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Yang L, Metzger GA, Padilla Del Valle R, Delgadillo Rubalcaba D, McLaughlin RN. Evolutionary insights from profiling LINE-1 activity at allelic resolution in a single human genome. EMBO J 2024; 43:112-131. [PMID: 38177314 PMCID: PMC10883270 DOI: 10.1038/s44318-023-00007-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/18/2023] [Accepted: 11/10/2023] [Indexed: 01/06/2024] Open
Abstract
Transposable elements have created the majority of the sequence in many genomes. In mammals, LINE-1 retrotransposons have been expanding for more than 100 million years as distinct, consecutive lineages; however, the drivers of this recurrent lineage emergence and disappearance are unknown. Most human genome assemblies provide a record of this ancient evolution, but fail to resolve ongoing LINE-1 retrotranspositions. Utilizing the human CHM1 long-read-based haploid assembly, we identified and cloned all full-length, intact LINE-1s, and found 29 LINE-1s with measurable in vitro retrotransposition activity. Among individuals, these LINE-1s varied in their presence, their allelic sequences, and their activity. We found that recently retrotransposed LINE-1s tend to be active in vitro and polymorphic in the population relative to more ancient LINE-1s. However, some rare allelic forms of old LINE-1s retain activity, suggesting older lineages can persist longer than expected. Finally, in LINE-1s with in vitro activity and in vivo fitness, we identified mutations that may have increased replication in ancient genomes and may prove promising candidates for mechanistic investigations of the drivers of LINE-1 evolution and which LINE-1 sequences contribute to human disease.
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Affiliation(s)
- Lei Yang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | - Ricky Padilla Del Valle
- Pacific Northwest Research Institute, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | | | - Richard N McLaughlin
- Pacific Northwest Research Institute, Seattle, WA, USA.
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA.
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2
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Romero MA, Mumford PW, Roberson PA, Osburn SC, Young KC, Sedivy JM, Roberts MD. Translational Significance of the LINE-1 Jumping Gene in Skeletal Muscle. Exerc Sport Sci Rev 2022; 50:185-193. [PMID: 35749745 PMCID: PMC9651911 DOI: 10.1249/jes.0000000000000301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Retrotransposons are gene segments that proliferate in the genome, and the Long INterspersed Element 1 (LINE-1 or L1) retrotransposon is active in humans. Although older mammals show enhanced skeletal muscle L1 expression, exercise generally reverses this trend. We hypothesize skeletal muscle L1 expression influences muscle physiology, and additional innovative investigations are needed to confirm this hypothesis.
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Affiliation(s)
- Matthew A. Romero
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California USA
| | - Petey W. Mumford
- Department of Exercise Science, Lindenwood University, St. Charles, Missouri USA
| | - Paul A. Roberson
- Department of Cellular and Molecular Physiology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania USA
| | | | - Kaelin C. Young
- School of Kinesiology, Auburn University, Auburn, Alabama USA
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine-Auburn, Auburn, Alabama, USA
| | - John M. Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Center on the Biology of Aging, Brown University, Providence, Rhode Island, USA
| | - Michael D. Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama USA
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine-Auburn, Auburn, Alabama, USA
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3
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Jeon S, Kim S, Oh MH, Liang P, Tang W, Han K. A comprehensive analysis of gorilla-specific LINE-1 retrotransposons. Genes Genomics 2021; 43:1133-1141. [PMID: 34406591 DOI: 10.1007/s13258-021-01146-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Long interspersed element-1 (LINE-1 or L1) is the most abundant retrotransposons in the primate genome. They have approximately 520,000 copies and make up ~ 17% of the primate genome. Full-length L1s can mobilize to a new genomic location using their enzymatic machinery. Gorilla is the second closest species to humans after the chimpanzee, and human-gorilla split 7-12 million years ago. The gorilla genome provides an opportunity to explore primate origins and evolution. OBJECTIVE L1s have contributed to genome diversity and variations during primate evolution. This study aimed to identify gorilla-specific L1s using a more recent version of the gorilla reference genome (Mar. 2016 GSMRT3/gorGor5). METHODS We collected gorilla-specific L1 candidates through computational analysis and manual inspection. L1Xplorer was used to identify whether full-length gorilla-specific L1s were intact. In addition, to determine the level of sequence conservation between intact fulllength gorilla-specific L1s, two ORFs of intact L1s were aligned with the L1PA2 consensus sequence. RESULTS 2002 gorilla-specific L1 candidates were identified through computational analysis. Among them, we manually inspected 1,883 gorilla-specific L1s, among which most of them belong to the L1PA2 subfamily and 12 were intact L1s that could influence genomic variations in the gorilla genome. Interestingly, the 12 intact full-length gorilla-specific L1s have 14 highly conserved nonsynonymous mutations, including 6 mutations and 8 mutations in ORF1 and ORF2, respectively. In comparison to the intact full-length chimpanzee-specific L1s and human-specific hot-L1s, two of these in ORF1 (L256F and E293G) were shown as gorilla-specific nonsynonymous mutations. CONCLUSION The gorilla-specific L1s may have had significantly affected the gorilla genome to compose a genome different form that of other primates during primate evolution.
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Affiliation(s)
- Soyeon Jeon
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Songmi Kim
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Man Hwan Oh
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada.,Centre of Biotechnologies, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Wanxiangfu Tang
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Kyudong Han
- Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea. .,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea.
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4
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Chen D, Cremona MA, Qi Z, Mitra RD, Chiaromonte F, Makova KD. Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. Mol Biol Evol 2021; 37:3576-3600. [PMID: 32722770 DOI: 10.1093/molbev/msaa194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. To fill this gap, we investigated three genome-wide data sets of L1s that integrated at different evolutionary times: 17,037 de novo L1s (from an L1 insertion cell-line experiment conducted in-house), and 1,212 polymorphic and 1,205 human-specific L1s (from public databases). We characterized 49 genomic features-proxying chromatin accessibility, transcriptional activity, replication, recombination, etc.-in the ±50 kb flanks of these elements. These features were contrasted between the three L1 data sets and L1-free regions using state-of-the-art Functional Data Analysis statistical methods, which treat high-resolution data as mathematical functions. Our results indicate that de novo, polymorphic, and human-specific L1s are surrounded by different genomic features acting at specific locations and scales. This led to an integrative model of L1 transposition, according to which L1s preferentially integrate into open-chromatin regions enriched in non-B DNA motifs, whereas they are fixed in regions largely free of purifying selection-depleted of genes and noncoding most conserved elements. Intriguingly, our results suggest that L1 insertions modify local genomic landscape by extending CpG methylation and increasing mononucleotide microsatellite density. Altogether, our findings substantially facilitate understanding of L1 integration and fixation preferences, pave the way for uncovering their role in aging and cancer, and inform their use as mutagenesis tools in genetic studies.
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Affiliation(s)
- Di Chen
- Intercollege Graduate Degree Program in Genetics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Marzia A Cremona
- Department of Statistics, The Pennsylvania State University, University Park, PA.,Department of Operations and Decision Systems, Université Laval, Québec, Canada
| | - Zongtai Qi
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Robi D Mitra
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, PA.,EMbeDS, Sant'Anna School of Advanced Studies, Pisa, Italy.,The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University, University Park, PA
| | - Kateryna D Makova
- The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
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5
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Reiner BC, Doyle GA, Weller AE, Levinson RN, Rao AM, Davila Perea E, Namoglu E, Pigeon A, Arauco-Shapiro G, Weickert CS, Turecki G, Crist RC, Berrettini WH. Inherited L1 Retrotransposon Insertions Associated With Risk for Schizophrenia and Bipolar Disorder. SCHIZOPHRENIA BULLETIN OPEN 2021; 2:sgab031. [PMID: 34901866 PMCID: PMC8650070 DOI: 10.1093/schizbullopen/sgab031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Studies of the genetic heritability of schizophrenia and bipolar disorder examining single nucleotide polymorphisms (SNPs) and copy number variations have failed to explain a large portion of the genetic liability, resulting in substantial missing heritability. Long interspersed element 1 (L1) retrotransposons are a type of inherited polymorphic variant that may be associated with risk for schizophrenia and bipolar disorder. We performed REBELseq, a genome wide assay for L1 sequences, on DNA from male and female persons with schizophrenia and controls (n = 63 each) to identify inherited L1 insertions and validated priority insertions. L1 insertions of interest were genotyped in DNA from a replication cohort of persons with schizophrenia, bipolar disorder, and controls (n = 2268 each) to examine differences in carrier frequencies. We identified an inherited L1 insertion in ARHGAP24 and a quadallelic SNP (rs74169643) inside an L1 insertion in SNTG2 that are associated with risk for developing schizophrenia and bipolar disorder (all odds ratios ~1.2). Pathway analysis identified 15 gene ontologies that were differentially affected by L1 burden, including multiple ontologies related to glutamatergic signaling and immune function, which have been previously associated with schizophrenia. These findings provide further evidence supporting the role of inherited repetitive genetic elements in the heritability of psychiatric disorders.
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Affiliation(s)
- Benjamin C Reiner
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Glenn A Doyle
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew E Weller
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel N Levinson
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aditya M Rao
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emilie Davila Perea
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Esin Namoglu
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alicia Pigeon
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabriella Arauco-Shapiro
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cyndi Shannon Weickert
- Schizophrenia Research Laboratory, Neuroscience Research Australia & School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Department of Neuroscience & Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Canada
| | - Richard C Crist
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wade H Berrettini
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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6
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Ewing AD, Smits N, Sanchez-Luque FJ, Faivre J, Brennan PM, Richardson SR, Cheetham SW, Faulkner GJ. Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling. Mol Cell 2020; 80:915-928.e5. [PMID: 33186547 DOI: 10.1016/j.molcel.2020.10.024] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) drive genome evolution and are a notable source of pathogenesis, including cancer. While CpG methylation regulates TE activity, the locus-specific methylation landscape of mobile human TEs has to date proven largely inaccessible. Here, we apply new computational tools and long-read nanopore sequencing to directly infer CpG methylation of novel and extant TE insertions in hippocampus, heart, and liver, as well as paired tumor and non-tumor liver. As opposed to an indiscriminate stochastic process, we find pronounced demethylation of young long interspersed element 1 (LINE-1) retrotransposons in cancer, often distinct to the adjacent genome and other TEs. SINE-VNTR-Alu (SVA) retrotransposons, including their internal tandem repeat-associated CpG island, are near-universally methylated. We encounter allele-specific TE methylation and demethylation of aberrantly expressed young LINE-1s in normal tissues. Finally, we recover the complete sequences of tumor-specific LINE-1 insertions and their retrotransposition hallmarks, demonstrating how long-read sequencing can simultaneously survey the epigenome and detect somatic TE mobilization.
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Affiliation(s)
- Adam D Ewing
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia.
| | - Nathan Smits
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Francisco J Sanchez-Luque
- GENYO, Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Jamila Faivre
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
| | - Paul M Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, Edinburgh EH16 4SB, UK
| | - Sandra R Richardson
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Seth W Cheetham
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia.
