransposition of engineered human L1 and Alu elements, an engineered mouse L1, and an engineered zebrafish LINE-2 element. Consistently, siRNA-mediated depletion of endogenous ZAP in HeLa cells led to a ~2-fold increase in human L1 retrotransposition. Fluorescence microscopy in cultured human cells demonstrated that ZAP co-localizes with L1 RNA, ORF1p, and stress granule associated proteins in cytoplasmic foci. Finally, molecular genetic and biochemical analyses indicate that ZAP reduces the accumulation of full-length L1 RNA and the L1-encoded proteins, yielding mechanistic insight about how ZAP may inhibit L1 retrotransposition. Together, these data suggest that ZAP inhibits the retrotransposition of LINE and Alu elements. Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous retrotransposon in the human genome. L1s comprise ~17% of human DNA and it is estimated that an average human genome has ~80–100 active L1s. L1 moves throughout the genome via a “copy-and-paste” mechanism known as retrotransposition. L1 retrotransposition is known to cause mutations; thus, it stands to reason that the host cell has evolved mechanisms to protect the cell from unabated retrotransposition. Here, we demonstrate that the zinc-finger antiviral protein (ZAP) inhibits the retrotransposition of human L1 and Alu retrotransposons, as well as related retrotransposons from mice and zebrafish. Biochemical and genetic data suggest that ZAP interacts with L1 RNA. Fluorescent microscopy demonstrates that ZAP associates with L1 in cytoplasmic foci that co-localize with stress granule proteins. Mechanistic analyses suggest that ZAP reduces the expression of full-length L1 RNA and the L1-encoded proteins, thereby providing mechanistic insight for how ZAP may restricts retrotransposition. Importantly, these data suggest that ZAP initially may have evolved to combat endogenous retrotransposons and subsequently was co-opted as a viral restriction factor.
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Affiliation(s)
- John B. Moldovan
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (JBM); (JVM)
| | - John V. Moran
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Departments of Human Genetics and Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail: (JBM); (JVM)
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19
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Singh PK, Bourque G, Craig NL, Dubnau JT, Feschotte C, Flasch DA, Gunderson KL, Malik HS, Moran JV, Peters JE, Slotkin RK, Levin HL. Mobile genetic elements and genome evolution 2014. Mob DNA 2014; 5:26. [PMID: 30117500 PMCID: PMC4363357 DOI: 10.1186/1759-8753-5-26] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 10/02/2014] [Indexed: 11/10/2022] Open
Abstract
The Mobile Genetic Elements and Genome Evolution conference was hosted by Keystone Symposia in Santa Fe, NM USA, 9 March through 14 March 2014. The goal of this conference was to bring together scientists from around the world who study transposable elements in diverse organisms and researchers who study the impact these elements have on genome evolution. The meeting included over 200 scientists who participated through poster presentations, short talks selected from abstracts, and invited speakers. The talks were organized into eight sessions and two workshops. The topics varied from diverse mechanisms of mobilization to the evolution of genomes and their defense strategies against transposable elements.
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Affiliation(s)
- Parmit Kumar Singh
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
| | - Guillaume Bourque
- McGill University and Genome Quebec Innovation Center, Montreal, Canada
| | - Nancy L Craig
- School of Medicine, The Johns Hopkins University, Baltimore, MD USA.,Howard Hughes Medical Institute, Chevy Chase, MD USA
| | - Josh T Dubnau
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring, NY USA
| | - Cédric Feschotte
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Diane A Flasch
- Department of Human Genetics, University of Michigan, Ann Arbor, MI USA
| | | | - Harmit Singh Malik
- Howard Hughes Medical Institute, Chevy Chase, MD USA.,Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - John V Moran
- Howard Hughes Medical Institute, Chevy Chase, MD USA.,Department of Human Genetics, University of Michigan, Ann Arbor, MI USA
| | - Joseph E Peters
- Department of Microbiology, Cornell University, Ithaca, NY USA
| | - R Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, OH USA
| | - Henry L Levin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD USA
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20
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Richardson SR, Narvaiza I, Planegger RA, Weitzman MD, Moran JV. APOBEC3A deaminates transiently exposed single-strand DNA during LINE-1 retrotransposition. eLife 2014; 3:e02008. [PMID: 24843014 PMCID: PMC4003774 DOI: 10.7554/elife.02008] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Long INterspersed Element-1 (LINE-1 or L1) retrotransposition poses a mutagenic threat to human genomes. Human cells have therefore evolved strategies to regulate L1 retrotransposition. The APOBEC3 (A3) gene family consists of seven enzymes that catalyze deamination of cytidine nucleotides to uridine nucleotides (C-to-U) in single-strand DNA substrates. Among these enzymes, APOBEC3A (A3A) is the most potent inhibitor of L1 retrotransposition in cultured cell assays. However, previous characterization of L1 retrotransposition events generated in the presence of A3A did not yield evidence of deamination. Thus, the molecular mechanism by which A3A inhibits L1 retrotransposition has remained enigmatic. Here, we have used in vitro and in vivo assays to demonstrate that A3A can inhibit L1 retrotransposition by deaminating transiently exposed single-strand DNA that arises during the process of L1 integration. These data provide a mechanistic explanation of how the A3A cytidine deaminase protein can inhibit L1 retrotransposition. DOI:http://dx.doi.org/10.7554/eLife.02008.001 Transposable elements are often referred to as ‘jumping genes’ because they can move between different locations within a genome. These sequences of DNA are found in many organisms and can make up a significant proportion of the genetic material: almost 50% of the DNA in the case of the human genome. Transposable elements are grouped by how they move to new locations in a genome. Some move by a cut-and-paste mechanism—whereby the transposable element DNA is removed from one location and inserted back at a new genomic location. Others, termed retrotransposons, move by a copy-and-paste mechanism: the DNA sequence is transcribed into an RNA intermediate, and then copied back into DNA before being inserted into a new location. Retrotransposons can accumulate to great numbers in genomes: and one retrotransposon, called LINE-1, is present at an estimated 500,000 copies in the human genome. Although most copies of LINE-1 are inactive, the average human genome contains about 80–100 that are predicted to be able to ‘jump’ to new locations. Given that these retrotransposons could insert into, and disrupt, vital genes, it follows that our cells