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Du Q, Stow EC, LaCoste D, Freeman B, Baddoo M, Shareef A, Miller KM, Belancio VP. A novel role of TRIM28 B box domain in L1 retrotransposition and ORF2p-mediated cDNA synthesis. Nucleic Acids Res 2023; 51:4429-4450. [PMID: 37070200 PMCID: PMC10201437 DOI: 10.1093/nar/gkad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 04/19/2023] Open
Abstract
The long interspersed element 1 (LINE-1 or L1) integration is affected by many cellular factors through various mechanisms. Some of these factors are required for L1 amplification, while others either suppress or enhance specific steps during L1 propagation. Previously, TRIM28 has been identified to suppress transposable elements, including L1 expression via its canonical role in chromatin remodeling. Here, we report that TRIM28 through its B box domain increases L1 retrotransposition and facilitates shorter cDNA and L1 insert generation in cultured cells. Consistent with the latter, we observe that tumor specific L1 inserts are shorter in endometrial, ovarian, and prostate tumors with higher TRIM28 mRNA expression than in those with lower TRIM28 expression. We determine that three amino acids in the B box domain that are involved in TRIM28 multimerization are critical for its effect on both L1 retrotransposition and cDNA synthesis. We provide evidence that B boxes from the other two members in the Class VI TRIM proteins, TRIM24 and TRIM33, also increase L1 retrotransposition. Our findings could lead to a better understanding of the host/L1 evolutionary arms race in the germline and their interplay during tumorigenesis.
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Affiliation(s)
- Qianhui Du
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Emily C Stow
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Dawn LaCoste
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Benjamin Freeman
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Melody Baddoo
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Afzaal M Shareef
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 100 E 24th Street, Austin, TX 78712, USA
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
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2
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Dumas F, Perelman PL, Biltueva L, Roelke-Parker ME. Retrotransposon mapping in spider monkey genomes of the family Atelidae (Platyrrhini, Primates) shows a high level of LINE-1 amplification. JOURNAL OF BIOLOGICAL RESEARCH - BOLLETTINO DELLA SOCIETÀ ITALIANA DI BIOLOGIA SPERIMENTALE 2022. [DOI: 10.4081/jbr.2022.10725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
To investigate the distribution of LINE-1 repeat sequences, a LINE-1 probe was Fluorescence In Situ Hybridized (FISH) on the chromosomes of Ateles geoffroyi and Ateles fusciceps (Atelidae); a LINE-1 probe was also mapped on Cebuella pygmaea (Cebidae) and used as an outgroup for phylogenetic comparison. Ateles spider monkeys have a highly rearranged genome and are an ideal model for testing whether LINE-1 is involved in genome evolution. The LINE-1 probe has been mapped in the two Atelidae species for the first time, revealing a high accumulation of LINE-1 sequences along chromosomal arms, including telomeres, and a scarcity of LINE-1 signals at centromere positions. LINE-1 mapping in C. pygmaea (Cebidae) revealed signals at centromere positions and along chromosome arms, which was consistent with previous published data from other Cebidae species. In a broader sense, the results were analyzed in light of published data on whole-chromosomal human probes mapped in these genomes. This analysis allows us to speculate about the presence of LINE-1 sequences at the junction of human chromosomal syntenies, as well as a possible link between these sequences and chromosomal rearrangements.
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Lee H, Min JW, Mun S, Han K. Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101583. [PMID: 36295018 PMCID: PMC9605557 DOI: 10.3390/life12101583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are classified into two classes according to their mobilization mechanism. Compared to DNA transposons that move by the "cut and paste" mechanism, retrotransposons mobilize via the "copy and paste" method. They have been an essential research topic because some of the active elements, such as Long interspersed element 1 (LINE-1), Alu, and SVA elements, have contributed to the genetic diversity of primates beyond humans. In addition, they can cause genetic disorders by altering gene expression and generating structural variations (SVs). The development and rapid technological advances in next-generation sequencing (NGS) have led to new perspectives on detecting retrotransposon-mediated SVs, especially insertions. Moreover, various computational methods have been developed based on NGS data to precisely detect the insertions and deletions in the human genome. Therefore, this review discusses details about the recently studied and utilized NGS technologies and the effective computational approaches for discovering retrotransposons through it. The final part covers a diverse range of computational methods for detecting retrotransposon insertions with human NGS data. This review will give researchers insights into understanding the TEs and how to investigate them and find connections with research interests.
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Affiliation(s)
- Haeun Lee
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea
| | - Jun Won Min
- Department of Surgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Seyoung Mun
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- Correspondence: (S.M.); (K.H.)
| | - Kyudong Han
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- HuNbiome Co., Ltd., R&D Center, Seoul 08507, Korea
- Correspondence: (S.M.); (K.H.)