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, St. Lucia, QLD 4067, Australia.
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7
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Qing R, Tao F, Chatterjee P, Yang G, Han Q, Chung H, Ni J, Suter BP, Kubicek J, Maertens B, Schubert T, Blackburn C, Zhang S. Non-full-length Water-Soluble CXCR4 QTY and CCR5 QTY Chemokine Receptors: Implication for Overlooked Truncated but Functional Membrane Receptors. iScience 2020; 23:101670. [PMID: 33376963 PMCID: PMC7756140 DOI: 10.1016/j.isci.2020.101670] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/12/2020] [Accepted: 10/08/2020] [Indexed: 01/06/2023] Open
Abstract
It was posited that functionalities of GPCRs require full-length sequences that are negated by residue deletions. Here we report that significantly truncated nfCCR5QTY and nfCXCR4QTY still bind native ligands. Receptor-ligand interactions were discovered from yeast 2-hybrid screening and confirmed by mating selection. Two nfCCR5QTY (SZ218a, SZ190b) and two nfCXCR4QTY (SZ158a, SZ146a) were expressed in E. coli. Synthesized receptors exhibited α-helical structures and bound respective ligands with reduced affinities. SZ190b and SZ158a were reconverted into non-QTY forms and expressed in HEK293T cells. Reconverted receptors localized on cell membranes and functioned as negative regulators for ligand-induced signaling when co-expressed with full-length receptors. CCR5-SZ190b individually can perform signaling at a reduced level with higher ligand concentration. Our findings provide insight into essential structural components for CCR5 and CXCR4 functionality, while raising the possibility that non-full-length receptors may be resulted from alternative splicing and that pseudo-genes in genomes may be present and functional in living organisms. Y2H screening reveals ligand interaction from truncated CXCR4 and CCR5 in QTY form Truncated CCR5QTY and CXCR4QTY can be produced in E. coli and bind native ligands Reconverted receptors localize on membranes and regulate cell signaling in HEK293 Our finding indicates potential presence and function for truncated receptors
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Affiliation(s)
- Rui Qing
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Fei Tao
- Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Pranam Chatterjee
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.,The Center for Bits and Atoms, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gaojie Yang
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Qiuyi Han
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Haeyoon Chung
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jun Ni
- Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
| | - Bernhard P Suter
- Next Interactions, Inc., 2600 Hilltop Drive, Building B, C332, Richmond, CA 94806, USA
| | - Jan Kubicek
- Cube Biotech, GmbH, Creative Campus, Alfred-Nobel Strasse 10, 40789 Monheim, Germany
| | - Barbara Maertens
- Cube Biotech, GmbH, Creative Campus, Alfred-Nobel Strasse 10, 40789 Monheim, Germany
| | | | - Camron Blackburn
- The Center for Bits and Atoms, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Shuguang Zhang
- Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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8
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Restriction Enzyme Based Enriched L1Hs Sequencing (REBELseq): A Scalable Technique for Detection of Ta Subfamily L1Hs in the Human Genome. G3-GENES GENOMES GENETICS 2020; 10:1647-1655. [PMID: 32132168 PMCID: PMC7202019 DOI: 10.1534/g3.119.400613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Long interspersed element-1 retrotransposons (LINE-1 or L1) are ∼6 kb mobile DNA elements implicated in the origins of many Mendelian and complex diseases. The actively retrotransposing L1s are mostly limited to the L1 human specific (L1Hs) transcriptional active (Ta) subfamily. In this manuscript, we present REBELseq as a method for the construction of Ta subfamily L1Hs-enriched next-generation sequencing libraries and bioinformatic identification. REBELseq was performed on DNA isolated from NeuN+ neuronal nuclei from postmortem brain samples of 177 individuals and empirically-driven bioinformatic and experimental cutoffs were established. Putative L1Hs insertions passing bioinformatics cutoffs were experimentally validated. REBELseq reliably identified both known and novel Ta subfamily L1Hs insertions distributed throughout the genome. Differences in the proportion of individuals possessing a given reference or non-reference retrotransposon insertion were identified. We conclude that REBELseq is an unbiased, whole genome approach to the amplification and detection of Ta subfamily L1Hs retrotransposons.
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9
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Wang W, Chen C, Wang X, Zhang L, Shen D, Wang S, Gao B, Mao J, Song C. Development of Molecular Markers Based on the L1 Retrotransposon Insertion Polymorphisms in Pigs (Sus scrofa) and Their Association with Economic Traits. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420020131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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10
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McKerrow W, Tang Z, Steranka JP, Payer LM, Boeke JD, Keefe D, Fenyö D, Burns KH, Liu C. Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190335. [PMID: 32075555 PMCID: PMC7061987 DOI: 10.1098/rstb.2019.0335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Long interspersed element-1 (LINE-1, L1) sequences, which comprise about 17% of human genome, are the product of one of the most active types of mobile DNAs in modern humans. LINE-1 insertion alleles can cause inherited and de novo genetic diseases, and LINE-1-encoded proteins are highly expressed in some cancers. Genome-wide LINE-1 mapping in single cells could be useful for defining somatic and germline retrotransposition rates, and for enabling studies to characterize tumour heterogeneity, relate insertions to transcriptional and epigenetic effects at the cellular level, or describe cellular phylogenies in development. Our laboratories have reported a genome-wide LINE-1 insertion site mapping method for bulk DNA, named transposon insertion profiling by sequencing (TIPseq). There have been significant barriers applying LINE-1 mapping to single cells, owing to the chimeric artefacts and features of repetitive sequences. Here, we optimize a modified TIPseq protocol and show its utility for LINE-1 mapping in single lymphoblastoid cells. Results from single-cell TIPseq experiments compare well to known LINE-1 insertions found by whole-genome sequencing and TIPseq on bulk DNA. Among the several approaches we tested, whole-genome amplification by multiple displacement amplification followed by restriction enzyme digestion, vectorette ligation and LINE-1-targeted PCR had the best assay performance. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Wilson McKerrow
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
| | - Zuojian Tang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
| | - Jared P Steranka
- Department of Pathology, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
| | - David Keefe
- Department of Obstetrics and Gynecology, New York University Langone School of Medicine, 462 First Avenue, New York, NY 10016, USA.,Department of Cell Biology, New York University Langone School of Medicine, 462 First Avenue, New York, NY 10016, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA.,High Throughput (HiT) Biology Center, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 401N Broadway, Baltimore, MD 21231, USA
| | - Chunhong Liu
- Department of Pathology, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA
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11
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Lou C, Goodier JL, Qiang R. A potential new mechanism for pregnancy loss: considering the role of LINE-1 retrotransposons in early spontaneous miscarriage. Reprod Biol Endocrinol 2020; 18:6. [PMID: 31964400 PMCID: PMC6971995 DOI: 10.1186/s12958-020-0564-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022] Open
Abstract
LINE1 retrotransposons are mobile DNA elements that copy and paste themselves into new sites in the genome. To ensure their evolutionary success, heritable new LINE-1 insertions accumulate in cells that can transmit genetic information to the next generation (i.e., germ cells and embryonic stem cells). It is our hypothesis that LINE1 retrotransposons, insertional mutagens that affect expression of genes, may be causal agents of early miscarriage in humans. The cell has evolved various defenses restricting retrotransposition-caused mutation, but these are occasionally relaxed in certain somatic cell types, including those of the early embryo. We predict that reduced suppression of L1s in germ cells or early-stage embryos may lead to excessive genome mutation by retrotransposon insertion, or to the induction of an inflammatory response or apoptosis due to increased expression of L1-derived nucleic acids and proteins, and so disrupt gene function important for embryogenesis. If correct, a novel threat to normal human development is revealed, and reverse transcriptase therapy could be one future strategy for controlling this cause of embryonic damage in patients with recurrent miscarriages.
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Affiliation(s)
- Chao Lou
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
| | - John L. Goodier
- 0000 0001 2171 9311grid.21107.35McKusick-Nathans Deartment of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Rong Qiang
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
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12
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Nguyen THM, Carreira PE, Sanchez-Luque FJ, Schauer SN, Fagg AC, Richardson SR, Davies CM, Jesuadian JS, Kempen MJHC, Troskie RL, James C, Beaven EA, Wallis TP, Coward JIG, Chetty NP, Crandon AJ, Venter DJ, Armes JE, Perrin LC, Hooper JD, Ewing AD, Upton KR, Faulkner GJ. L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution. Cell Rep 2019; 23:3730-3740. [PMID: 29949758 DOI: 10.1016/j.celrep.2018.05.090] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 01/04/2018] [Accepted: 05/26/2018] [Indexed: 01/07/2023] Open
Abstract
LINE-1 (L1) retrotransposons are a source of insertional mutagenesis in tumor cells. However, the clinical significance of L1 mobilization during tumorigenesis remains unclear. Here, we applied retrotransposon capture sequencing (RC-seq) to multiple single-cell clones isolated from five ovarian cancer cell lines and HeLa cells and detected endogenous L1 retrotransposition in vitro. We then applied RC-seq to ovarian tumor and matched blood samples from 19 patients and identified 88 tumor-specific L1 insertions. In one tumor, an intronic de novo L1 insertion supplied a novel cis-enhancer to the putative chemoresistance gene STC1. Notably, the tumor subclone carrying the STC1 L1 mutation increased in prevalence after chemotherapy, further increasing STC1 expression. We also identified hypomethylated donor L1s responsible for new L1 insertions in tumors and cultivated cancer cells. These congruent in vitro and in vivo results highlight L1 insertional mutagenesis as a common component of ovarian tumorigenesis and cancer genome heterogeneity.