would have evolved ways to limit their movement. An enzyme named APOBEC3A is known to limit the movement of LINE-1 retrotransposons in cells. APOBEC3A can alter the letters, or bases, that make up the genetic code. This enzyme acts on single-strand DNA to change ‘C’ bases to ‘U’ bases, which could explain how APOBEC3A combats LINE-1. However, no evidence for such mutation of LINE-1 sequences by APOBEC3A had been found to date. Now, Richardson et al. recreate the copying of LINE-1 RNA back into DNA in a test tube—and reveal that APOBEC3A can mutate single-strand LINE-1 DNA. Critically, as long as the RNA intermediate and DNA copy remain together, the LINE-1 DNA is protected. However, when LINE-1 inserts into a new location the temporarily exposed single strand of LINE-1 DNA becomes susceptible to mutation by APOBEC3A. Human cells can detect and destroy ‘U’ bases in DNA—and only by inhibiting this ability were Richardson et al. able to observe APOBEC3A mutations in new LINE-1 copies within the genomes of living cells. Richardson et al. speculate that the activity of APOBEC3 enzymes must strike a balance between limiting the spread of retrotransposons and minimizing the mutation of the cell's own DNA. Future work could address important questions, such as: do APOBEC enzymes affect the ‘jumping’ of LINE-1 retrotransposons in human reproductive cells and the early embryo, where new LINE-1 insertions could be passed on to subsequent generations? Also, does a loss of APOBEC3 activity lead to new LINE-1 insertions in cancerous cells? And does this effect how tumors form and/or progress? Since APOBEC3 enzymes can cause mutations in cancers, they have been proposed as new targets for anti-cancer drugs—therefore, it is crucial to uncover any harmful effects of inhibiting APOBEC3 enzymes that might limit the effectiveness of such treatments. DOI:http://dx.doi.org/10.7554/eLife.02008.002
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Affiliation(s)
- Sandra R Richardson
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, United States
| | - Iñigo Narvaiza
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, United States
| | - Randy A Planegger
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, United States
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine and the Children's Hospital of Philadelphia, Philadelphia, United States
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, United States Department of Internal Medicine, Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, United States
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21
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Moran JV. 2013 Curt Stern Award Address. Am J Hum Genet 2014; 94:340-8. [PMID: 24607386 DOI: 10.1016/j.ajhg.2014.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 01/28/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- John V Moran
- Departments of Human Genetics and Internal Medicine, 1241 East Catherine Street, University of Michigan Medical School, Ann Arbor, MI 48109-5618, USA; Howard Hughes Medical Institute.
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22
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Zhang A, Dong B, Doucet AJ, Moldovan JB, Moran JV, Silverman RH. RNase L restricts the mobility of engineered retrotransposons in cultured human cells. Nucleic Acids Res 2013; 42:3803-20. [PMID: 24371271 PMCID: PMC3973342 DOI: 10.1093/nar/gkt1308] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Retrotransposons are mobile genetic elements, and their mobility can lead to genomic instability. Retrotransposon insertions are associated with a diverse range of sporadic diseases, including cancer. Thus, it is not a surprise that multiple host defense mechanisms suppress retrotransposition. The 2′,5′-oligoadenylate (2-5A) synthetase (OAS)-RNase L system is a mechanism for restricting viral infections during the interferon antiviral response. Here, we investigated a potential role for the OAS-RNase L system in the restriction of retrotransposons. Expression of wild type (WT) and a constitutively active form of RNase L (NΔ385), but not a catalytically inactive RNase L mutant (R667A), impaired the mobility of engineered human LINE-1 (L1) and mouse intracisternal A-type particle retrotransposons in cultured human cells. Furthermore, WT RNase L, but not an inactive RNase L mutant (R667A), reduced L1 RNA levels and subsequent expression of the L1-encoded proteins (ORF1p and ORF2p). Consistently, confocal immunofluorescent microscopy demonstrated that WT RNase L, but not RNase L R667A, prevented formation of L1 cytoplasmic foci. Finally, siRNA-mediated depletion of endogenous RNase L in a human ovarian cancer cell line (Hey1b) increased the levels of L1 retrotransposition by ∼2-fold. Together, these data suggest that RNase L might function as a suppressor of structurally distinct retrotransposons.
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Affiliation(s)
- Ao Zhang
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland Clinic, Cleveland, OH, 44195, USA, Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA, Department of Human Genetics, Ann Arbor, MI 48109, USA, Cellular and Molecular Biology Program, Ann Arbor, MI 48109, USA, Department of Internal Medicine, Ann Arbor, MI 48109, USA and Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
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23
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Macfarlane CM, Collier P, Rahbari R, Beck CR, Wagstaff JF, Igoe S, Moran JV, Badge RM. Transduction-specific ATLAS reveals a cohort of highly active L1 retrotransposons in human populations. Hum Mutat 2013; 34:974-85. [PMID: 23553801 DOI: 10.1002/humu.22327] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 03/15/2013] [Indexed: 11/09/2022]
Abstract
Long INterspersed Element-1 (LINE-1 or L1) retrotransposons are the only autonomously active transposable elements in the human genome. The average human genome contains ∼80-100 active L1s, but only a subset of these L1s are highly active or 'hot'. Human L1s are closely related in sequence, making it difficult to decipher progenitor/offspring relationships using traditional phylogenetic methods. However, L1 mRNAs can sometimes bypass their own polyadenylation signal and instead utilize fortuitous polyadenylation signals in 3' flanking genomic DNA. Retrotransposition of the resultant mRNAs then results in lineage specific sequence "tags" (i.e., 3' transductions) that mark the descendants of active L1 progenitors. Here, we developed a method (Transduction-Specific Amplification Typing of L1 Active Subfamilies or TS-ATLAS) that exploits L1 3' transductions to identify active L1 lineages in a genome-wide context. TS-ATLAS enabled the characterization of a putative active progenitor of one L1 lineage that includes the disease causing L1 insertion L1RP , and the identification of new retrotransposition events within two other "hot" L1 lineages. Intriguingly, the analysis of the newly discovered transduction lineage members suggests that L1 polyadenylation, even within a lineage, is highly stochastic. Thus, TS-ATLAS provides a new tool to explore the dynamics of L1 lineage evolution and retrotransposon biology.