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4
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Ceraulo S, Perelman PL, Dumas F. Massive LINE‐1 retrotransposon enrichment in tamarins of the Cebidae family (Platyrrhini, Primates) and its significance for genome evolution. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simona Ceraulo
- Department of “Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF)” University of Palermo Palermo Italy
| | | | - Francesca Dumas
- Department of “Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF)” University of Palermo Palermo Italy
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5
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RNA m 6A modification orchestrates a LINE-1-host interaction that facilitates retrotransposition and contributes to long gene vulnerability. Cell Res 2021; 31:861-885. [PMID: 34108665 PMCID: PMC8324889 DOI: 10.1038/s41422-021-00515-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
The molecular basis underlying the interaction between retrotransposable elements (RTEs) and the human genome remains poorly understood. Here, we profiled N6-methyladenosine (m6A) deposition on nascent RNAs in human cells by developing a new method MINT-Seq, which revealed that many classes of RTE RNAs, particularly intronic LINE-1s (L1s), are strongly methylated. These m6A-marked intronic L1s (MILs) are evolutionarily young, sense-oriented to hosting genes, and are bound by a dozen RNA binding proteins (RBPs) that are putative novel readers of m6A-modified RNAs, including a nuclear matrix protein SAFB. Notably, m6A positively controls the expression of both autonomous L1s and co-transcribed L1 relics, promoting L1 retrotransposition. We showed that MILs preferentially reside in long genes with critical roles in DNA damage repair and sometimes in L1 suppression per se, where they act as transcriptional "roadblocks" to impede the hosting gene expression, revealing a novel host-weakening strategy by the L1s. In counteraction, the host uses the SAFB reader complex to bind m6A-L1s to reduce their levels, and to safeguard hosting gene transcription. Remarkably, our analysis identified thousands of MILs in multiple human fetal tissues, enlisting them as a novel category of cell-type-specific regulatory elements that often compromise transcription of long genes and confer their vulnerability in neurodevelopmental disorders. We propose that this m6A-orchestrated L1-host interaction plays widespread roles in gene regulation, genome integrity, human development and diseases.
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Neuberger EWI, Brahmer A, Ehlert T, Kluge K, Philippi KFA, Boedecker SC, Weinmann-Menke J, Simon P. Validating quantitative PCR assays for cfDNA detection without DNA extraction in exercising SLE patients. Sci Rep 2021; 11:13581. [PMID: 34193884 PMCID: PMC8245561 DOI: 10.1038/s41598-021-92826-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 06/07/2021] [Indexed: 01/10/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has been investigated as a screening tool for many diseases. To avoid expensive and time-consuming DNA isolation, direct quantification PCR assays can be established. However, rigorous validation is required to provide reliable data in the clinical and non-clinical context. Considering the International Organization for Standardization, as well as bioanalytical method validation guidelines, we provide a comprehensive procedure to validate assays for cfDNA quantification from blood plasma without DNA isolation. A 90 and 222 bp assay was validated to study the kinetics of cfDNA after exercise in patients with systemic lupus erythematosus (SLE). The assays showed ultra-low limit of quantification (LOQ) with 0.47 and 0.69 ng/ml, repeatability ≤ 11.6% (95% CI 8.1-20.3), and intermediate precision ≤ 12.1% (95% CI 9.2-17.7). Incurred sample reanalysis confirmed the precision of the procedure. The additional consideration of pre-analytical factors shows that centrifugation speed and temperature do not change cfDNA concentrations. In SLE patients cfDNA increases ~ twofold after a walking exercise, normalizing after 60 min of rest. The established assays allow reliable and cost-efficient quantification of cfDNA in minute amounts of plasma in the clinical setting. Additionally, the assay can be used as a tool to determine the impact of pre-analytical factors and validate cfDNA quantity and quality of isolated samples.
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Affiliation(s)
- Elmo W I Neuberger
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Alexandra Brahmer
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Tobias Ehlert
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Katrin Kluge
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Keito F A Philippi
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany
| | - Simone C Boedecker
- Department of Rheumatology and Nephrology, University Medical Center Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Julia Weinmann-Menke
- Department of Rheumatology and Nephrology, University Medical Center Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, University of Mainz, Albert-Schweitzer Str. 22, 55128, Mainz, Germany.
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7
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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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8
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Abstract
I have been fortunate and privileged to have participated in amazing breakthroughs in human genetics since the 1960s. I was lucky to have trained in medical school at Dartmouth and Johns Hopkins, in pediatrics at the University of Minnesota and Johns Hopkins, and in genetics and molecular biology with Dr. Barton Childs at Johns Hopkins and Dr. Harvey Itano at the National Institutes of Health. Later, the collaborative spirit at Johns Hopkins and the University of Pennsylvania were important to my career. Here, I describe the thrill of scientific discovery in two diverse areas of human genetics: DNA haplotypes and their role in solving the molecular basis of beta thalassemia and the role of retrotransposons (jumping genes) in human biology. I hope that this article may inspire others who love human genetics as much as I do.