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Affiliation(s)
- Thu H M Nguyen
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Patricia E Carreira
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Francisco J Sanchez-Luque
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PT Ciencias de la Salud, Granada 18016, Spain
| | - Stephanie N Schauer
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Allister C Fagg
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Sandra R Richardson
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | | | - J Samuel Jesuadian
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Marie-Jeanne H C Kempen
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Robin-Lee Troskie
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Cini James
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | | | | | - Jermaine I G Coward
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Mater Health Services, South Brisbane, QLD 4101, Australia
| | - Naven P Chetty
- Mater Health Services, South Brisbane, QLD 4101, Australia
| | | | - Deon J Venter
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Mater Health Services, South Brisbane, QLD 4101, Australia
| | - Jane E Armes
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Mater Health Services, South Brisbane, QLD 4101, Australia
| | - Lewis C Perrin
- Mater Health Services, South Brisbane, QLD 4101, Australia
| | - John D Hooper
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Adam D Ewing
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Kyle R Upton
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
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13
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Tang W, Liang P. Comparative Genomics Analysis Reveals High Levels of Differential Retrotransposition among Primates from the Hominidae and the Cercopithecidae Families. Genome Biol Evol 2019; 11:3309-3325. [PMID: 31651947 PMCID: PMC6934888 DOI: 10.1093/gbe/evz234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2019] [Indexed: 12/11/2022] Open
Abstract
Mobile elements (MEs), making ∼50% of primate genomes, are known to be responsible for generating inter- and intra-species genomic variations and play important roles in genome evolution and gene function. Using a bioinformatics comparative genomics approach, we performed analyses of species-specific MEs (SS-MEs) in eight primate genomes from the families of Hominidae and Cercopithecidae, focusing on retrotransposons. We identified a total of 230,855 SS-MEs, with which we performed normalization based on evolutionary distances, and we also analyzed the most recent SS-MEs in these genomes. Comparative analysis of SS-MEs reveals striking differences in ME transposition among these primate genomes. Interesting highlights of our results include: 1) the baboon genome has the highest number of SS-MEs with a strong bias for SINEs, while the crab-eating macaque genome has a sustained extremely low transposition for all ME classes, suggesting the existence of a genome-wide mechanism suppressing ME transposition; 2) while SS-SINEs represent the dominant class in general, the orangutan genome stands out by having SS-LINEs as the dominant class; 3) the human genome stands out among the eight genomes by having the largest number of recent highly active ME subfamilies, suggesting a greater impact of ME transposition on its recent evolution; and 4) at least 33% of the SS-MEs locate to genic regions, including protein coding regions, presenting significant potentials for impacting gene function. Our study, as the first of its kind, demonstrates that mobile elements evolve quite differently among these primates, suggesting differential ME transposition as an important mechanism in primate evolution.
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Affiliation(s)
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
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14
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Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH. SQuIRE reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Res 2019; 47:e27. [PMID: 30624635 PMCID: PMC6411935 DOI: 10.1093/nar/gky1301] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/18/2018] [Accepted: 01/03/2019] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) are interspersed repeat sequences that make up much of the human genome. Their expression has been implicated in development and disease. However, TE-derived RNA-seq reads are difficult to quantify. Past approaches have excluded these reads or aggregated RNA expression to subfamilies shared by similar TE copies, sacrificing quantitative accuracy or the genomic context necessary to understand the basis of TE transcription. As a result, the effects of TEs on gene expression and associated phenotypes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), the first RNA-seq analysis pipeline that provides a quantitative and locus-specific picture of TE expression (https://github.com/wyang17/SQuIRE). SQuIRE is an accurate and user-friendly tool that can be used for a variety of species. We applied SQuIRE to RNA-seq from normal mouse tissues and a Drosophila model of amyotrophic lateral sclerosis. In both model organisms, we recapitulated previously reported TE subfamily expression levels and revealed locus-specific TE expression. We also identified differences in TE transcription patterns relating to transcript type, gene expression and RNA splicing that would be lost with other approaches using subfamily-level analyses. Altogether, our findings illustrate the importance of studying TE transcription with locus-level resolution.
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Affiliation(s)
- Wan R Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel Ardeljan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clarissa N Pacyna
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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15
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Chale RS, Ghiam N, McNamara SA, Jimenez JJ. Transmissible Cancers and Immune Downregulation in Tasmanian Devil ( Sacrophilus harrisii) and Canine Populations. Comp Med 2019; 69:291-298. [PMID: 31387668 DOI: 10.30802/aalas-cm-18-000129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Known as devil facial tumor disease (DFTD) and canine transmissible venereal tumor (CTVT), transmissible cancer occurs in both Tasmanian devil and canine populations, respectively. Both malignancies show remarkable ability to be transmitted as allografts into subsequent hosts. How DFTD and CTVT avoid detection by immunocompetent hosts is of particular interest, given that these malignancies are rarely seen in other species in nature. Both of these transmissible cancers can downregulate the host immune system, enabling proliferation. DFTD is characterized by epigenetic modifications to the DNA promoter regions of β₂microglobulin, transporters associated with antigen processing 1 and 2, MHC I, and MHC II-crucial proteins required in the detection and surveillance of foreign material. Downregulation during DFTD may be achieved by altering the activity of histone deacetylases. DFTD has caused widespread destruction of devil populations, placing the species on the brink of extinction. CTVT demonstrates a proliferative phase, during which the tumor evades immune detection, allowing it to proliferate, and a regressive phase when hosts mount an effective immune response. Alteration of TGFβ signaling in CTVT likely impedes the antigen-processing capabilities of canine hosts in addition to hindering the ability of natural killer cells to detect immune system downregulation. Immunosuppressive cytokines such as CXCL7 may contribute to a favorable microenvironment that supports the proliferation of CTVT. When viewed from an evolutionary paradigm, both DFTD and CTVT may conform to a model of host-parasite coevolution. Furthermore, various genetic features, such as genetically active transposons in CTVT and chromosomal rearrangements in DFTD, play important roles in promoting the survival of these disease agents. Understanding the mode of transmission for these transmissible cancers may shed light on mechanisms for human malignancies and reveal opportunities for treatment in the future.
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16
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Sanchez-Luque FJ, Kempen MJHC, Gerdes P, Vargas-Landin DB, Richardson SR, Troskie RL, Jesuadian JS, Cheetham SW, Carreira PE, Salvador-Palomeque C, García-Cañadas M, Muñoz-Lopez M, Sanchez L, Lundberg M, Macia A, Heras SR, Brennan PM, Lister R, Garcia-Perez JL, Ewing AD, Faulkner GJ. LINE-1 Evasion of Epigenetic Repression in Humans. Mol Cell 2019; 75:590-604.e12. [PMID: 31230816 DOI: 10.1016/j.molcel.2019.05.024] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 04/08/2019] [Accepted: 05/15/2019] [Indexed: 02/07/2023]
Abstract
Epigenetic silencing defends against LINE-1 (L1) retrotransposition in mammalian cells. However, the mechanisms that repress young L1 families and how L1 escapes to cause somatic genome mosaicism in the brain remain unclear. Here we report that a conserved Yin Yang 1 (YY1) transcription factor binding site mediates L1 promoter DNA methylation in pluripotent and differentiated cells. By analyzing 24 hippocampal neurons with three distinct single-cell genomic approaches, we characterized and validated a somatic L1 insertion bearing a 3' transduction. The source (donor) L1 for this insertion was slightly 5' truncated, lacked the YY1 binding site, and was highly mobile when tested in vitro. Locus-specific bisulfite sequencing revealed that the donor L1 and other young L1s with mutated YY1 binding sites were hypomethylated in embryonic stem cells, during neurodifferentiation, and in liver and brain tissue. These results explain how L1 can evade repression and retrotranspose in the human body.
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Affiliation(s)
- Francisco J Sanchez-Luque
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain.
| | - Marie-Jeanne H C Kempen
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Patricia Gerdes
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Dulce B Vargas-Landin
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, the University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Sandra R Richardson
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Robin-Lee Troskie
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - J Samuel Jesuadian
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Seth W Cheetham
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Patricia E Carreira
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Carmen Salvador-Palomeque
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Marta García-Cañadas
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain
| | - Martin Muñoz-Lopez
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain
| | - Laura Sanchez
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain
| | - Mischa Lundberg
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Angela Macia
- Department of Pediatrics/Rady Children's Hospital San Diego, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sara R Heras
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain; Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Paul M Brennan
- Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, EH4 2XR, UK
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, the University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Jose L Garcia-Perez
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Adam D Ewing
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
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17
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Bodea GO, McKelvey EGZ, Faulkner GJ. Retrotransposon-induced mosaicism in the neural genome. Open Biol 2019; 8:rsob.180074. [PMID: 30021882 PMCID: PMC6070720 DOI: 10.1098/rsob.180074] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022] Open
Abstract
Over the past decade, major discoveries in retrotransposon biology have depicted the neural genome as a dynamic structure during life. In particular, the retrotransposon LINE-1 (L1) has been shown to be transcribed and mobilized in the brain. Retrotransposition in the developing brain, as well as during adult neurogenesis, provides a milieu in which neural diversity can arise. Dysregulation of retrotransposon activity may also contribute to neurological disease. Here, we review recent reports of retrotransposon activity in the brain, and discuss the temporal nature of retrotransposition and its regulation in neural cells in response to stimuli. We also put forward hypotheses regarding the significance of retrotransposons for brain development and neurological function, and consider the potential implications of this phenomenon for neuropsychiatric and neurodegenerative conditions.
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Affiliation(s)
- Gabriela O Bodea
- Mater Research Institute-University of Queensland, TRI Building, Brisbane, Queensland 4102, Australia .,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Eleanor G Z McKelvey
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, TRI Building, Brisbane, Queensland 4102, Australia .,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
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18
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Dynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation. Mol Cell Biol 2019; 39:MCB.00499-18. [PMID: 30692270 PMCID: PMC6425141 DOI: 10.1128/mcb.00499-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/11/2019] [Indexed: 01/28/2023] Open
Abstract
The retrotransposon LINE-1 (L1) is a significant source of endogenous mutagenesis in humans. In each individual genome, a few retrotransposition-competent L1s (RC-L1s) can generate new heritable L1 insertions in the early embryo, primordial germ line, and germ cells. L1 retrotransposition can also occur in the neuronal lineage and cause somatic mosaicism. Although DNA methylation mediates L1 promoter repression, the temporal pattern of methylation applied to individual RC-L1s during neurogenesis is unclear. Here, we identified a de novo L1 insertion in a human induced pluripotent stem cell (hiPSC) line via retrotransposon capture sequencing (RC-seq). The L1 insertion was full-length and carried 5' and 3' transductions. The corresponding donor RC-L1 was part of a large and recently active L1 transduction family and was highly mobile in a cultured-cell L1 retrotransposition reporter assay. Notably, we observed distinct and dynamic DNA methylation profiles for the de novo L1 and members of its extended transduction family during neuronal differentiation. These experiments reveal how a de novo L1 insertion in a pluripotent stem cell is rapidly recognized and repressed, albeit incompletely, by the host genome during neurodifferentiation, while retaining potential for further retrotransposition.