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24
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Arkhipova IR, Batzer MA, Brosius J, Feschotte C, Moran JV, Schmitz J, Jurka J. Genomic impact of eukaryotic transposable elements. Mob DNA 2012; 3:19. [PMID: 23171443 PMCID: PMC3520738 DOI: 10.1186/1759-8753-3-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/07/2012] [Indexed: 11/10/2022] Open
Abstract
The third international conference on the genomic impact of eukaryotic transposable elements (TEs) was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come.
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Affiliation(s)
- Irina R Arkhipova
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster D-48149, Germany.
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25
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Abstract
The completion of the human genome reference sequence ushered in a new era for the study and discovery of human transposable elements. It now is undeniable that transposable elements, historically dismissed as junk DNA, have had an instrumental role in sculpting the structure and function of our genomes. In particular, long interspersed element-1 (LINE-1 or L1) and short interspersed elements (SINEs) continue to affect our genome, and their movement can lead to sporadic cases of disease. Here, we briefly review the types of transposable elements present in the human genome and their mechanisms of mobility. We next highlight how advances in DNA sequencing and genomic technologies have enabled the discovery of novel retrotransposons in individual genomes. Finally, we discuss how L1-mediated retrotransposition events impact human genomes.
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Affiliation(s)
- Christine R Beck
- Department of Human Genetics, University of MIchigan Medical School, Ann Arbor, Michigan 48109-5618, USA.
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26
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Wissing S, Muñoz-Lopez M, Macia A, Yang Z, Montano M, Collins W, Garcia-Perez JL, Moran JV, Greene WC. Reprogramming somatic cells into iPS cells activates LINE-1 retroelement mobility. Hum Mol Genet 2011; 21:208-18. [PMID: 21989055 DOI: 10.1093/hmg/ddr455] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Long interspersed element-1 (LINE-1 or L1) retrotransposons account for nearly 17% of human genomic DNA and represent a major evolutionary force that has reshaped the structure and function of the human genome. However, questions remain concerning both the frequency and the developmental timing of L1 retrotransposition in vivo and whether the mobility of these retroelements commonly results in insertional and post-insertional mechanisms of genomic injury. Cells exhibiting high rates of L1 retrotransposition might be especially at risk for such injury. We assessed L1 mRNA expression and L1 retrotransposition in two biologically relevant cell types, human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs), as well as in control parental human dermal fibroblasts (HDFs). Full-length L1 mRNA and the L1 open reading frame 1-encoded protein (ORF1p) were readily detected in hESCs and iPSCs, but not in HDFs. Sequencing analysis proved the expression of human-specific L1 element mRNAs in iPSCs. Bisulfite sequencing revealed that the increased L1 expression observed in iPSCs correlates with an overall decrease in CpG methylation in the L1 promoter region. Finally, retrotransposition of an engineered human L1 element was ~10-fold more efficient in iPSCs than in parental HDFs. These findings indicate that somatic cell reprogramming is associated with marked increases in L1 expression and perhaps increases in endogenous L1 retrotransposition, which could potentially impact the genomic integrity of the resultant iPSCs.
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Affiliation(s)
- Silke Wissing
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA, USA
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27
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Wissing S, Montano M, Garcia-Perez JL, Moran JV, Greene WC. Endogenous APOBEC3B restricts LINE-1 retrotransposition in transformed cells and human embryonic stem cells. J Biol Chem 2011; 286:36427-37. [PMID: 21878639 DOI: 10.1074/jbc.m111.251058] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Members of the APOBEC3 (A3) family of cytidine deaminase enzymes act as host defense mechanisms limiting both infections by exogenous retroviruses and mobilization of endogenous retrotransposons. Previous studies revealed that the overexpression of some A3 proteins could restrict engineered human Long INterspersed Element-1 (LINE-1 or L1) retrotransposition in HeLa cells. However, whether endogenous A3 proteins play a role in restricting L1 retrotransposition remains largely unexplored. Here, we show that HeLa cells express endogenous A3B and A3C, whereas human embryonic stem cells (hESCs) express A3B, A3C, A3DE, A3F, and A3G. To study the relative contribution of endogenous A3 proteins in restricting L1 retrotransposition, we first generated small hairpin RNAs (shRNAs) to suppress endogenous A3 mRNA expression, and then assessed L1 mobility using a cell-based L1 retrotransposition assay. We demonstrate that in both HeLa and hESCs, shRNA-based knockdown of A3B promotes a ∼2-3.7-fold increase in the retrotransposition efficiency of an engineered human L1. Knockdown of the other A3s produced no significant increase in L1 activity. Thus, A3B appears to restrict engineered L1 retrotransposition in a broad range of cell types, including pluripotent cells.
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Affiliation(s)
- Silke Wissing
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California 94158, USA
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28
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Abstract
Transposable elements (TEs) have a unique ability to mobilize to new genomic locations, and the major advance of second-generation DNA sequencing has provided insights into the dynamic relationship between TEs and their hosts. It now is clear that TEs have adopted diverse strategies - such as specific integration sites or patterns of activity - to thrive in host environments that are replete with mechanisms, such as small RNAs or epigenetic marks, that combat TE amplification. Emerging evidence suggests that TE mobilization might sometimes benefit host genomes by enhancing genetic diversity, although TEs are also implicated in diseases such as cancer. Here, we discuss recent findings about how, where and when TEs insert in diverse organisms.