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Affiliation(s)
- Haig H Kazazian
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
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9
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Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model. Sci Rep 2021; 11:8083. [PMID: 33850167 PMCID: PMC8044218 DOI: 10.1038/s41598-021-86395-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
While transposons are generally silenced in somatic tissues, many transposons escape epigenetic repression in epithelial cancers, become transcriptionally active and contribute to the regulation of human gene expression. We have developed a bioinformatic pipeline for the integrated analysis of transcription factor binding and transcriptomic data to identify transposon-derived promoters that are activated in specific diseases and developmental states. We applied this pipeline to a breast cancer model, and found that the L1PA2 transposon subfamily contributes abundant regulatory sequences to co-ordinated transcriptional regulation in breast cancer. Transcription factor profiling demonstrates that over 27% of L1PA2 transposons harbour co-localised binding sites of functionally interacting, cancer-associated transcription factors in MCF7 cells, a cell line used to model breast cancer. Transcriptomic analysis reveals that L1PA2 transposons also contribute transcription start sites to up-regulated transcripts in MCF7 cells, including some transcripts with established oncogenic properties. In addition, we verified the utility of our pipeline on other transposon subfamilies, as well as on leukemia and lung carcinoma cell lines. We demonstrate that the normally quiescent regulatory activities of transposons can be activated and alter the cancer transcriptome. In particular, the L1PA2 subfamily contributes abundant regulatory sequences, and likely plays a global role in modulating breast cancer transcriptional regulation. Understanding the regulatory impact of L1PA2 on breast cancer genomes provides additional insights into cancer genome regulation, and may provide novel biomarkers for disease diagnosis, prognosis and therapy.
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10
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Newkirk SJ, Kong L, Jones MM, Habben CE, Dilts VL, Ye P, An W. Subfamily-specific quantification of endogenous mouse L1 retrotransposons by droplet digital PCR. Anal Biochem 2020; 601:113779. [PMID: 32442414 DOI: 10.1016/j.ab.2020.113779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/06/2020] [Accepted: 05/14/2020] [Indexed: 11/18/2022]
Abstract
Long interspersed element type 1 (LINE-1; L1) mobilizes during early embryogenesis, neurogenesis, and germ cell development, accounting for 25% of disease-causing heritable insertions and 98% of somatic insertions in cancer. To better understand the regulation and impact of L1 mobilization in the genome, reliable methods for measuring L1 copy number variation (CNV) are needed. Here we present a comprehensive analysis of a droplet digital PCR (ddPCR) based method for quantifying endogenous mouse L1. We provide experimental evidence that ddPCR assays can be designed to target specific L1 subfamilies using diagnostic single nucleotide polymorphisms (SNPs). The target and off-target L1 subfamilies form distinct droplet clusters, which were experimentally verified using both synthetic gene fragments and endogenous L1 derived plasmid clones. We further provide a roadmap for in silico assay design and evaluation of target specificity, ddPCR testing, and optimization for L1 CNV quantification. The assay can achieve a sensitivity of 5% CNV with 8 technical replicates. With 24 technical replicates, it can detect 2% CNV because of the increased precision. The same approach will serve as a guide for the development of ddPCR based assays for quantifying human L1 copy number and any other high copy genomic target sequences.
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Affiliation(s)
- Simon J Newkirk
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Lingqi Kong
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Mason M Jones
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Chase E Habben
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Victoria L Dilts
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
| | - Ping Ye
- Department of Pharmacy Practice, South Dakota State University, Brookings, SD, 57007, United States; Avera Research Institute, Sioux Falls, SD, 57108, United States.
| | - Wenfeng An
- Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD, 57007, United States.
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11
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Zhou W, Emery SB, Flasch DA, Wang Y, Kwan KY, Kidd JM, Moran JV, Mills RE. Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. Nucleic Acids Res 2020; 48:1146-1163. [PMID: 31853540 PMCID: PMC7026601 DOI: 10.1093/nar/gkz1173] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/14/2019] [Accepted: 12/05/2019] [Indexed: 11/13/2022] Open
Abstract
Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; however, they have limitations in detecting insertions in complex repetitive genomic regions. Here, we developed a computational tool (PALMER) and used it to identify 203 non-reference L1Hs insertions in the NA12878 benchmark genome. Using PacBio long-read sequencing data, we identified L1Hs insertions that were absent in previous short-read studies (90/203). Approximately 81% (73/90) of the L1Hs insertions reside within endogenous LINE-1 sequences in the reference assembly and the analysis of unique breakpoint junction sequences revealed 63% (57/90) of these L1Hs insertions could be genotyped in 1000 Genomes Project sequences. Moreover, we observed that amplification biases encountered in single-cell WGS experiments led to a wide variation in L1Hs insertion detection rates between four individual NA12878 cells; under-amplification limited detection to 32% (65/203) of insertions, whereas over-amplification increased false positive calls. In sum, these data indicate that L1Hs insertions are often missed using standard short-read sequencing approaches and long-read sequencing approaches can significantly improve the detection of L1Hs insertions present in individual genomes.