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19
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Steranka JP, Tang Z, Grivainis M, Huang CRL, Payer LM, Rego FOR, Miller TLA, Galante PAF, Ramaswami S, Heguy A, Fenyö D, Boeke JD, Burns KH. Transposon insertion profiling by sequencing (TIPseq) for mapping LINE-1 insertions in the human genome. Mob DNA 2019; 10:8. [PMID: 30899333 PMCID: PMC6407172 DOI: 10.1186/s13100-019-0148-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/14/2019] [Indexed: 12/14/2022] Open
Abstract
Background Transposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as a source of structural variation and somatic mutation. To this end, laboratories have developed strategies to selectively amplify or otherwise enrich transposable element insertion sites in genomic DNA. Results Here we describe a technique, Transposon Insertion Profiling by sequencing (TIPseq), to map Long INterspersed Element 1 (LINE-1, L1) retrotransposon insertions in the human genome. This method uses vectorette PCR to amplify species-specific L1 (L1PA1) insertion sites followed by paired-end Illumina sequencing. In addition to providing a step-by-step molecular biology protocol, we offer users a guide to our pipeline for data analysis, TIPseqHunter. Our recent studies in pancreatic and ovarian cancer demonstrate the ability of TIPseq to identify invariant (fixed), polymorphic (inherited variants), as well as somatically-acquired L1 insertions that distinguish cancer genomes from a patient’s constitutional make-up. Conclusions TIPseq provides an approach for amplifying evolutionarily young, active transposable element insertion sites from genomic DNA. Our rationale and variations on this protocol may be useful to those mapping L1 and other mobile elements in complex genomes. Electronic supplementary material The online version of this article (10.1186/s13100-019-0148-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jared P Steranka
- 1Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Zuojian Tang
- 3Department for Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016 USA.,4Institute for Systems Genetics, NYU Langone Health, New York, NY 10016 USA
| | - Mark Grivainis
- 3Department for Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016 USA.,4Institute for Systems Genetics, NYU Langone Health, New York, NY 10016 USA
| | - Cheng Ran Lisa Huang
- 2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Lindsay M Payer
- 1Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Fernanda O R Rego
- 5Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Thiago Luiz Araujo Miller
- 5Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil.,Departamento de Bioquímica, Instituto de Química, Universidade de São Paul, São Paulo, Brazil
| | - Pedro A F Galante
- 5Centro de Oncologia Molecular, Hospital Sírio-Libanês, São Paulo, Brazil
| | - Sitharam Ramaswami
- 7Genome Technology Center, Division of Advanced Research Technologies, NYU Langone Health, New York, NY USA
| | - Adriana Heguy
- 7Genome Technology Center, Division of Advanced Research Technologies, NYU Langone Health, New York, NY USA
| | - David Fenyö
- 3Department for Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016 USA.,4Institute for Systems Genetics, NYU Langone Health, New York, NY 10016 USA
| | - Jef D Boeke
- 4Institute for Systems Genetics, NYU Langone Health, New York, NY 10016 USA
| | - Kathleen H Burns
- 1Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA.,2McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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20
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Rey-Iglesia A, Gopalakrishan S, Carøe C, Alquezar-Planas DE, Ahlmann Nielsen A, Röder T, Bruhn Pedersen L, Naesborg-Nielsen C, Sinding MHS, Fredensborg Rath M, Li Z, Petersen B, Gilbert MTP, Bunce M, Mourier T, Hansen AJ. MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements. Mol Ecol Resour 2019; 19:512-525. [PMID: 30575257 DOI: 10.1111/1755-0998.12984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022]
Abstract
In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome-scale studies to characterize both model and non-model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome-wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site-associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms-enabling the exploration of diverse evolutionary and conservation questions.
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Affiliation(s)
- Alba Rey-Iglesia
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Shyam Gopalakrishan
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - David E Alquezar-Planas
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Anne Ahlmann Nielsen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Timo Röder
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lene Bruhn Pedersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Mikkel-Holger S Sinding
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | | | - Zhipeng Li
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Kedah, Malaysia
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Tobias Mourier
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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21
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Abstract
Transposable elements (TEs) are low-complexity elements (e.g., LINEs, SINEs, SVAs, and HERVs) that make up to two-thirds of the human genome. There is mounting evidence that TEs play an essential role in molecular functions that influence genomic plasticity and gene expression regulation. With the advent of next-generation sequencing approaches, our understanding of the relationship between TEs and psychiatric disorders will greatly improve. In this chapter, the Authors comprehensively summarize the state-of the-art of TE research in animal models and humans supporting a framework in which TEs play a functional role in mechanisms affecting a variety of behaviors, including neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Finally, the Authors discuss recent therapeutic applications raised from the increasing experimental evidence on TE functional mechanisms.
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Affiliation(s)
- G Guffanti
- McLean Hospital - Harvard Medical School, Belmont, MA, USA.
| | - A Bartlett
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA
| | - P DeCrescenzo
- McLean Hospital - Harvard Medical School, Belmont, MA, USA
| | - F Macciardi
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, USA
| | - R Hunter
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA
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22
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Stringer JM, Forster SC, Qu Z, Prokopuk L, O'Bryan MK, Gardner DK, White SJ, Adelson D, Western PS. Reduced PRC2 function alters male germline epigenetic programming and paternal inheritance. BMC Biol 2018; 16:104. [PMID: 30236109 PMCID: PMC6149058 DOI: 10.1186/s12915-018-0569-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/28/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Defining the mechanisms that establish and regulate the transmission of epigenetic information from parent to offspring is critical for understanding disease heredity. Currently, the molecular pathways that regulate epigenetic information in the germline and its transmission to offspring are poorly understood. RESULTS Here we provide evidence that Polycomb Repressive Complex 2 (PRC2) regulates paternal inheritance. Reduced PRC2 function in mice resulted in male sub-fertility and altered epigenetic and transcriptional control of retrotransposed elements in foetal male germ cells. Males with reduced PRC2 function produced offspring that over-expressed retrotransposed pseudogenes and had altered preimplantation embryo cleavage rates and cell cycle control. CONCLUSION This study reveals a novel role for the histone-modifying complex, PRC2, in paternal intergenerational transmission of epigenetic effects on offspring, with important implications for understanding disease inheritance.
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Affiliation(s)
- Jessica M Stringer
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia
- Department of Anatomy and Developmental Biology, Ovarian Biology Laboratory, Biomedicine Discovery Institute, Monash University, Melbourne, 3168, Australia
| | - Samuel C Forster
- Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia
- Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia
| | - Zhipeng Qu
- Bioinformatics and Computational Genetics, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Lexie Prokopuk
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia
- Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia
| | - Moira K O'Bryan
- School of Biological Sciences, Monash University, Clayton, Victoria, 3168, Australia
| | - David K Gardner
- School of BioSciences, University of Melbourne, Parkville, Australia
| | - Stefan J White
- Department of Human Genetics, Leiden Genome Technology Centre, Leiden University Medical Center, Leiden, the Netherlands
| | - David Adelson
- Bioinformatics and Computational Genetics, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Patrick S Western
- Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, Victoria, 3168, Australia.
- Molecular and Translational Science, Monash University, Clayton, Victoria, 3168, Australia.
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23
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Faulkner GJ, Billon V. L1 retrotransposition in the soma: a field jumping ahead. Mob DNA 2018; 9:22. [PMID: 30002735 PMCID: PMC6035798 DOI: 10.1186/s13100-018-0128-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/27/2018] [Indexed: 12/13/2022] Open
Abstract
Retrotransposons are transposable elements (TEs) capable of "jumping" in germ, embryonic and tumor cells and, as is now clearly established, in the neuronal lineage. Mosaic TE insertions form part of a broader landscape of somatic genome variation and hold significant potential to generate phenotypic diversity, in the brain and elsewhere. At present, the LINE-1 (L1) retrotransposon family appears to be the most active autonomous TE in most mammals, based on experimental data obtained from disease-causing L1 mutations, engineered L1 reporter systems tested in cultured cells and transgenic rodents, and single-cell genomic analyses. However, the biological consequences of almost all somatic L1 insertions identified thus far remain unknown. In this review, we briefly summarize the current state-of-the-art in the field, including estimates of L1 retrotransposition rate in neurons. We bring forward the hypothesis that an extensive subset of retrotransposition-competent L1s may be de-repressed and mobile in the soma but largely inactive in the germline. We discuss recent reports of non-canonical L1-associated sequence variants in the brain and propose that the elevated L1 DNA content reported in several neurological disorders may predominantly comprise accumulated, unintegrated L1 nucleic acids, rather than somatic L1 insertions. Finally, we consider the main objectives and obstacles going forward in elucidating the biological impact of somatic retrotransposition.
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Affiliation(s)
- Geoffrey J. Faulkner
- Mater Research Institute – University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072 Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
| | - Victor Billon
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
- Biology Department, École Normale Supérieure Paris-Saclay, 61 Avenue du Président Wilson, 94230 Cachan, France
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24
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Yu Q, Zhang W, Zhang X, Zeng Y, Wang Y, Wang Y, Xu L, Huang X, Li N, Zhou X, Lu J, Guo X, Li G, Hou Y, Liu S, Li B. Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection. Gigascience 2018; 6:1-11. [PMID: 28938719 PMCID: PMC5603766 DOI: 10.1093/gigascience/gix066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 07/20/2017] [Indexed: 12/20/2022] Open
Abstract
Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs. We demonstrate that SID is suitable for high-depth whole-genome sequencing data using paired-end reads obtained from simulated and real datasets. We construct a comprehensive RIP database using a large population of 90 Han Chinese individuals with a mean ×68 depth per individual. In total, we identify 9342 recent RIPs, and 8433 of these RIPs are novel compared with dbRIP, including 5826 Alu, 2169 long interspersed nuclear element 1 (L1), 383 SVA, and 55 long terminal repeats. Among the 9342 RIPs, 4828 were located in gene regions and 5 were located in protein-coding regions. We demonstrate that RIPs can, in principle, be an informative resource to perform population evolution and phylogenetic analyses. Taking the demographic effects into account, we identify a weak negative selection on SVA and L1 but an approximately neutral selection for Alu elements based on the frequency spectrum of RIPs. SID is a powerful open-source program for the detection of non-reference RIPs. We built a non-reference RIP dataset that greatly enhanced the diversity of RIPs detected in the general population, and it should be invaluable to researchers interested in many aspects of human evolution, genetics, and disease. As a proof of concept, we demonstrate that the RIPs can be used as biomarkers in a similar way as single nucleotide polymorphisms.
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Affiliation(s)
- Qichao Yu
- BGI Education Center, UCAS: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Wei Zhang
- BGI Education Center, UCAS: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Xiaolong Zhang
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yongli Zeng
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yeming Wang
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yanhui Wang
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Liqin Xu
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Xiaoyun Huang
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Nannan Li
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Xinlan Zhou
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Jie Lu
- BGI College: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Xiaosen Guo
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Guibo Li
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,Department of Biology, University of Copenhagen: Nørregade 10, Copenhagen 1165, Denmark
| | - Yong Hou
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,Department of Biology, University of Copenhagen: Nørregade 10, Copenhagen 1165, Denmark
| | - Shiping Liu
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,School of Biology and Biological Engineering, SCUT: Postdoctoral Apartment Building, South China University of Technology, Wushan RD., TianHe District, Guangzhou, 510640, China
| | - Bo Li
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,BGI-Forensics: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
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25
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Rajagopalan M, Balasubramanian S, Ramaswamy A. Insights into the RNA binding mechanism of human L1-ORF1p: a molecular dynamics study. MOLECULAR BIOSYSTEMS 2018; 13:1728-1743. [PMID: 28714502 DOI: 10.1039/c7mb00358g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The recognition and binding of nucleic acids by ORF1p, an L1 retrotransposon protein, have not yet been clearly understood due to the lack of structural knowledge. The present study attempts to identify the probable single-stranded RNA binding pathway of trimeric ORF1p using computational methods like ligand mapping methodology combined with molecular dynamics simulations. Using the ligand mapping methodology, the possible RNA interacting sites on the surface of the trimeric ORF1p were identified. The crystal structure of the ORF1p timer and an RNA molecule of 29 nucleotide bases in length were used to generate the structure of the ORF1p complex based on information on predicted binding sites as well as the functional states of the CTD. The various complexes of ORF1p-RNA were generated using polyU, polyA and L1RNA sequences and were simulated for a period of 75 ns. The observed stable interaction pattern was used to propose the possible binding pathway. Based on the binding free energy for complex formation, both polyU and L1RNA complexes were identified as stable complexes, while the complex formed with polyA was the least stable one. Furthermore, the importance of the residues in the CC domain (Lys137 and Arg141), the RRM loop (Arg206, Arg210 and Arg211) and the CTD (Arg 261 and Arg262) of all three chains in stabilizing the wrapped RNA has been highlighted in this study. The presence of several electrostatic interactions including H-bond interactions increases the affinity towards RNA and hence plays a vital role in retaining the wrapped position of RNA around ORF1p. Altogether, this study presents one of the possible RNA binding pathways of ORF1p and clearly highlights the functional state of ORF1p visited during RNA binding.