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Affiliation(s)
- Henry L Levin
- Section on Eukaryotic Transposable Elements, Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
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29
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Doucet AJ, Sahinovic E, Bucheton A, Moran JV, Gilbert N. Identification of the 'basal' human LINE-1 retrotransposition complex. Retrovirology 2009. [PMCID: PMC2767015 DOI: 10.1186/1742-4690-6-s2-p32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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30
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Costanzo V, Chaudhuri J, Fung JC, Moran JV. Dealing with dangerous accidents: DNA double-strand breaks take centre stage. Symposium on Genome Instability and DNA Repair. EMBO Rep 2009; 10:837-42. [PMID: 19609319 PMCID: PMC2726687 DOI: 10.1038/embor.2009.173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 06/23/2009] [Indexed: 11/08/2022] Open
Affiliation(s)
- Vincenzo Costanzo
- Genome Stability, London Research Institute, South Mimms, Hertfordshire EN63LD, UK
| | - Jayanta Chaudhuri
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Jennifer C Fung
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, California 94158, USA
| | - John V Moran
- Howard Hughes Medical Institute, Departments of Human Genetics and Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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31
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Bennett EA, Keller H, Mills RE, Schmidt S, Moran JV, Weichenrieder O, Devine SE. Active Alu retrotransposons in the human genome. Genes Dev 2008; 18:1875-83. [PMID: 18836035 PMCID: PMC2593586 DOI: 10.1101/gr.081737.108] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 09/30/2008] [Indexed: 12/16/2022]
Abstract
Alu retrotransposons evolved from 7SL RNA approximately 65 million years ago and underwent several rounds of massive expansion in primate genomes. Consequently, the human genome currently harbors 1.1 million Alu copies. Some of these copies remain actively mobile and continue to produce both genetic variation and diseases by "jumping" to new genomic locations. However, it is unclear how many active Alu copies exist in the human genome and which Alu subfamilies harbor such copies. Here, we present a comprehensive functional analysis of Alu copies across the human genome. We cloned Alu copies from a variety of genomic locations and tested these copies in a plasmid-based mobilization assay. We show that functionally intact core Alu elements are highly abundant and far outnumber all other active transposons in humans. A range of Alu lineages were found to harbor such copies, including all modern AluY subfamilies and most AluS subfamilies. We also identified two major determinants of Alu activity: (1) The primary sequence of a given Alu copy, and (2) the ability of the encoded RNA to interact with SRP9/14 to form RNA/protein (RNP) complexes. We conclude that Alu elements pose the largest transposon-based mutagenic threat to the human genome. On the basis of our data, we have begun to identify Alu copies that are likely to produce genetic variation and diseases in humans.
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Affiliation(s)
- E. Andrew Bennett
- Genetics and Molecular Biology Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Center for Bioinformatics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Heiko Keller
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ryan E. Mills
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Center for Bioinformatics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Steffen Schmidt
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - John V. Moran
- Howard Hughes Medical Institute, Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Scott E. Devine
- Genetics and Molecular Biology Graduate Program, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Center for Bioinformatics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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Garcia-Perez JL, Marchetto MCN, Muotri AR, Coufal NG, Gage FH, O'Shea KS, Moran JV. LINE-1 retrotransposition in human embryonic stem cells. Hum Mol Genet 2007; 16:1569-77. [PMID: 17468180 DOI: 10.1093/hmg/ddm105] [Citation(s) in RCA: 179] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
LINE-1 elements comprise approximately 17% of human DNA and their mobility continues to impact genome evolution. However, little is known about the types of non-transformed cells that can support LINE-1 retrotransposition. Here, we show that human embryonic stem cells express endogenous LINE-1 elements and can accommodate LINE-1 retrotransposition in vitro. The resultant retrotransposition events can occur into genes and can result in the concomitant deletion of genomic DNA at the target site. Thus, these data suggest that LINE-1 retrotransposition events may occur during early stages of human development.
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Affiliation(s)
- Jose L Garcia-Perez
- Departments of Human Genetics and Internal Medicine, University of Michigan Medical School, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
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Garcia-Perez JL, Doucet AJ, Bucheton A, Moran JV, Gilbert N. Distinct mechanisms for trans-mediated mobilization of cellular RNAs by the LINE-1 reverse transcriptase. Genome Res 2007; 17:602-11. [PMID: 17416749 PMCID: PMC1855177 DOI: 10.1101/gr.5870107] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Long Interspersed Element-1 (LINE-1 or L1) sequences comprise approximately 17% of human DNA and ongoing L1 retrotransposition continues to impact genome evolution. The L1-encoded proteins also can mobilize other cellular RNAs (e.g., Alu retrotransposons, SVA retrotransposons, and U6 snRNAs), which comprise approximately 13% of human DNA. Here, we demonstrate that the trans-mediated mobilization of non-L1 RNAs can occur by either template choice or template-switching mechanisms. Remarkably, these mechanisms are not mutually exclusive, as both processes can operate sequentially on the same RNA template. Finally, we provide evidence that efficient U6 snRNA retrotransposition requires both ORF1p and ORF2p, providing indirect evidence for the action of ORF1p in U6 snRNA retrotransposition. Thus, we propose that the LINE-1-encoded reverse transcriptase can mediate the retrotransposition of non-L1 RNAs by distinct mechanisms.