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Affiliation(s)
- Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Diane A Flasch
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Kenneth Y Kwan
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA.,Molecular and Behavioral Neuroscience Institute, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
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12
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Navarro FCP, Hoops J, Bellfy L, Cerveira E, Zhu Q, Zhang C, Lee C, Gerstein MB. TeXP: Deconvolving the effects of pervasive and autonomous transcription of transposable elements. PLoS Comput Biol 2019; 15:e1007293. [PMID: 31425522 PMCID: PMC6715295 DOI: 10.1371/journal.pcbi.1007293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 08/29/2019] [Accepted: 07/26/2019] [Indexed: 11/19/2022] Open
Abstract
The Long interspersed nuclear element 1 (LINE-1) is a primary source of genetic variation in humans and other mammals. Despite its importance, LINE-1 activity remains difficult to study because of its highly repetitive nature. Here, we developed and validated a method called TeXP to gauge LINE-1 activity accurately. TeXP builds mappability signatures from LINE-1 subfamilies to deconvolve the effect of pervasive transcription from autonomous LINE-1 activity. In particular, it apportions the multiple reads aligned to the many LINE-1 instances in the genome into these two categories. Using our method, we evaluated well-established cell lines, cell-line compartments and healthy tissues and found that the vast majority (91.7%) of transcriptome reads overlapping LINE-1 derive from pervasive transcription. We validated TeXP by independently estimating the levels of LINE-1 autonomous transcription using ddPCR, finding high concordance. Next, we applied our method to comprehensively measure LINE-1 activity across healthy somatic cells, while backing out the effect of pervasive transcription. Unexpectedly, we found that LINE-1 activity is present in many normal somatic cells. This finding contrasts with earlier studies showing that LINE-1 has limited activity in healthy somatic tissues, except for neuroprogenitor cells. Interestingly, we found that the amount of LINE-1 activity was associated with the with the amount of cell turnover, with tissues with low cell turnover rates (e.g. the adult central nervous system) showing lower LINE-1 activity. Altogether, our results show how accounting for pervasive transcription is critical to accurately quantify the activity of highly repetitive regions of the human genome. Repetitive sequences, such as LINEs, comprise more than half of the human genome. Due to their repetitive nature, LINEs are hard to grasp. In particular, we find that pervasive transcription is a major confounding factor in transcriptome data. We observe that, on average, more than 90% of LINE signal derives from pervasive transcription. To investigate this issue, we developed and validated a new method called TeXP. TeXP accounts and removes the effects of pervasive transcription when quantifying LINE activity. Our method uses the broad distribution of LINEs to estimate the effects of pervasive transcription. Using TeXP, we processed thousands of transcriptome datasets to uniformly, and unbiasedly measure LINE-1 activity across healthy somatic cells. By removing the pervasive transcription component, we find that (1) LINE-1 is broadly expressed in healthy somatic tissues; (2) Adult brain show small levels of LINE transcription and; (3) LINE-1 transcription level is correlated with tissue cell turnover. Our method thus offers insights into how repetitive sequences and influenced by pervasive transcription. Moreover, we uncover the activity of LINE-1 in somatic tissues at an unmatched scale.
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Affiliation(s)
- Fabio CP Navarro
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jacob Hoops
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Lauren Bellfy
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Eliza Cerveira
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Chengsheng Zhang
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, Michigan, United States of America
- Department of Life Sciences, Ewha Womans University, Seoul, Korea
| | - Mark B. Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Computer Science, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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13
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A comprehensive analysis of chimpanzee (Pan troglodytes)-specific LINE-1 retrotransposons. Gene 2019; 693:46-51. [DOI: 10.1016/j.gene.2019.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/08/2019] [Accepted: 01/22/2019] [Indexed: 01/08/2023]
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14
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Shin W, Mun S, Kim J, Lee W, Park DG, Choi S, Lee TY, Cha S, Han K. Novel Discovery of LINE-1 in a Korean Individual by a Target Enrichment Method. Mol Cells 2019; 42:87-95. [PMID: 30699287 PMCID: PMC6354063 DOI: 10.14348/molcells.2018.0351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/10/2018] [Accepted: 10/26/2018] [Indexed: 11/27/2022] Open
Abstract
Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.
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Affiliation(s)
- Wonseok Shin
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Junse Kim
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Wooseok Lee
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Dong-Guk Park
- Department of Surgery, Dankook University College of Medicine, Cheonan 31116,
Korea
| | - Seungkyu Choi
- Department of Pathology, Dankook University College of Medicine, Cheonan 31116,
Korea
| | - Tae Yoon Lee
- Department of Technology Education and Department of Biomedical Engineering, Chungnam National University, Daejeon 34134,
Korea
| | - Seunghee Cha
- Department of Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, FL 32610,
USA
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
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15
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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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16
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Abstract
The field of genomic biomarkers in melanoma has evolved dramatically in the past few decades. Whereas much of the prior focus was on molecular assessment of tumor tissue, circulating tumor cells (CTCs), and cell-free circulating tumor DNA (ctDNA) as sources of a "liquid biopsy" in cancer patients provide promising potential as a method to assess tumor progression, identify targets for therapy, and evaluate clinical response to treatment. Blood biomarker assays have the advantage of being noninvasive, allow for dynamic evaluation of disease over a serial time frame, and help to address the issue of tissue sampling bias and tumor heterogeneity. However, there remains an assortment of technologies and techniques to isolate and detect CTCs and ctDNA and a standardized method has yet to be established. Despite these challenges, multiple studies have already demonstrated the clinical prognostic utility of blood-based genomic biomarker assays. With the advent of next-generation sequencing and genome-wide ctDNA analysis, this will undoubtedly lead to an improved understanding of tumor progression, help to identify new targets for treatment, and improve monitoring of treatment response and development of resistance.