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Affiliation(s)
- Muthukumaran Rajagopalan
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry 605014, India.
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26
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Kvikstad EM, Piazza P, Taylor JC, Lunter G. A high throughput screen for active human transposable elements. BMC Genomics 2018; 19:115. [PMID: 29390960 PMCID: PMC5796560 DOI: 10.1186/s12864-018-4485-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/16/2018] [Indexed: 11/30/2022] Open
Abstract
Background Transposable elements (TEs) are mobile genetic sequences that randomly propagate within their host’s genome. This mobility has the potential to affect gene transcription and cause disease. However, TEs are technically challenging to identify, which complicates efforts to assess the impact of TE insertions on disease. Here we present a targeted sequencing protocol and computational pipeline to identify polymorphic and novel TE insertions using next-generation sequencing: TE-NGS. The method simultaneously targets the three subfamilies that are responsible for the majority of recent TE activity (L1HS, AluYa5/8, and AluYb8/9) thereby obviating the need for multiple experiments and reducing the amount of input material required. Results Here we describe the laboratory protocol and detection algorithm, and a benchmark experiment for the reference genome NA12878. We demonstrate a substantial enrichment for on-target fragments, and high sensitivity and precision to both reference and NA12878-specific insertions. We report 17 previously unreported loci for this individual which are supported by orthogonal long-read evidence, and we identify 1470 polymorphic and novel TEs in 12 additional samples that were previously undocumented in databases of insertion polymorphisms. Conclusions We anticipate that future applications of TE-NGS alongside exome sequencing of patients with sporadic disease will reduce the number of unresolved cases, and improve estimates of the contribution of TEs to human genetic disease. Electronic supplementary material The online version of this article (10.1186/s12864-018-4485-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erika M Kvikstad
- Wellcome Trust Centre for Human Genetics, Oxford, UK. .,National Institute for Health Research Comprehensive Biomedical Research Centre, Oxford, UK.
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, Oxford, UK.,Department of Medicine, Imperial College London, London, UK
| | - Jenny C Taylor
- Wellcome Trust Centre for Human Genetics, Oxford, UK.,National Institute for Health Research Comprehensive Biomedical Research Centre, Oxford, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, Oxford, UK
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27
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Analysis of LINE-1 Elements in DNA from Postmortem Brains of Individuals with Schizophrenia. Neuropsychopharmacology 2017; 42:2602-2611. [PMID: 28585566 PMCID: PMC5686486 DOI: 10.1038/npp.2017.115] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 05/10/2017] [Accepted: 05/31/2017] [Indexed: 11/08/2022]
Abstract
Whereas some rare genetic variants convey high risk for schizophrenia (SZ), common alleles conveying even moderate risk remain elusive. Long interspersed element-1s (L1) are mobile retrotransposons comprising ~17% of the human genome. L1 retrotransposition can cause somatic mosaicism during neurodevelopment by insertional mutagenesis. We hypothesized that, compared to controls, patients diagnosed with schizophrenia (PDS) may have increased numbers of deleterious L1 insertions, perhaps occurring de novo, in brain-expressed genes of dorsolateral prefrontal cortex (DLPFC) neurons. Neuronal and non-neuronal nuclei were separated by fluorescence-activated cell sorting from postmortem DLPFC of 36 PDS and 26 age-matched controls. Genomic sequences flanking the 3'-side of L1s were amplified from neuronal DNA, and neuronal L1 libraries were sequenced. Aligned sequences were analyzed for L1 insertions using custom bioinformatics programs. Ontology and pathway analyses were done on lists of genes putatively disrupted by L1s in PDS and controls. Cellular or population allele frequencies of L1s were assessed by droplet digital PCR or Taqman genotyping. We observed a statistically significant increase in the proportion of intragenic novel L1s in DLPFC of PDS. We found over-representation of L1 insertions within the gene ontologies 'cell projection' and 'postsynaptic membrane' in the gene lists derived from PDS samples, but not from controls. Cellular allele frequencies of examined L1 insertions indicated heterozygosity in genomes of DLPFC cells. An L1 within ERI1 exoribonuclease family member 3 (ERI3) was found to associate with SZ. These results extend prior work documenting increased L1 genetic burden in the brains of PDS and also identify unique genes that may provide new insight into the pathophysiology of schizophrenia.
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28
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Sokolowski M, Chynces M, deHaro D, Christian CM, Belancio VP. Truncated ORF1 proteins can suppress LINE-1 retrotransposition in trans. Nucleic Acids Res 2017; 45:5294-5308. [PMID: 28431148 PMCID: PMC5605252 DOI: 10.1093/nar/gkx211] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/12/2017] [Indexed: 01/15/2023] Open
Abstract
Long interspersed element 1 (L1) is an autonomous non-LTR retroelement that is active in mammalian genomes. Although retrotranspositionally incompetent and functional L1 loci are present in the same genomes, it remains unknown whether non-functional L1s have any trans effect on mobilization of active elements. Using bioinformatic analysis, we identified over a thousand of human L1 loci containing at least one stop codon in their ORF1 sequence. RNAseq analysis confirmed that many of these loci are expressed. We demonstrate that introduction of equivalent stop codons in the full-length human L1 sequence leads to the expression of truncated ORF1 proteins. When supplied in trans some truncated human ORF1 proteins suppress human L1 retrotransposition. This effect requires the N-terminus and coiled-coil domain (C-C) as mutations within the ORF1p C-C domain abolish the suppressive effect of truncated proteins on L1 retrotransposition. We demonstrate that the expression levels and length of truncated ORF1 proteins influence their ability to suppress L1 retrotransposition. Taken together these findings suggest that L1 retrotransposition may be influenced by coexpression of defective L1 loci and that these L1 loci may reduce accumulation of de novo L1 integration events.
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Affiliation(s)
- Mark Sokolowski
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - May Chynces
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Dawn deHaro
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Claiborne M Christian
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Victoria P Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
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29
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Lai X, Schnable JC, Liao Z, Xu J, Zhang G, Li C, Hu E, Rong T, Xu Y, Lu Y. Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize. BMC Genomics 2017; 18:702. [PMID: 28877662 PMCID: PMC5588714 DOI: 10.1186/s12864-017-4103-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/31/2017] [Indexed: 12/20/2022] Open
Abstract
Background Maize was originally domesticated in a tropical environment but is now widely cultivated at temperate latitudes. Temperate and tropical maize populations have diverged both genotypically and phenotypically. Tropical maize lines grown in temperate environments usually exhibit delayed flowering, pollination, and seed set, which reduces their grain yield relative to temperate adapted maize lines. One potential mechanism by which temperate maize may have adapted to a new environment is novel transposable element insertions, which can influence gene regulation. Recent advances in sequencing technology have made it possible to study variation in transposon content and insertion location in large sets of maize lines. Results In total, 274,408 non-redundant TEs (NRTEs) were identified using resequencing data generated from 83 maize inbred lines. The locations of DNA TEs and copia-superfamily retrotransposons showed significant positive correlations with gene density and genetic recombination rates, whereas gypsy-superfamily retrotransposons showed a negative correlation with these two parameters. Compared to tropical maize, temperate maize had fewer unique NRTEs but higher insertion frequency, lower background recombination rates, and higher linkage disequilibrium, with more NRTEs close to flowering and stress-related genes in the genome. Association mapping demonstrated that the presence/absence of 48 NRTEs was associated with flowering time and that expression of neighboring genes differed between haplotypes where a NRTE was present or absent. Conclusions This study suggests that NRTEs may have played an important role in creating the variation in gene regulation that enabled the rapid adaptation of maize to diverse environments. Electronic supplementary material The online version of this article (10.1186/s12864-017-4103-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xianjun Lai
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Zhengqiao Liao
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Gengyun Zhang
- Bejing Genomics Institute (BGI)-Shenzhen, Shenzhen, 518083, China
| | - Chuan Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Erliang Hu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Tingzhao Rong
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Haidian, Beijing, 100081, China. .,International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, CP, 56130, México.
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, 611130, China.
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30
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L1 Mosaicism in Mammals: Extent, Effects, and Evolution. Trends Genet 2017; 33:802-816. [PMID: 28797643 DOI: 10.1016/j.tig.2017.07.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/30/2017] [Accepted: 07/14/2017] [Indexed: 10/19/2022]
Abstract
The retrotransposon LINE-1 (long interspersed element 1, L1) is a transposable element that has extensively colonized the mammalian germline. L1 retrotransposition can also occur in somatic cells, causing genomic mosaicism, as well as in cancer. However, the extent of L1-driven mosaicism arising during ontogenesis is unclear. We discuss here recent experimental data which, at a minimum, fully substantiate L1 mosaicism in early embryonic development and neural cells, including post-mitotic neurons. We also consider the possible biological impact of somatic L1 insertions in neurons, the existence of donor L1s that are highly active ('hot') in specific spatiotemporal niches, and the evolutionary selection of donor L1s driving neuronal mosaicism.
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31
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McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data. G3-GENES GENOMES GENETICS 2017. [PMID: 28637810 PMCID: PMC5555480 DOI: 10.1534/g3.117.043893] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Transposable element (TE) insertions are among the most challenging types of variants to detect in genomic data because of their repetitive nature and complex mechanisms of replication . Nevertheless, the recent availability of large resequencing data sets has spurred the development of many new methods to detect TE insertions in whole-genome shotgun sequences. Here we report an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote, Saccharomyces cerevisiae We find substantial variation among McClintock component methods in their ability to detect nonreference TEs in the yeast genome, but show that nonreference TEs at nearly all biologically realistic locations can be detected in simulated data by combining multiple methods that use split-read and read-pair evidence. In general, our results reveal that split-read methods detect fewer nonreference TE insertions than read-pair methods, but generally have much higher positional accuracy. Analysis of a large sample of real yeast genomes reveals that most McClintock component methods can recover known aspects of TE biology in yeast such as the transpositional activity status of families, target preferences, and target site duplication structure, albeit with varying levels of accuracy. Our work provides a general framework for integrating and analyzing results from multiple TE detection methods, as well as useful guidance for researchers studying TEs in yeast resequencing data.