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Affiliation(s)
- José L. Garcia-Perez
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109-0618, USA
| | - Aurélien J. Doucet
- Institut de Génétique Humaine, CNRS, UPR 1142, 34396 Montpellier cedex 5, France
| | - Alain Bucheton
- Institut de Génétique Humaine, CNRS, UPR 1142, 34396 Montpellier cedex 5, France
| | - John V. Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109-0618, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109-0618, USA
- Corresponding authors.E-mail ; fax (734) 763-3784.E-mail ; fax (33) 4-99-61-99-01
| | - Nicolas Gilbert
- Institut de Génétique Humaine, CNRS, UPR 1142, 34396 Montpellier cedex 5, France
- Corresponding authors.E-mail ; fax (734) 763-3784.E-mail ; fax (33) 4-99-61-99-01
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Morrish TA, Garcia-Perez JL, Stamato TD, Taccioli GE, Sekiguchi J, Moran JV. Endonuclease-independent LINE-1 retrotransposition at mammalian telomeres. Nature 2007; 446:208-12. [PMID: 17344853 DOI: 10.1038/nature05560] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 01/02/2007] [Indexed: 11/08/2022]
Abstract
Long interspersed element-1 (LINE-1 or L1) elements are abundant, non-long-terminal-repeat (non-LTR) retrotransposons that comprise approximately 17% of human DNA. The average human genome contains approximately 80-100 retrotransposition-competent L1s (ref. 2), and they mobilize by a process that uses both the L1 endonuclease and reverse transcriptase, termed target-site primed reverse transcription. We have previously reported an efficient, endonuclease-independent L1 retrotransposition pathway (EN(i)) in certain Chinese hamster ovary (CHO) cell lines that are defective in the non-homologous end-joining (NHEJ) pathway of DNA double-strand-break repair. Here we have characterized EN(i) retrotransposition events generated in V3 CHO cells, which are deficient in DNA-dependent protein kinase catalytic subunit (DNA-PKcs) activity and have both dysfunctional telomeres and an NHEJ defect. Notably, approximately 30% of EN(i) retrotransposition events insert in an orientation-specific manner adjacent to a perfect telomere repeat (5'-TTAGGG-3'). Similar insertions were not detected among EN(i) retrotransposition events generated in controls or in XR-1 CHO cells deficient for XRCC4, an NHEJ factor that is required for DNA ligation but has no known function in telomere maintenance. Furthermore, transient expression of a dominant-negative allele of human TRF2 (also called TERF2) in XRCC4-deficient XR-1 cells, which disrupts telomere capping, enables telomere-associated EN(i) retrotransposition events. These data indicate that L1s containing a disabled endonuclease can use dysfunctional telomeres as an integration substrate. The findings highlight similarities between the mechanism of EN(i) retrotransposition and the action of telomerase, because both processes can use a 3' OH for priming reverse transcription at either internal DNA lesions or chromosome ends. Thus, we propose that EN(i) retrotransposition is an ancestral mechanism of RNA-mediated DNA repair associated with non-LTR retrotransposons that may have been used before the acquisition of an endonuclease domain.
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Affiliation(s)
- Tammy A Morrish
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109-0618, USA.
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Hulme AE, Bogerd HP, Cullen BR, Moran JV. Selective inhibition of Alu retrotransposition by APOBEC3G. Gene 2006; 390:199-205. [PMID: 17079095 PMCID: PMC2917221 DOI: 10.1016/j.gene.2006.08.032] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 08/23/2006] [Accepted: 08/24/2006] [Indexed: 11/30/2022]
Abstract
The non-LTR retrotransposon LINE-1 (L1) comprises approximately 17% of the human genome, and the L1-encoded proteins can function in trans to mediate the retrotransposition of non-autonomous retrotransposons (i.e., Alu and probably SVA elements) and cellular mRNAs to generate processed pseudogenes. Here, we have examined the effect of APOBEC3G and APOBEC3F, cytidine deaminases that inhibit Vif-deficient HIV-1 replication, on Alu retrotransposition and other L1-mediated retrotransposition processes. We demonstrate that APOBEC3G selectively inhibits Alu retrotransposition in an ORF1p-independent manner. An active cytidine deaminase site is not required for the inhibition of Alu retrotransposition and the resultant integration events lack G to A or C to T hypermutation. These data demonstrate a differential restriction of L1 and Alu retrotransposition by APOBEC3G, and suggest that the Alu ribonucleoprotein complex may be targeted by APOBEC3G.
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Affiliation(s)
- Amy E. Hulme
- Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Paper correspondence should be addressed to or
| | - Hal P. Bogerd
- Center for Virology and Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Bryan R. Cullen
- Center for Virology and Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - John V. Moran
- Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, The University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Paper correspondence should be addressed to or
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Gasior SL, Preston G, Hedges DJ, Gilbert N, Moran JV, Deininger PL. Characterization of pre-insertion loci of de novo L1 insertions. Gene 2006; 390:190-8. [PMID: 17067767 PMCID: PMC1850991 DOI: 10.1016/j.gene.2006.08.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 08/21/2006] [Accepted: 08/22/2006] [Indexed: 10/24/2022]
Abstract
The human Long Interspersed Element-1 (LINE-1) and the Short Interspersed Element (SINE) Alu comprise 28% of the human genome. They share the same L1-encoded endonuclease for insertion, which recognizes an A+T-rich sequence. Under a simple model of insertion distribution, this nucleotide preference would lead to the prediction that the populations of both elements would be biased towards A+T-rich regions. Genomic L1 elements do show an A+T-rich bias. In contrast, Alu is biased towards G+C-rich regions when compared to the genome average. Several analyses have demonstrated that relatively recent insertions of both elements show less G+C content bias relative to older elements. We have analyzed the repetitive element and G+C composition of more than 100 pre-insertion loci derived from de novo L1 insertions in cultured human cancer cells, which should represent an evolutionarily unbiased set of insertions. An A+T-rich bias is observed in the 50 bp flanking the endonuclease target site, consistent with the known target site for the L1 endonuclease. The L1, Alu, and G+C content of 20 kb of the de novo pre-insertion loci shows a different set of biases than that observed for fixed L1s in the human genome. In contrast to the insertion sites of genomic L1s, the de novo L1 pre-insertion loci are relatively L1-poor, Alu-rich and G+C neutral. Finally, a statistically significant cluster of de novo L1 insertions was localized in the vicinity of the c-myc gene. These results suggest that the initial insertion preference of L1, while A+T-rich in the initial vicinity of the break site, can be influenced by the broader content of the flanking genomic region and have implications for understanding the dynamics of L1 and Alu distributions in the human genome.