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Affiliation(s)
- Kelly Huynh
- Department of Surgical Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA 90404
| | - Dave S B Hoon
- Department of Molecular Oncology John Wayne Cancer Institute at Providence Saint John's Health Center Santa Monica, California
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17
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Guler GD, Tindell CA, Pitti R, Wilson C, Nichols K, KaiWai Cheung T, Kim HJ, Wongchenko M, Yan Y, Haley B, Cuellar T, Webster J, Alag N, Hegde G, Jackson E, Nance TL, Giresi PG, Chen KB, Liu J, Jhunjhunwala S, Settleman J, Stephan JP, Arnott D, Classon M. Repression of Stress-Induced LINE-1 Expression Protects Cancer Cell Subpopulations from Lethal Drug Exposure. Cancer Cell 2017; 32:221-237.e13. [PMID: 28781121 DOI: 10.1016/j.ccell.2017.07.002] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 05/02/2017] [Accepted: 07/05/2017] [Indexed: 12/30/2022]
Abstract
Maintenance of phenotypic heterogeneity within cell populations is an evolutionarily conserved mechanism that underlies population survival upon stressful exposures. We show that the genomes of a cancer cell subpopulation that survives treatment with otherwise lethal drugs, the drug-tolerant persisters (DTPs), exhibit a repressed chromatin state characterized by increased methylation of histone H3 lysines 9 and 27 (H3K9 and H3K27). We also show that survival of DTPs is, in part, maintained by regulators of H3K9me3-mediated heterochromatin formation and that the observed increase in H3K9me3 in DTPs is most prominent over long interspersed repeat element 1 (LINE-1). Disruption of the repressive chromatin over LINE-1 elements in DTPs results in DTP ablation, which is partially rescued by reducing LINE-1 expression or function.
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Affiliation(s)
- Gulfem Dilek Guler
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Robert Pitti
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Catherine Wilson
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Katrina Nichols
- Protein Chemistry, Genentech Inc., South San Francisco, CA, USA
| | | | - Hyo-Jin Kim
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - Yibing Yan
- LS Biomarker Development, Genentech Inc., South San Francisco, CA, USA
| | - Benjamin Haley
- Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | - Trinna Cuellar
- Molecular Biology, Genentech Inc., South San Francisco, CA, USA
| | | | - Navneet Alag
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ganapati Hegde
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Erica Jackson
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | | | | | - Jinfeng Liu
- Bioinformatics, Genentech Inc., South San Francisco, CA, USA
| | | | - Jeff Settleman
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | | | - David Arnott
- Protein Chemistry, Genentech Inc., South San Francisco, CA, USA
| | - Marie Classon
- Molecular Oncology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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18
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Paul S, Bhattacharjee P, Giri AK, Bhattacharjee P. Arsenic toxicity and epimutagenecity: the new LINEage. Biometals 2017; 30:505-515. [PMID: 28516305 DOI: 10.1007/s10534-017-0021-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 05/09/2017] [Indexed: 12/15/2022]
Abstract
Global methylation pattern regulates the normal functioning of a cell. Research have shown arsenic alter these methylation landscapes within the genome leading to aberrant gene expression and inducts various pathophysiological outcomes. Long interspersed nuclear elements (LINE-1) normally remains inert due to heavy methylation of it's promoters, time and various environmental insults, they lose these methylation signatures and begin retro-transposition that has been associated with genomic instability and cancerous outcomes. Of the various high throughput technologies available to detect global methylation profile, development of LINE-1 methylation index shall provide a cost effect-screening tool to detect epimutagenic events in the wake of toxic exposure in a large number of individuals. In the present review, we tried to discuss the state of research and whether LINE-1 methylation can be considered as a potent epigenetic signature for arsenic toxicity.
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Affiliation(s)
- Somnath Paul
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India. .,Department of Epigenetics & Molecular Carcinogenesis, The Virginia Harris Cockrell Cancer Center, The University of Texas, M.D. Anderson Cancer Center, Science Park, 1808 Park Road 1C, Smithville, TX, 78957, USA.
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Ashok K Giri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032, India.
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India.
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19
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Penzkofer T, Jäger M, Figlerowicz M, Badge R, Mundlos S, Robinson PN, Zemojtel T. L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. Nucleic Acids Res 2016; 45:D68-D73. [PMID: 27924012 PMCID: PMC5210629 DOI: 10.1093/nar/gkw925] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/28/2016] [Accepted: 10/05/2016] [Indexed: 12/28/2022] Open
Abstract
LINE-1 (L1) insertions comprise as much as 17% of the human genome sequence, and similar proportions have been recorded for other mammalian species. Given the established role of L1 retrotransposons in shaping mammalian genomes, it becomes an important task to track and annotate the sources of this activity: full length elements, able to encode the cis and trans acting components of the retrotransposition machinery. The L1Base database (http://l1base.charite.de) contains annotated full-length sequences of LINE-1 transposons including putatively active L1s. For the new version of L1Base, a LINE-1 annotation tool, L1Xplorer, has been used to mine potentially active L1 retrotransposons from the reference genome sequences of 17 mammals. The current release of the human genome, GRCh38, contains 146 putatively active L1 elements or full length intact L1 elements (FLIs). The newest versions of the mouse, GRCm38 and the rat, Rnor_6.0, genomes contain 2811 and 492 FLIs, respectively. Most likely reflecting the current level of completeness of the genome project, the latest reference sequence of the common chimpanzee genome, PT 2.19, only contains 19 FLIs. Of note, the current assemblies of the dog, CF 3.1 and the sheep, OA 3.1, genomes contain 264 and 598 FLIs, respectively. Further developments in the new version of L1Base include an updated website with implementation of modern web server technologies. including a more responsive design for an improved user experience, as well as the addition of data sharing capabilities for L1Xplorer annotation.