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32
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Abstract
Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1). LINE-1 sequences are self-propagating, protein-coding retrotransposons, and their activity results in somatically acquired insertions in cancer genomes. Altered expression of transposable elements and animation of genomic LINE-1 sequences appear to be hallmarks of cancer, and can be responsible for driving mutations in tumorigenesis.
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Affiliation(s)
- Kathleen H Burns
- Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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33
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Transposable elements in cancer. NATURE REVIEWS. CANCER 2017. [PMID: 28642606 DOI: 10.1038/nrc.2017.35+[doi]] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1). LINE-1 sequences are self-propagating, protein-coding retrotransposons, and their activity results in somatically acquired insertions in cancer genomes. Altered expression of transposable elements and animation of genomic LINE-1 sequences appear to be hallmarks of cancer, and can be responsible for driving mutations in tumorigenesis.
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34
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Doyle GA, Doucet-O'Hare TT, Hammond MJ, Crist RC, Ewing AD, Ferraro TN, Mash DC, Kazazian HH, Berrettini WH. Reading LINEs within the cocaine addicted brain. Brain Behav 2017; 7:e00678. [PMID: 28523221 PMCID: PMC5434184 DOI: 10.1002/brb3.678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 01/19/2017] [Accepted: 02/13/2017] [Indexed: 12/22/2022] Open
Abstract
INTRODUCTION Long interspersed element (LINE)-1 (L1) is a type of retrotransposon capable of mobilizing into new genomic locations. Often studied in Mendelian diseases or cancer, L1s may also cause somatic mutation in the developing central nervous system. Recent reports showed L1 transcription was activated in brains of cocaine-treated mice, and L1 retrotransposition was increased in cocaine-treated neuronal cell cultures. We hypothesized that the predisposition to cocaine addiction may result from inherited L1s or somatic L1 mobilization in the brain. METHODS Postmortem medial prefrontal cortex (mPFC) tissue from 30 CA and 30 control individuals was studied. An Alexafluor488-labeled NeuN antibody and fluorescence activated nuclei sorting were used to separate neuronal from non-neuronal cell nuclei. L1s and their 3' flanking sequences were amplified from neuronal and non-neuronal genomic DNA (gDNA) using L1-seq. L1 DNA libraries from the neuronal gDNA were sequenced on an Illumina HiSeq2000. Sequences aligned to the hg19 human genome build were analyzed for L1 insertions using custom "L1-seq" bioinformatics programs. RESULTS Previously uncataloged L1 insertions, some validated by PCR, were detected in neurons from both CA and control brain samples. Steady-state L1 mRNA levels in CA and control mPFC were also assessed. Gene ontology and pathway analyses were used to assess relationships between genes putatively disrupted by novel L1s in CA and control individuals. L1 insertions in CA samples were enriched in gene ontologies and pathways previously associated with CA. CONCLUSIONS We conclude that neurons in the mPFC harbor L1 insertions that have the potential to influence predisposition to CA.
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Affiliation(s)
- Glenn A Doyle
- Department of Psychiatry Center for Neurobiology and Behavior University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | | | - Matthew J Hammond
- Department of Psychiatry Center for Neurobiology and Behavior University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Richard C Crist
- Department of Psychiatry Center for Neurobiology and Behavior University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
| | - Adam D Ewing
- Mater Research Institute - University of Queensland Brisbane Qld Australia
| | - Thomas N Ferraro
- Department of Biomedical Sciences Cooper Medical School of Rowan University Camden NJ USA
| | - Deborah C Mash
- Department of Neurology, Brain Endowment Bank™ University of Miami Miller School of Medicine Miami FL USA
| | - Haig H Kazazian
- Johns Hopkins School of Medicine Institute of Genetic Medicine Baltimore MD USA
| | - Wade H Berrettini
- Department of Psychiatry Center for Neurobiology and Behavior University of Pennsylvania Perelman School of Medicine Philadelphia PA USA
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35
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Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer. Proc Natl Acad Sci U S A 2017; 114:E733-E740. [PMID: 28096347 DOI: 10.1073/pnas.1619797114] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mammalian genomes are replete with interspersed repeats reflecting the activity of transposable elements. These mobile DNAs are self-propagating, and their continued transposition is a source of both heritable structural variation as well as somatic mutation in human genomes. Tailored approaches to map these sequences are useful to identify insertion alleles. Here, we describe in detail a strategy to amplify and sequence long interspersed element-1 (LINE-1, L1) retrotransposon insertions selectively in the human genome, transposon insertion profiling by next-generation sequencing (TIPseq). We also report the development of a machine-learning-based computational pipeline, TIPseqHunter, to identify insertion sites with high precision and reliability. We demonstrate the utility of this approach to detect somatic retrotransposition events in high-grade ovarian serous carcinoma.
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36
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Muñoz-Lopez M, Vilar-Astasio R, Tristan-Ramos P, Lopez-Ruiz C, Garcia-Pérez JL. Study of Transposable Elements and Their Genomic Impact. Methods Mol Biol 2016; 1400:1-19. [PMID: 26895043 DOI: 10.1007/978-1-4939-3372-3_1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Transposable elements (TEs) have been considered traditionally as junk DNA, i.e., DNA sequences that despite representing a high proportion of genomes had no evident cellular functions. However, over the last decades, it has become undeniable that not only TE-derived DNA sequences have (and had) a fundamental role during genome evolution, but also TEs have important implications in the origin and evolution of many genomic disorders. This concise review provides a brief overview of the different types of TEs that can be found in genomes, as well as a list of techniques and methods used to study their impact and mobilization. Some of these techniques will be covered in detail in this Method Book.
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Affiliation(s)
- Martin Muñoz-Lopez
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), Avda Ilustracion 114, PTS Granada, 18016, Granada, Spain.
| | - Raquel Vilar-Astasio
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), Avda Ilustracion 114, PTS Granada, 18016, Granada, Spain
| | - Pablo Tristan-Ramos
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), Avda Ilustracion 114, PTS Granada, 18016, Granada, Spain
| | - Cesar Lopez-Ruiz
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), Avda Ilustracion 114, PTS Granada, 18016, Granada, Spain
| | - Jose L Garcia-Pérez
- -Genyo (Center for Genomics and Oncological Research), Pfizer/Universidad de Granada/Junta de Andalucia. PTS Granada, Spain-Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh,, Edinburgh, UK
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Carreira PE, Ewing AD, Li G, Schauer SN, Upton KR, Fagg AC, Morell S, Kindlova M, Gerdes P, Richardson SR, Li B, Gerhardt DJ, Wang J, Brennan PM, Faulkner GJ. Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme. Mob DNA 2016; 7:21. [PMID: 27843499 PMCID: PMC5105311 DOI: 10.1186/s13100-016-0076-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/13/2016] [Indexed: 01/23/2023] Open
Abstract
Background LINE-1 (L1) retrotransposons are a notable endogenous source of mutagenesis in mammals. Notably, cancer cells can support unusual L1 retrotransposition and L1-associated sequence rearrangement mechanisms following DNA damage. Recent reports suggest that L1 is mobile in epithelial tumours and neural cells but, paradoxically, not in brain cancers. Results Here, using retrotransposon capture sequencing (RC-seq), we surveyed L1 mutations in 14 tumours classified as glioblastoma multiforme (GBM) or as a lower grade glioma. In four GBM tumours, we characterised one probable endonuclease-independent L1 insertion, two L1-associated rearrangements and one likely Alu-Alu recombination event adjacent to an L1. These mutations included PCR validated intronic events in MeCP2 and EGFR. Despite sequencing L1 integration sites at up to 250× depth by RC-seq, we found no tumour-specific, endonuclease-dependent L1 insertions. Whole genome sequencing analysis of the tumours carrying the MeCP2 and EGFR L1 mutations also revealed no endonuclease-dependent L1 insertions. In a complementary in vitro assay, wild-type and endonuclease mutant L1 reporter constructs each mobilised very inefficiently in four cultured GBM cell lines. Conclusions These experiments altogether highlight the consistent absence of canonical L1 retrotransposition in GBM tumours and cultured cell lines, as well as atypical L1-associated sequence rearrangements following DNA damage in vivo. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0076-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Patricia E Carreira
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Adam D Ewing
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Guibo Li
- BGI-Shenzhen, Shenzhen, 518083 China.,Department of Biology and the Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, 1599 Denmark
| | - Stephanie N Schauer
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Kyle R Upton
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia.,School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072 Australia
| | - Allister C Fagg
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Santiago Morell
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Michaela Kindlova
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Patricia Gerdes
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Sandra R Richardson
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Bo Li
- BGI-Shenzhen, Shenzhen, 518083 China
| | - Daniel J Gerhardt
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083 China.,Department of Biology and the Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, 1599 Denmark
| | - Paul M Brennan
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, EH42XR UK
| | - Geoffrey J Faulkner
- Mater Research Institute - University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia.,Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
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Chawla V, Kumar R, Shankar R. Identifying wrong assemblies in de novo short read primary sequence assembly contigs. J Biosci 2016; 41:455-74. [PMID: 27581937 DOI: 10.1007/s12038-016-9630-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
With the advent of short-reads-based genome sequencing approaches, large number of organisms are being sequenced all over the world. Most of these assemblies are done using some de novo short read assemblers and other related approaches. However, the contigs produced this way are prone to wrong assembly. So far, there is a conspicuous dearth of reliable tools to identify mis-assembled contigs. Mis-assemblies could result from incorrectly deleted or wrongly arranged genomic sequences. In the present work various factors related to sequence, sequencing and assembling have been assessed for their role in causing mis-assembly by using different genome sequencing data. Finally, some mis-assembly detecting tools have been evaluated for their ability to detect the wrongly assembled primary contigs, suggesting a lot of scope for improvement in this area. The present work also proposes a simple unsupervised learning-based novel approach to identify mis-assemblies in the contigs which was found performing reasonably well when compared to the already existing tools to report mis-assembled contigs. It was observed that the proposed methodology may work as a complementary system to the existing tools to enhance their accuracy.