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Affiliation(s)
- Stephen L. Gasior
- Tulane Cancer Center and Dept. of Epidemiology, Tulane University Health Sciences Center SL-66, 1430 Tulane Ave., New Orleans, LA 70112, Phone: (504) 988-6385, Fax: (504) 988-5516,
| | - Graeme Preston
- Tulane Cancer Center and Dept. of Epidemiology, Tulane University Health Sciences Center SL-66, 1430 Tulane Ave., New Orleans, LA 70112, Phone: (504) 988-6385, Fax: (504) 988-5516,
| | - Dale J. Hedges
- Tulane Cancer Center and Dept. of Epidemiology, Tulane University Health Sciences Center SL-66, 1430 Tulane Ave., New Orleans, LA 70112, Phone: (504) 988-6385, Fax: (504) 988-5516,
| | - Nicolas Gilbert
- Institut de Génétique Humaine, CNRS, UPR 1142, 141 rue de la Cardonille, 34396 Montpellier cedex 5, France
| | - John V. Moran
- Departments of Human Genetics and Internal Medicine, 1241 E. Catherine St., University of Michigan Medical School, Ann Arbor, Michigan 48109-0618
| | - Prescott L. Deininger
- Tulane Cancer Center and Dept. of Epidemiology, Tulane University Health Sciences Center SL-66, 1430 Tulane Ave., New Orleans, LA 70112, Phone: (504) 988-6385, Fax: (504) 988-5516,
- *Address for Correspondence: Tulane Cancer Center, SL66, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112, 504-988-6385,
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Batzer MA, Deininger PL, Jurka J, Moran JV. Introduction for the Gene special issue dedicated to the meeting "Genomic impact of eukaryotic transposable elements" at Asilomar. Gene 2006; 390:1-2. [PMID: 17027200 DOI: 10.1016/j.gene.2006.07.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Accepted: 07/31/2006] [Indexed: 11/30/2022]
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Lin L, Wang Z, Prescott MS, van Dekken H, Thomas DG, Giordano TJ, Chang AC, Orringer MB, Gruber SB, Moran JV, Glover TW, Beer DG. Multiple forms of genetic instability within a 2-Mb chromosomal segment of 3q26.3-q27 are associated with development of esophageal adenocarcinoma. Genes Chromosomes Cancer 2006; 45:319-31. [PMID: 16320248 DOI: 10.1002/gcc.20293] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Gene amplification is one of the mechanisms to activate oncogenes in many cancers, including esophageal adenocarcinoma (EA). In the present study, we used two-dimensional restriction landmark genome scanning to clone a NotI/DpnII fragment that showed increased genomic dosage in 1 of 44 EAs analyzed. This fragment maps to 3q26.3-q27, and subsequent experiments identified two intrachromosomal amplicons within a 10-Mb DNA segment in 7 of 75 (9%) EAs. The distal amplified-core region maps centromeric to the PIK3CA locus, and a microsatellite (D3S1754) within this region exhibited significant instability (MSI), in stark contrast to the genomewide microsatellite stability found in EA. D3S1754-MSI arises in premalignant Barrett's dysplastic cells and preceded amplification of the nascent MSI allele in the corresponding EA. Seven ESTs within the amplified-core were overexpressed in amplicon-containing EAs. One of these, EST AW513672, represents a chimeric transcript that initiated from an antisense promoter sequence in the 5'UTR of a full-length LINE-1 element (L1-5'ASP). Similar chimeric transcripts encoding portions of the MET oncogene and the BCAS3 gene also were overexpressed in EAs, suggesting that L1-5'ASP activation may occur at a broad level in primary EAs. Thus, the fine dissection of a 2-Mb amplified DNA segment in 3q26.3-q27 in EA revealed multiple genetic alterations that had occurred sequentially and/or concurrently during EA development.
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Affiliation(s)
- Lin Lin
- Department of Surgery Thoracic Section, University of Michigan Medical School, B560 MSRB2, Box 0686, Ann Arbor, MI 48109, USA.
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Kulpa DA, Moran JV. Cis-preferential LINE-1 reverse transcriptase activity in ribonucleoprotein particles. Nat Struct Mol Biol 2006; 13:655-60. [PMID: 16783376 DOI: 10.1038/nsmb1107] [Citation(s) in RCA: 215] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 05/11/2006] [Indexed: 11/09/2022]
Abstract
LINE-1 retrotransposons (L1s) constitute approximately 17% of human DNA, and their activity continues to affect genome evolution. Retrotransposition-competent human L1s encode two proteins required for their mobility (ORF1p and ORF2p); however, biochemical activities associated with ORF2p have been difficult to detect in cells. Here, we show for the first time the colocalization of L1 RNA, ORF1p and ORF2p to a putative ribonucleoprotein retrotransposition intermediate. We further demonstrate that ORF2p preferentially uses its encoding RNA as a template for reverse transcription. Thus, our data provide the first biochemical evidence supporting the cis-preferential action of the L1 reverse transcriptase.
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Affiliation(s)
- Deanna A Kulpa
- Department of Human Genetics 1241 E. Catherine St., University of Michigan Medical School, Ann Arbor, Michigan 48109-0618, USA.
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40
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Bogerd HP, Wiegand HL, Hulme AE, Garcia-Perez JL, O’Shea KS, Moran JV, Cullen BR. Cellular inhibitors of long interspersed element 1 and Alu retrotransposition. Proc Natl Acad Sci U S A 2006; 103:8780-5. [PMID: 16728505 PMCID: PMC1482655 DOI: 10.1073/pnas.0603313103] [Citation(s) in RCA: 298] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Indexed: 12/18/2022] Open
Abstract
Long interspersed element (LINE) 1 retrotransposons are major genomic parasites that represent approximately 17% of the human genome. The LINE-1 ORF2 protein is also responsible for the mobility of Alu elements, which constitute a further approximately 11% of genomic DNA. Representative members of each element class remain mobile, and deleterious retrotransposition events can induce spontaneous genetic diseases. Here, we demonstrate that APOBEC3A and APOBEC3B, two members of the APOBEC3 family of human innate antiretroviral resistance factors, can enter the nucleus, where LINE-1 and Alu reverse transcription occurs, and specifically inhibit both LINE-1 and Alu retrotransposition. These data suggest that the APOBEC3 protein family may have evolved, at least in part, to defend the integrity of the human genome against endogenous retrotransposons.