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Affiliation(s)
- Tobias Penzkofer
- Department of Radiology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Marten Jäger
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-569 Poznan, Poland
| | - Richard Badge
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | - Stefan Mundlos
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.,The Jackson Laboratory for Genomic medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Tomasz Zemojtel
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-569 Poznan, Poland
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20
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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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21
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Streva VA, Jordan VE, Linker S, Hedges DJ, Batzer MA, Deininger PL. Sequencing, identification and mapping of primed L1 elements (SIMPLE) reveals significant variation in full length L1 elements between individuals. BMC Genomics 2015; 16:220. [PMID: 25887476 PMCID: PMC4381410 DOI: 10.1186/s12864-015-1374-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There are over a half a million copies of L1 retroelements in the human genome which are responsible for as much as 0.5% of new human genetic diseases. Most new L1 inserts arise from young source elements that are polymorphic in the human genome. Highly active polymorphic "hot" L1 source elements have been shown to be capable of extremely high levels of mobilization and result in numerous instances of disease. Additionally, hot polymorphic L1s have been described to be highly active within numerous cancer genomes. These hot L1s result in mutagenesis by insertion of new L1 copies elsewhere in the genome, but also have been shown to generate additional full length L1 insertions which are also hot and able to further retrotranspose. Through this mechanism, hot L1s may amplify within a tumor and result in a continued cycle of mutagenesis. RESULTS AND CONCLUSIONS We have developed a method to detect full-length, polymorphic L1 elements using a targeted next generation sequencing approach, Sequencing Identification and Mapping of Primed L1 Elements (SIMPLE). SIMPLE has 94% sensitivity and detects nearly all full-length L1 elements in a genome. SIMPLE will allow researchers to identify hot mutagenic full-length L1s as potential drivers of genome instability. Using SIMPLE we find that the typical individual has approximately 100 non-reference, polymorphic L1 elements in their genome. These elements are at relatively low population frequencies relative to previously identified polymorphic L1 elements and demonstrate the tremendous diversity in potentially active L1 elements in the human population.
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Affiliation(s)
- Vincent A Streva
- Tulane Cancer Center and Department of Epidemiology, Tulane University, New Orleans, LA, USA. .,Present Address: Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Vallmer E Jordan
- Department of Biology, Louisiana State University, Baton Rouge, LA, USA.
| | - Sara Linker
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA.
| | - Dale J Hedges
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA.
| | - Mark A Batzer
- Department of Biology, Louisiana State University, Baton Rouge, LA, USA.
| | - Prescott L Deininger
- Tulane Cancer Center and Department of Epidemiology, Tulane University, New Orleans, LA, USA.
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22
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White TB, McCoy AM, Streva VA, Fenrich J, Deininger PL. A droplet digital PCR detection method for rare L1 insertions in tumors. Mob DNA 2014; 5:30. [PMID: 25598847 PMCID: PMC4297411 DOI: 10.1186/s13100-014-0030-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/19/2014] [Indexed: 01/17/2023] Open
Abstract
Background The active human mobile element, long interspersed element 1 (L1) currently populates human genomes in excess of 500,000 copies per haploid genome. Through its mobility via a process called target primed reverse transcription (TPRT), L1 mobilization has resulted in over 100 de novo cases of human disease and has recently been associated with various cancer types. Large advances in high-throughput sequencing (HTS) technology have allowed for an increased understanding of the role of L1 in human cancer; however, researchers are still limited by the ability to validate potentially rare L1 insertion events detected by HTS that may occur in only a small fraction of tumor cells. Additionally, HTS detection of rare events varies greatly as a function of read depth, and new tools for de novo element discovery are needed to fill in gaps created by HTS. Results We have employed droplet digital PCR (ddPCR) to detect rare L1 loci in mosaic human genomes. Our assay allows for the detection of L1 insertions as rare as one cell in every 10,000. Conclusions ddPCR represents a robust method to be used alongside HTS techniques for detecting, validating and quantitating rare L1 insertion events in tumors and other tissues. Electronic supplementary material The online version of this article (doi:10.1186/s13100-014-0030-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Travis B White
- Tulane Cancer Center, 1430 Tulane Avenue, New Orleans, LA 70112 USA
| | - Adam M McCoy
- Bio-Rad Laboratories, 750 Alfred Nobel Drive, Hercules, CA 94547 USA.,Present Address: Eureka Genomics, 2000 Alfred Nobel Drive, Hercules, CA 94547 USA
| | - Vincent A Streva
- Tulane Cancer Center, 1430 Tulane Avenue, New Orleans, LA 70112 USA.,Present Address: Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115 USA
| | - Joshua Fenrich
- Bio-Rad Laboratories, 750 Alfred Nobel Drive, Hercules, CA 94547 USA
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23
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Ngamphiw C, Tongsima S, Mutirangura A. Roles of intragenic and intergenic L1s in mouse and human. PLoS One 2014; 9:e113434. [PMID: 25409429 PMCID: PMC4237456 DOI: 10.1371/journal.pone.0113434] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/28/2014] [Indexed: 02/02/2023] Open
Abstract
Long INterspersed Element-1 (LINE-1 or L1) is a retrotransposable element that has shaped the evolution of mammalian genomes. There is increasing evidence that transcriptionally active L1 could have been co-opted through evolution to play various roles including X-inactivation, homologous recombination and gene regulation. Here, we compare putatively active L1 distributions in the mouse with human. L1 density is higher in the mouse except for the Y-chromosome. L1 density is the highest in X-chromosome, implying an X-inactivation role. L1 is more common outside genes (intergenic) except for the Y-chromosome in both species. The structure of mouse L1 is distinguished from human L1 by the presence of a 200 bp repeat in the 5' UTR of the former. We found that mouse intragenic L1 has significantly higher repeat copy numbers than intergenic L1, suggesting that this is important for control of L1 expression. Furthermore, a significant association between the presence of intragenic L1s and down-regulated genes in early embryogenesis was found in both species. In conclusion, the distribution of L1 in the mouse genome points to biological roles of L1 in mouse similar to human.