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Affiliation(s)
- Vandna Chawla
- Studio of Computational Biology and Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
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Wei B, Liu H, Liu X, Xiao Q, Wang Y, Zhang J, Hu Y, Liu Y, Yu G, Huang Y. Genome-wide characterization of non-reference transposons in crops suggests non-random insertion. BMC Genomics 2016; 17:536. [PMID: 27485608 PMCID: PMC4971691 DOI: 10.1186/s12864-016-2847-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 06/20/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Transposons (transposable elements or TEs) are DNA sequences that can change their position within the genome. A large number of TEs have been identified in reference genome of each crop(named accumulated TEs), which are the important part of genome. However, whether there existed TEs with different insert positions in resequenced crop accession genomes from those of reference genome (named non-reference transposable elements, non-ref TEs), and what the characteristics (such as the number, type and distribution) are. To identify and characterize crop non-ref TEs, we analyzed non-ref TEs in more than 125 accessions from rice (Oryza sativa), maize (Zea mays) and sorghum (Sorghum bicolor) using resequenced data with paired-end mapping methods. RESULTS We identified 13,066, 23,866 and 35,679 non-ref TEs in rice, maize and sorghum, respectively. Genome-wide characterization analysis shows that most of non-ref TEs were unique and non-ref TE classes shows different among rice, maize and sorghum. We found that non-ref TEs have a strong positive correlation with gene number and have a bias toward insertion near genes, but with a preference for avoiding coding regions in maize and sorghum. The genes affected by non-ref TE insertion were functionally enriched for stress response mechanisms in all three crops. CONCLUSIONS These observations suggest that transposon insertion is not a random event and it makes genomic diversity, which may affect the intraspecific adaption and evolution of crops.
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Affiliation(s)
- Bin Wei
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hanmei Liu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xin Liu
- Beijing Genome Institute and the Key Laboratory of Genomics of the Minister of Agriculture, Shenzhen, 518083, China
| | - Qianlin Xiao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yongbin Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yinghong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guowu Yu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yubi Huang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China.
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40
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Nätt D, Thorsell A. Stress-induced transposon reactivation: a mediator or an estimator of allostatic load? ENVIRONMENTAL EPIGENETICS 2016; 2:dvw015. [PMID: 29492295 PMCID: PMC5804529 DOI: 10.1093/eep/dvw015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 06/16/2016] [Accepted: 07/27/2016] [Indexed: 05/04/2023]
Abstract
Transposons are playing an important role in the evolution of eukaryotic genomes. These endogenous virus-like elements often amplify within their host genomes in a species specific manner. Today we have limited understanding when and how these amplification events happens. What we do know is that cells have evolved multiple line of defenses to keep these potentially invasive elements under control, often involving epigenetic mechanisms such as DNA-methylation and histone modifications. Emerging evidence shows a strong link between transposon activity and human aging and diseases, as well as a role for transposons in normal brain development. Controlling transposon activity may therefore uphold the fine balance between health and disease. In this article we investigate this balance, and sets it in relation to allostatic load, which conceptualize the link between stress and the "wear and tear" of the organism that leads to aging and disease. We hypothesize that stress-induced retrotransposon reactivation in humans may be used to estimate allostatic load, and may be a possible mechanism in which transposons amplify within species genomes.
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Affiliation(s)
- Daniel Nätt
- Department of Clinical and Experimental Medicine (IKE), Linkoping University, Center for Social and Affective Neuroscience (CSAN), Linkoping, Sweden
- *Correspondence address. Tel:
+46-10-103 06 71
; E-mail:
| | - Annika Thorsell
- Department of Clinical and Experimental Medicine (IKE), Linkoping University, Center for Social and Affective Neuroscience (CSAN), Linkoping, Sweden
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Bandyopadhyay AK, Paul S, Adak S, Giri AK. Reduced LINE-1 methylation is associated with arsenic-induced genotoxic stress in children. Biometals 2016; 29:731-41. [DOI: 10.1007/s10534-016-9950-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/08/2016] [Indexed: 10/21/2022]
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Gaudi S, Guffanti G, Fallon J, Macciardi F. Epigenetic mechanisms and associated brain circuits in the regulation of positive emotions: A role for transposable elements. J Comp Neurol 2016; 524:2944-54. [PMID: 27224878 DOI: 10.1002/cne.24046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 07/21/2015] [Accepted: 05/23/2016] [Indexed: 01/12/2023]
Abstract
Epigenetic programming and reprogramming are at the heart of cellular differentiation and represent developmental and evolutionary mechanisms in both germline and somatic cell lines. Only about 2% of our genome is composed of protein-coding genes, while the remaining 98%, once considered "junk" DNA, codes for regulatory/epigenetic elements that control how genes are expressed in different tissues and across time from conception to death. While we already know that epigenetic mechanisms are at play in cancer development and in regulating metabolism (cellular and whole body), the role of epigenetics in the developing prenatal and postnatal brain, and in maintaining a proper brain activity throughout the various stages of life, in addition to having played a critical role in human evolution, is a relatively new domain of knowledge. Here we present the current state-of-the-art techniques and results of these studies within the domain of emotions, and then speculate on how genomic and epigenetic mechanisms can modify and potentially alter our emotional (limbic) brain and affect our social interactions. J. Comp. Neurol. 524:2944-2954, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Simona Gaudi
- Department of Infectious, Parasitic, and Immune-Mediated Diseases, Italian National Institute of Health, 00161, Rome, Italy
| | - Guia Guffanti
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, 02478, MA
| | - James Fallon
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, 92617, California
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, 92617, California.,Center for Autism Research and Treatment (CART), University of California Irvine, Irvine, 92617, California.,Center for Epigenetics and Metabolism, University of California Irvine, Irvine, 92617, California.,Department of Health Sciences, University of Milan, 20133, Milan, Italy
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Rangasamy D, Lenka N, Ohms S, Dahlstrom JE, Blackburn AC, Board PG. Activation of LINE-1 Retrotransposon Increases the Risk of Epithelial-Mesenchymal Transition and Metastasis in Epithelial Cancer. Curr Mol Med 2016; 15:588-97. [PMID: 26321759 PMCID: PMC5384359 DOI: 10.2174/1566524015666150831130827] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 07/31/2015] [Accepted: 08/27/2015] [Indexed: 12/12/2022]
Abstract
Epithelial cancers comprise 80-90% of human cancers. During the process of cancer progression, cells lose their epithelial characteristics and acquire stem-like mesenchymal features that are resistant to chemotherapy. This process, termed the epithelial-mesenchymal transition (EMT), plays a critical role in the development of metastases. Because of the unique migratory and invasive properties of cells undergoing the EMT, therapeutic control of the EMT offers great hope and new opportunities for treating cancer. In recent years, a plethora of genes and noncoding RNAs, including miRNAs, have been linked to the EMT and the acquisition of stem cell-like properties. Despite these advances, questions remain unanswered about the molecular processes underlying such a cellular transition. In this article, we discuss how expression of the normally repressed LINE-1 (or L1) retrotransposons activates the process of EMT and the development of metastases. L1 is rarely expressed in differentiated stem cells or adult somatic tissues. However, its expression is widespread in almost all epithelial cancers and in stem cells in their undifferentiated state, suggesting a link between L1 activity and the proliferative and metastatic behaviour of cancer cells. We present an overview of L1 activity in cancer cells including how genes involved in proliferation, invasive and metastasis are modulated by L1 expression. The role of L1 in the differential expression of the let-7 family of miRNAs (that regulate genes involved in the EMT and metastasis) is also discussed. We also summarize recent novel insights into the role of the L1-encoded reverse transcriptase enzyme in epithelial cell plasticity that suggest it might be a potential therapeutic target that could reverse the EMT and the metastasis-associated stem cell-like properties of cancer cells.
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Affiliation(s)
- D Rangasamy
- John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia.
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Guffanti G, Gaudi S, Klengel T, Fallon JH, Mangalam H, Madduri R, Rodriguez A, DeCrescenzo P, Glovienka E, Sobell J, Klengel C, Pato M, Ressler KJ, Pato C, Macciardi F. LINE1 insertions as a genomic risk factor for schizophrenia: Preliminary evidence from an affected family. Am J Med Genet B Neuropsychiatr Genet 2016; 171:534-45. [PMID: 26990047 DOI: 10.1002/ajmg.b.32437] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 02/11/2016] [Indexed: 02/02/2023]
Abstract
Recent studies show that human-specific LINE1s (L1HS) play a key role in the development of the central nervous system (CNS) and its disorders, and that their transpositions within the human genome are more common than previously thought. Many polymorphic L1HS, that is, present or absent across individuals, are not annotated in the current release of the genome and are customarily termed "non-reference L1s." We developed an analytical workflow to identify L1 polymorphic insertions with next-generation sequencing (NGS) using data from a family in which SZ segregates. Our workflow exploits two independent algorithms to detect non-reference L1 insertions, performs local de novo alignment of the regions harboring predicted L1 insertions and resolves the L1 subfamily designation from the de novo assembled sequence. We found 110 non-reference L1 polymorphic loci exhibiting Mendelian inheritance, the vast majority of which are already reported in dbRIP and/or euL1db, thus, confirming their status as non-reference L1 polymorphic insertions. Four previously undetected L1 polymorphic loci were confirmed by PCR amplification and direct sequencing of the insert. A large fraction of our non-reference L1s is located within the open reading frame of protein-coding genes that belong to pathways already implicated in the pathogenesis of schizophrenia. The finding of these polymorphic variants among SZ offsprings is intriguing and suggestive of putative pathogenic role. Our data show the utility of NGS to uncover L1 polymorphic insertions, a neglected type of genetic variants with the potential to influence the risk to develop schizophrenia like SNVs and CNVs. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Guia Guffanti
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - Simona Gaudi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Italian National Institute of Health, Rome, Italy
| | - Torsten Klengel
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - James H Fallon
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California
| | - Harry Mangalam
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California
| | - Ravi Madduri
- Division of Mathematics and Computer Science, Argonne National Laboratory, Lemont, Illinois.,Computation Institute, University of Chicago, Chicago, Illinois
| | - Alex Rodriguez
- Division of Mathematics and Computer Science, Argonne National Laboratory, Lemont, Illinois.,Computation Institute, University of Chicago, Chicago, Illinois
| | - Paula DeCrescenzo
- Department of Psychiatry, Columbia University Medical Center and New York State Psychiatric Institute, New York, New York
| | - Emily Glovienka
- Department of Psychiatry, Columbia University Medical Center and New York State Psychiatric Institute, New York, New York
| | - Janet Sobell
- SUNY Downstate, College of Medicine, Brooklyn, New York
| | - Claudia Klengel
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - Michele Pato
- SUNY Downstate, College of Medicine, Brooklyn, New York
| | - Kerry J Ressler
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - Carlos Pato
- SUNY Downstate, College of Medicine, Brooklyn, New York
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California.,Center for Autism Research and Treatment (CART), University of California, Irvine, California.,Center for Epigenetics and Metabolism, University of California, Irvine, California
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Philippe C, Vargas-Landin DB, Doucet AJ, van Essen D, Vera-Otarola J, Kuciak M, Corbin A, Nigumann P, Cristofari G. Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci. eLife 2016; 5. [PMID: 27016617 PMCID: PMC4866827 DOI: 10.7554/elife.13926] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/25/2016] [Indexed: 12/26/2022] Open
Abstract