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Affiliation(s)
- Hal P. Bogerd
- Center for Virology and Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710; and
| | - Heather L. Wiegand
- Center for Virology and Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710; and
| | - Amy E. Hulme
- Departments of Human Genetics and Internal Medicine and
| | | | - K. Sue O’Shea
- Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - John V. Moran
- Departments of Human Genetics and Internal Medicine and
| | - Bryan R. Cullen
- Center for Virology and Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710; and
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Kubo S, del Carmen Seleme M, Soifer HS, Perez JLG, Moran JV, Kazazian HH, Kasahara N. L1 retrotransposition in nondividing and primary human somatic cells. Proc Natl Acad Sci U S A 2006; 103:8036-41. [PMID: 16698926 PMCID: PMC1472425 DOI: 10.1073/pnas.0601954103] [Citation(s) in RCA: 139] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Whether long interspersed element-1 (L1 or LINE-1) retrotransposition can occur in quiescent, nondividing, and/or terminally differentiated somatic cells has remained an unanswered fundamental question in human genetics. Here, we used a ubiquitously active phosphoglycerate kinase-1 promoter to drive the expression of a highly active human L1 element from an adenovirus-L1 hybrid vector. This vector system achieved retrotransposition in up to 91% of actively growing immortalized cells, and we demonstrated that L1 retrotransposition can be suppressed by the reverse transcriptase inhibitor 3'-azido-3'-deoxythymidine. This adenovirus vector enabled efficient delivery of the L1 element into differentiated primary human somatic cells and G1/S-arrested cells, resulting in retrotransposition in both cases; however, it was not detected in G0-arrested cells. Thus, these data indicate that L1 retrotransposition can occur in nondividing somatic cells.
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Affiliation(s)
- Shuji Kubo
- *Department of Medicine, UCLA School of Medicine, 675 Charles E. Young Drive South, MRL-1551, Los Angeles, CA 90095-7019
| | - Maria del Carmen Seleme
- Department of Genetics, University of Pennsylvania School of Medicine, 475 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104-6145
| | - Harris S. Soifer
- Division of Molecular Biology, Beckman Research Institute, City of Hope National Medical Center, 1450 East Duarte Road, Duarte, CA 91010-3011; Departments of
| | | | - John V. Moran
- Human Genetics and
- Internal Medicine, University of Michigan Medical School, 1241 East Catherine Street, Room 4909 Buhl, Ann Arbor, MI 48109-0618
| | - Haig H. Kazazian
- Department of Genetics, University of Pennsylvania School of Medicine, 475 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104-6145
| | - Noriyuki Kasahara
- *Department of Medicine, UCLA School of Medicine, 675 Charles E. Young Drive South, MRL-1551, Los Angeles, CA 90095-7019
- To whom correspondence should be addressed. E-mail:
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Abstract
Long Interspersed Element-1 (LINE-1 or L1) retrotransposons encode proteins required for their mobility (ORF1p and ORF2p), yet little is known about how L1 mRNA is translated. Here, we show that ORF2 translation generally initiates from the first in-frame methionine codon of ORF2, and that both ORF1 and the inter-ORF spacer are dispensable for ORF2 translation. Remarkably, changing the ORF2 AUG codon to any other coding triplet is compatible with retrotransposition. However, introducing a premature termination codon in ORF1 or a thermostable hairpin in the inter-ORF spacer reduces ORF2p translation or L1 retrotransposition to approximately 5% of wild-type levels. Similar data obtained from "natural" and codon optimized "synthetic" mouse L1s lead us to propose that ORF2 is translated by an unconventional termination/reinitiation mechanism.
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Affiliation(s)
- Reid S Alisch
- Department of Human Genetics and Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109-0618, USA
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43
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Abstract
Long interspersed elements (LINE-1s or L1s) are abundant non-LTR retrotransposons that mobilize through an RNA intermediate by target site primed reverse transcription. The L1-encoded proteins (ORF1p and ORF2p) preferentially associate with their encoding transcript to form a ribonucleoprotein particle (RNP), which is a proposed retrotransposition intermediate. Here, we have used epitope tagging to discriminate the proteins encoded by engineered L1s from those encoded by endogenously expressed L1s. We demonstrate that an L1 containing an epitope tag at the carboxyl terminus of ORF1p remains retrotransposition-competent and that tagged ORF1p and its encoding RNA localize to cytoplasmic RNPs. We also identified two classes of ORF1p mutants, one that severely decreased RNP formation and blocked retrotransposition, and another that allows RNP formation but reduces retrotransposition by 100-fold. Thus, these data indicate that RNP formation is important but not sufficient for L1 retrotransposition and suggest that ORF1p also may function at downstream steps in the L1 retrotransposition pathway.
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Affiliation(s)
- Deanna A Kulpa
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109-0618, USA
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44
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Abstract
LINE-1 (L1) retrotransposons comprise approximately 17% of human DNA, yet little is known about L1 integration. Here, we characterized 100 retrotransposition events in HeLa cells and show that distinct DNA repair pathways can resolve L1 cDNA retrotransposition intermediates. L1 cDNA resolution can lead to various forms of genetic instability including the generation of chimeric L1s, intrachromosomal deletions, intrachromosomal duplications, and intra-L1 rearrangements as well as a possible interchromosomal translocation. The L1 retrotransposition machinery also can mobilize U6 snRNA to new genomic locations, increasing the repertoire of noncoding RNAs that are mobilized by L1s. Finally, we have determined that the L1 reverse transcriptase can faithfully replicate its own transcript and has a base misincorporation error rate of approximately 1/7,000 bases. These data indicate that L1 retrotransposition in transformed human cells can lead to a variety of genomic rearrangements and suggest that host processes act to restrict L1 integration in cultured human cells. Indeed, the initial steps in L1 retrotransposition may define a host/parasite battleground that serves to limit the number of active L1s in the genome.