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Affiliation(s)
- Chumpol Ngamphiw
- Inter-Department Program of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
- Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sissades Tongsima
- Genome Technology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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24
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Belkhiri A, El-Rifai W. 5-Methylcytosine hydroxylation-mediated LINE-1 hypomethylation: a novel mechanism of proto-oncogenes activation in colorectal cancer? Gut 2014; 63:538-9. [PMID: 23812322 PMCID: PMC4035300 DOI: 10.1136/gutjnl-2013-305176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Abbes Belkhiri
- Department of Surgery and Department of Cancer Biology,
Vanderbilt University Medical Center, Nashville TN 37232
| | - Wael El-Rifai
- Department of Surgery and Department of Cancer Biology,
Vanderbilt University Medical Center, Nashville TN 37232,Department of Veterans Affairs, Tennessee Valley Healthcare
System, Nashville, TN 37232
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25
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Grandi FC, An W. Non-LTR retrotransposons and microsatellites: Partners in genomic variation. Mob Genet Elements 2013; 3:e25674. [PMID: 24195012 PMCID: PMC3812793 DOI: 10.4161/mge.25674] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/07/2013] [Accepted: 07/09/2013] [Indexed: 01/10/2023] Open
Abstract
The human genome is laden with both non-LTR (long-terminal repeat) retrotransposons and microsatellite repeats. Both types of sequences are able to, either actively or passively, mutagenize the genomes of human individuals and are therefore poised to dynamically alter the human genomic landscape across generations. Non-LTR retrotransposons, such as L1 and Alu, are a major source of new microsatellites, which are born both concurrently and subsequently to L1 and Alu integration into the genome. Likewise, the mutation dynamics of microsatellite repeats have a direct impact on the fitness of their non-LTR retrotransposon parent owing to microsatellite expansion and contraction. This review explores the interactions and dynamics between non-LTR retrotransposons and microsatellites in the context of genomic variation and evolution.
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Affiliation(s)
- Fiorella C Grandi
- School of Molecular Biosciences and Center for Reproductive Biology; Washington State University; Pullman, WA USA
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Single-neuron sequencing analysis of L1 retrotransposition and somatic mutation in the human brain. Cell 2013; 151:483-96. [PMID: 23101622 DOI: 10.1016/j.cell.2012.09.035] [Citation(s) in RCA: 403] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 08/02/2012] [Accepted: 09/19/2012] [Indexed: 11/22/2022]
Abstract
A major unanswered question in neuroscience is whether there exists genomic variability between individual neurons of the brain, contributing to functional diversity or to an unexplained burden of neurological disease. To address this question, we developed a method to amplify genomes of single neurons from human brains. Because recent reports suggest frequent LINE-1 (L1) retrotransposition in human brains, we performed genome-wide L1 insertion profiling of 300 single neurons from cerebral cortex and caudate nucleus of three normal individuals, recovering >80% of germline insertions from single neurons. While we find somatic L1 insertions, we estimate <0.6 unique somatic insertions per neuron, and most neurons lack detectable somatic insertions, suggesting that L1 is not a major generator of neuronal diversity in cortex and caudate. We then genotyped single cortical cells to characterize the mosaicism of a somatic AKT3 mutation identified in a child with hemimegalencephaly. Single-neuron sequencing allows systematic assessment of genomic diversity in the human brain.
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Grandi FC, Rosser JM, An W. LINE-1-derived poly(A) microsatellites undergo rapid shortening and create somatic and germline mosaicism in mice. Mol Biol Evol 2012; 30:503-12. [PMID: 23125228 DOI: 10.1093/molbev/mss251] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Interspersed and tandem repeat sequences comprise the bulk of mammalian genomes. Interspersed repeats result from successive replication by transposable elements, such as Alu and long interspersed element type 1 (L1). Microsatellites are tandem repeats of 1-6 base pairs, among which poly(A) microsatellites are the most abundant in the human genome. The rise and fall of a microsatellite has been depicted as a life cycle. Previous studies have demonstrated that Alu and L1 insertions are a major source of A-rich microsatellites owing to the concurrent formation of a poly(A) DNA tract at the 3'-end of each insertion. The fate of such poly(A) tracts has been studied by surveying the length distribution of genomic resident Alu and L1 insertions. However, these cross-sectional studies provide no information about the tempo of mutation immediately after birth. In this study, de novo L1 insertions were created using a transgenic L1 mouse model and traced through generations to investigate the early life of poly(A) microsatellites. High frequencies of intra-individual and intergenerational shortening were observed for long poly(A) tracts, creating somatic and germline mosaicism at the insertion site, whereas little variation was observed for short poly(A) alleles. As poly(A) microsatellites are the major intrinsic signal for nucleosome positioning, their remarkable abundance and variability make them a significant source of epigenetic variation. Thus, the birth of poly(A) microsatellites from retrotransposons and the subsequent rapid and variable shortening represent a new way with which retrotransposons can modify the genetic and epigenetic architecture of our genome.