LINE-1 (L1) retrotransposons represent approximately one sixth of the human genome, but only the human-specific L1HS-Ta subfamily acts as an endogenous mutagen in modern humans, reshaping both somatic and germline genomes. Due to their high levels of sequence identity and the existence of many polymorphic insertions absent from the reference genome, the transcriptional activation of individual genomic L1HS-Ta copies remains poorly understood. Here we comprehensively mapped fixed and polymorphic L1HS-Ta copies in 12 commonly-used somatic cell lines, and identified transcriptional and epigenetic signatures allowing the unambiguous identification of active L1HS-Ta copies in their genomic context. Strikingly, only a very restricted subset of L1HS-Ta loci - some being polymorphic among individuals - significantly contributes to the bulk of L1 expression, and these loci are differentially regulated among distinct cell lines. Thus, our data support a local model of L1 transcriptional activation in somatic cells, governed by individual-, locus-, and cell-type-specific determinants. DOI:http://dx.doi.org/10.7554/eLife.13926.001 Retrotransposons, also known as jumping genes, have invaded the genomes of most living organisms. These fragments of DNA have the ability to move or copy themselves from one location of a chromosome to another. Depending on where they insert themselves, retrotransposons can modify the sequence of nearby genes, which can alter or even abolish their activity. Although these genetic modifications have contributed significantly to the evolution of different species, retrotransposons can also have detrimental effects; for example, by causing new cases of genetic diseases. Adult human cells have a number of mechanisms that work to keep the activity of retrotransposons at a very low level. However, in many types of cancers retrotransposons escape these defense mechanisms and ‘jump’ actively. This is thought to contribute to the development and spread of cancerous tumors. To understand how jumping genes are mobilized, a fundamental question must be answered: is the high jumping gene activity observed in some cell types a result of activating many copies of the retrotransposons, or only a few of them? This question has been difficult to address because there are more than one hundred copies of retrotransposons that could potentially move in humans, many of which have not even been referenced in the human genome map. Furthermore, each copy is almost identical to another one, making it difficult to discriminate between them. Philippe et al. have now developed an approach that can map where individual retrotransposons are located in the genome of normal and cancerous cells and measure how active these jumping genes are. This revealed that only a very restricted number of them are active in any given cell type. Moreover, different subsets of jumping genes are active in different cell types, and their locations in the genome often do not overlap. Thus, whether jumping genes are activated depends on the cell type and their position in the genome. These results are in contrast to the prevalent view that retrotransposons are activated in a more widespread manner across the genome, at least in cancerous cells. Overall, Philippe et al.’s findings pave the way towards characterizing the chromosome regions in which retrotransposons are frequently activated and understanding how they contribute to cancer and other diseases. DOI:http://dx.doi.org/10.7554/eLife.13926.002
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Affiliation(s)
- Claude Philippe
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
| | - Dulce B Vargas-Landin
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,Ecole Normale Supérieure, Paris, France
| | - Aurélien J Doucet
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
| | - Dominic van Essen
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Jorge Vera-Otarola
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Monika Kuciak
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,Ecole Normale Supérieure de Lyon, Lyon, France
| | | | - Pilvi Nigumann
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Gaël Cristofari
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
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46
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Nazaryan-Petersen L, Bertelsen B, Bak M, Jønson L, Tommerup N, Hancks DC, Tümer Z. Germline Chromothripsis Driven by L1-Mediated Retrotransposition and Alu/Alu Homologous Recombination. Hum Mutat 2016; 37:385-95. [PMID: 26929209 DOI: 10.1002/humu.22953] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 01/03/2016] [Indexed: 12/20/2022]
Abstract
Chromothripsis (CTH) is a phenomenon where multiple localized double-stranded DNA breaks result in complex genomic rearrangements. Although the DNA-repair mechanisms involved in CTH have been described, the mechanisms driving the localized "shattering" process remain unclear. High-throughput sequence analysis of a familial germline CTH revealed an inserted SVAE retrotransposon associated with a 110-kb deletion displaying hallmarks of L1-mediated retrotransposition. Our analysis suggests that the SVAE insertion did not occur prior to or after, but concurrent with the CTH event. We also observed L1-endonuclease potential target sites in other breakpoints. In addition, we found four Alu elements flanking the 110-kb deletion and associated with an inversion. We suggest that chromatin looping mediated by homologous Alu elements may have brought distal DNA regions into close proximity facilitating DNA cleavage by catalytically active L1-endonuclease. Our data provide the first evidence that active and inactive human retrotransposons can serve as endogenous mutagens driving CTH in the germline.
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Affiliation(s)
- Lusine Nazaryan-Petersen
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, 2600, Denmark.,Department of Cellular and Molecular Medicine (ICMM), Faculty of Health Science, University of Copenhagen, Copenhagen, N. 2200, Denmark
| | - Birgitte Bertelsen
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, 2600, Denmark
| | - Mads Bak
- Department of Cellular and Molecular Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, N. 2200, Denmark
| | - Lars Jønson
- Center for Genomic Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, O. 2100, Denmark
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, N. 2200, Denmark
| | - Dustin C Hancks
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, 84112
| | - Zeynep Tümer
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, 2600, Denmark
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47
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Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Cañadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A, Grabundzija I, Merkert S, Gerdes P, Pulgarin JA, Bock A, Held U, Witthuhn A, Haase A, Sarkadi B, Löwer J, Wolvetang EJ, Martin U, Ivics Z, Izsvák Z, Garcia-Perez JL, Faulkner GJ, Schumann GG. Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells. Nat Commun 2016; 7:10286. [PMID: 26743714 PMCID: PMC4729875 DOI: 10.1038/ncomms10286] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/26/2015] [Indexed: 02/08/2023] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) are capable of unlimited proliferation and can differentiate in vitro to generate derivatives of the three primary germ layers. Genetic and epigenetic abnormalities have been reported by Wissing and colleagues to occur during hiPSC derivation, including mobilization of engineered LINE-1 (L1) retrotransposons. However, incidence and functional impact of endogenous retrotransposition in hiPSCs are yet to be established. Here we apply retrotransposon capture sequencing to eight hiPSC lines and three human embryonic stem cell (hESC) lines, revealing endogenous L1, Alu and SINE-VNTR-Alu (SVA) mobilization during reprogramming and pluripotent stem cell cultivation. Surprisingly, 4/7 de novo L1 insertions are full length and 6/11 retrotransposition events occurred in protein-coding genes expressed in pluripotent stem cells. We further demonstrate that an intronic L1 insertion in the CADPS2 gene is acquired during hiPSC cultivation and disrupts CADPS2 expression. These experiments elucidate endogenous retrotransposition, and its potential consequences, in hiPSCs and hESCs. Genetic and epigenetic abnormalities have been found to result from reprogramming of differentiated cells into human induced pluripotent stem cells (hiPSCs). Here, Klawitter et al. identify endogenous L1, Alu and SVA mobilization during reprogramming, highlighting the risk of insertional mutagens in hiPSCs.
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Affiliation(s)
- Sabine Klawitter
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | - Nina V Fuchs
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany.,Max-Delbrück-Center for Molecular Medicine, D-13125 Berlin, Germany
| | - Kyle R Upton
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Martin Muñoz-Lopez
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), PTS Granada, 18016 Granada, Spain
| | - Ruchi Shukla
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Jichang Wang
- Max-Delbrück-Center for Molecular Medicine, D-13125 Berlin, Germany
| | - Marta Garcia-Cañadas
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), PTS Granada, 18016 Granada, Spain
| | - Cesar Lopez-Ruiz
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), PTS Granada, 18016 Granada, Spain
| | - Daniel J Gerhardt
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Attila Sebe
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | | | - Sylvia Merkert
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation, and Vascular Surgery; REBIRTH, Cluster of Excellence, Hannover Medical School, D-30625 Hannover, Germany
| | - Patricia Gerdes
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - J Andres Pulgarin
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), PTS Granada, 18016 Granada, Spain
| | - Anja Bock
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | - Ulrike Held
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | - Anett Witthuhn
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation, and Vascular Surgery; REBIRTH, Cluster of Excellence, Hannover Medical School, D-30625 Hannover, Germany
| | - Alexandra Haase
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation, and Vascular Surgery; REBIRTH, Cluster of Excellence, Hannover Medical School, D-30625 Hannover, Germany
| | - Balázs Sarkadi
- Department of Biophysics and Radiation Biology, Semmelweis University, H-1094 Budapest, Hungary
| | - Johannes Löwer
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation, and Vascular Surgery; REBIRTH, Cluster of Excellence, Hannover Medical School, D-30625 Hannover, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | - Zsuzsanna Izsvák
- Max-Delbrück-Center for Molecular Medicine, D-13125 Berlin, Germany
| | - Jose L Garcia-Perez
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), PTS Granada, 18016 Granada, Spain
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Brisbane, Queensland 4102, Australia.,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
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48
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Thung DT, de Ligt J, Vissers LEM, Steehouwer M, Kroon M, de Vries P, Slagboom EP, Ye K, Veltman JA, Hehir-Kwa JY. Mobster: accurate detection of mobile element insertions in next generation sequencing data. Genome Biol 2015; 15:488. [PMID: 25348035 PMCID: PMC4228151 DOI: 10.1186/s13059-014-0488-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Indexed: 01/15/2023] Open
Abstract
Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster.
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Affiliation(s)
- Djie Tjwan Thung
- Department of Human Genetics, RadboudUMC, P.O. Box 9101, 6500, HB, Nijmegen, the Netherlands
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49
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Habibi L, Pedram M, AmirPhirozy A, Bonyadi K. Mobile DNA Elements: The Seeds of Organic Complexity on Earth. DNA Cell Biol 2015. [DOI: 10.1089/dna.2015.2938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Laleh Habibi
- Department of Pharmaceutics, School of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Nutrition Department, School of Nutritional Science and Dietetics, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Pedram
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Akbar AmirPhirozy
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Bonyadi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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50
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The Fine LINE: Methylation Drawing the Cancer Landscape. BIOMED RESEARCH INTERNATIONAL 2015; 2015:131547. [PMID: 26448926 PMCID: PMC4584040 DOI: 10.1155/2015/131547] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 11/17/2014] [Accepted: 11/25/2014] [Indexed: 01/08/2023]
Abstract
LINE-1 (L1) is the most abundant mammalian transposable element that comprises nearly 20% of the genome, and nearly half of the mammalian genome has stemmed from L1-mediated mobilization. Expression and retrotransposition of L1 are suppressed by complex mechanisms, where the key role belongs to DNA methylation. Alterations in L1 methylation may lead to aberrant expression of L1 and have been described in numerous diseases. Accumulating evidence clearly indicates that loss of global DNA methylation observed in cancer development and progression is tightly associated with hypomethylation of L1 elements. Significant progress achieved in the last several years suggests that such parameters as L1 methylation status can be potentially utilized as clinical biomarkers for determination of the disease stage and in predicting the disease-free survival in cancer patients. In this paper, we summarize the current knowledge on L1 methylation, with specific emphasis given to success and challenges on the way of introduction of L1 into clinical practice.
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