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Affiliation(s)
- Nicolas Gilbert
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, 48109-0618, USA
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45
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Muotri AR, Chu VT, Marchetto MCN, Deng W, Moran JV, Gage FH. Somatic mosaicism in neuronal precursor cells mediated by L1 retrotransposition. Nature 2005; 435:903-10. [PMID: 15959507 DOI: 10.1038/nature03663] [Citation(s) in RCA: 664] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 04/20/2005] [Indexed: 11/08/2022]
Abstract
Revealing the mechanisms for neuronal somatic diversification remains a central challenge for understanding individual differences in brain organization and function. Here we show that an engineered human LINE-1 (for long interspersed nuclear element-1; also known as L1) element can retrotranspose in neuronal precursors derived from rat hippocampus neural stem cells. The resulting retrotransposition events can alter the expression of neuronal genes, which, in turn, can influence neuronal cell fate in vitro. We further show that retrotransposition of a human L1 in transgenic mice results in neuronal somatic mosaicism. The molecular mechanism of action is probably mediated through Sox2, because a decrease in Sox2 expression during the early stages of neuronal differentiation is correlated with increases in both L1 transcription and retrotransposition. Our data therefore indicate that neuronal genomes might not be static, but some might be mosaic because of de novo L1 retrotransposition events.
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Affiliation(s)
- Alysson R Muotri
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA
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46
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Abstract
The initial step in Long Interspersed Element-1 (LINE-1) retrotransposition requires transcription from an internal promoter located within its 5'-untranslated region (5'-UTR). Previous studies have identified a YY1 (Yin Yang 1)-binding site as an important sequence in LINE-1 transcription. Here, we demonstrate that mutations in the YY1-binding site have only minor effects on transcription activation of the full-length 5'-UTR and LINE-1 mobility in a single round cultured cell retrotransposition assay. Instead, these mutations disrupt proper initiation of transcription from the +1 site of the 5'-UTR. Thus, we propose that the YY1-binding site functions as a component of the LINE-1 core promoter to direct accurate transcription initiation. Indeed, this sequence may explain the evolutionary success of LINE-1 by enabling full-length retrotransposed copies to undergo autonomous retrotransposition in subsequent generations.
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Affiliation(s)
- Jyoti N Athanikar
- Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, MI 48109-0618, USA
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47
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Abstract
Mobile elements make up large portions of most eukaryotic genomes. They create genetic instability, not only through insertional mutation but also by contributing recombination substrates, both during and long after their insertion. The combination of whole-genome sequences and the development of innovative new assays to test the function of mobile elements have increased our understanding of how these elements mobilize and how their insertion impacts genome diversity and human disease.
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Affiliation(s)
- Prescott L Deininger
- Department of Environmental Health Sciences, Tulane University Health Sciences Center, New Orleans, LA 70112, USA.
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48
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Abstract
B1 elements are an abundant class of short interspersed elements (SINEs) in the mouse genome and mobilize by a process known as retrotransposition. Here, we report the characterization of a mutagenic B1 insertion into exon 4 of the Atcay gene, which was previously shown to be responsible for the jittery mouse. Mutations in the human ortholog of this gene, ATCAY, are responsible for Cayman ataxia. The B1 insertion is approximately 150-bp long, ends in a 45-50-bp polyadenylic acid (poly A) tail, is flanked by a perfect 13-bp target-site duplication, and is inserted into a sequence that resembles a LINE-1 endonuclease consensus cleavage site. Computational analysis indicates that the mutagenic insertion is most closely related to elements of the B1-C subfamily, and we have identified two possible progenitor B1 sequences on mouse chromosome 19. Together, these data demonstrate that B1 retrotransposition is ongoing in the mouse genome and is consistent with the hypothesis that the reverse transcriptase and endonuclease encoded by LINE-1 elements mediate B1 mobility.
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Affiliation(s)
- Nicolas Gilbert
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA.
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49
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Lutz SM, Vincent BJ, Kazazian HH, Batzer MA, Moran JV. Allelic heterogeneity in LINE-1 retrotransposition activity. Am J Hum Genet 2003; 73:1431-7. [PMID: 14610717 PMCID: PMC1180405 DOI: 10.1086/379744] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2003] [Accepted: 09/09/2003] [Indexed: 11/03/2022] Open
Abstract
De novo LINE-1 (long interspersed element-1, or L1) retrotransposition events are responsible for approximately 1/1,000 disease-causing mutations in humans. Previously, L1.2 was identified as the likely progenitor of a mutagenic insertion in the factor VIII gene in a patient with hemophilia A. It subsequently was shown to be one of a small number of active L1s in the human genome. Here, we demonstrate that L1.2 is present at an intermediate insertion allele frequency in worldwide human populations and that common alleles (L1.2A and L1.2B) exhibit an approximately 16-fold difference in their ability to retrotranspose in cultured human HeLa cells. Chimera analysis revealed that two amino acid substitutions (S1259L and I1220M) downstream of the conserved cysteine-rich motif in L1 open reading frame 2 are largely responsible for the observed reduction in L1.2A retrotransposition efficiency. Thus, common L1 alleles can vary widely in their retrotransposition potential. We propose that such allelic heterogeneity can influence the potential L1 mutational load present in an individual genome.
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Affiliation(s)
- Sheila M Lutz
- Departments of Human Genetics and Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109-0618, USA.
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50
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Brouha B, Schustak J, Badge RM, Lutz-Prigge S, Farley AH, Moran JV, Kazazian HH. Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A 2003; 100:5280-5. [PMID: 12682288 PMCID: PMC154336 DOI: 10.1073/pnas.0831042100] [Citation(s) in RCA: 764] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although LINE-1 (long interspersed nucleotide element-1, L1) retrotransposons comprise 17% of the human genome, an exhaustive search of the December 2001 "freeze" of the haploid human genome working draft sequence (95% complete) yielded only 90 L1s with intact ORFs. We demonstrate that 38 of 86 (44%) L1s are polymorphic as to their presence in human populations. We cloned 82 (91%) of the 90 L1s and found that 40 of the 82 (49%) are active in a cultured cell retrotransposition assay. From these data, we predict that there are 80-100 retrotransposition-competent L1s in an average human being. Remarkably, 84% of assayed retrotransposition capability was present in six highly active L1s (hot L1s). By comparison, four of five full-length L1s involved in recent human insertions had retrotransposition activity comparable to the six hot L1s in the human genome working draft sequence. Thus, our data indicate that most L1 retrotransposition in the human population stems from hot L1s, with the remaining elements playing a lesser role in genome plasticity.
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Affiliation(s)
- Brook Brouha
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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