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Affiliation(s)
- Fiorella C Grandi
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, USA
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Hoshimoto S, Kuo CT, Chong KK, Takeshima TL, Takei Y, Li MW, Huang SK, Sim MS, Morton DL, Hoon DSB. AIM1 and LINE-1 epigenetic aberrations in tumor and serum relate to melanoma progression and disease outcome. J Invest Dermatol 2012; 132:1689-97. [PMID: 22402438 PMCID: PMC3352986 DOI: 10.1038/jid.2012.36] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aberrations in the methylation status of non-coding genomic repeat DNA sequences and specific gene promoter region are important epigenetic events in melanoma progression. Promoter methylation status in LINE-1 and Absent in melanoma-1(AIM1;6q21) associated with melanoma progression and disease outcome was assessed. LINE-1 and AIM1 methylation status was assessed in paraffin-embedded archival tissues(PEAT)(n=133) and melanoma patients’ serum(n=56). LINE-1 U-Index(hypomethylation) and AIM1 were analyzed in microdissected melanoma PEAT sections. The LINE-1 U-Index of melanoma(n=100) was significantly higher than that of normal skin(n=14) and nevi(n=12)(P=0.0004). LINE-1 U-Index level was elevated with increasing AJCC stage(P<0.0001). AIM1 promoter hypermethylation was found in higher frequency(P=0.005) in metastatic melanoma(65%) than in primary melanomas(38%). When analyzed, high LINE-1 U-Index and/or AIM1 methylation in melanomas were associated with disease-free survival(DFS) and overall survival(OS) in Stage I/II patients (P=0.017, 0.027; respectively). In multivariate analysis, melanoma AIM1 methylation status was a significant prognostic factor of OS(P=0.032). Furthermore, serum unmethylated LINE-1 was at higher levels in both stage III(n=20) and stage IV(n=36) patients compared to healthy donors(n=14)(P=0.022). Circulating methylated AIM1 was detected in patients’ serum and was predictive of OS in Stage IV patients (P=0.009). LINE-1 hypomethylation and AIM1 hypermethylation have prognostic utility in both melanoma patients’ tumors and serum.
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Affiliation(s)
- Sojun Hoshimoto
- Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center, Santa Monica, California 90404, USA
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Harris CR, Normart R, Yang Q, Stevenson E, Haffty BG, Ganesan S, Cordon-Cardo C, Levine AJ, Tang LH. Association of nuclear localization of a long interspersed nuclear element-1 protein in breast tumors with poor prognostic outcomes. Genes Cancer 2011; 1:115-24. [PMID: 20948976 DOI: 10.1177/1947601909360812] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Within healthy human somatic cells, retrotransposition by long interspersed nuclear element-1 (also known as LINE-1 or L1) is thought to be held in check by a variety of mechanisms, including DNA methylation and RNAi. The expression of L1-ORF1 protein, which is rarely found in normal tissue, was assayed using antibodies with a variety of clinical cancer specimens and cancer cell lines. L1-ORF1p expression was detected in nearly all breast tumors that the authors examined, and the protein was also present in a high percentage of ileal carcinoids, bladder, and pancreatic neuroendocrine tumors, as well as in a smaller percentage of prostate and colorectal tumors. Tumors generally demonstrated cytoplasmic L1-ORF1p; however, in several breast cancers, L1-ORF1p was nuclear. Patients with breast tumors displaying nuclear L1-ORF1p had a greater incidence of both local recurrence and distal metastases and also showed poorer overall survival when compared with patients with tumors displaying cytoplasmic L1-ORF1p. These data suggest that expression of L1-ORF1p is widespread in many cancers and that redistribution from cytoplasm to nucleus could be a poor prognostic indicator during breast cancer. High expression and nuclear localization of L1-ORF1p may result in a higher rate of L1 retrotransposition, which could increase genomic instability.
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Beck CR, Garcia-Perez JL, Badge RM, Moran JV. LINE-1 elements in structural variation and disease. Annu Rev Genomics Hum Genet 2011; 12:187-215. [PMID: 21801021 DOI: 10.1146/annurev-genom-082509-141802] [Citation(s) in RCA: 394] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The completion of the human genome reference sequence ushered in a new era for the study and discovery of human transposable elements. It now is undeniable that transposable elements, historically dismissed as junk DNA, have had an instrumental role in sculpting the structure and function of our genomes. In particular, long interspersed element-1 (LINE-1 or L1) and short interspersed elements (SINEs) continue to affect our genome, and their movement can lead to sporadic cases of disease. Here, we briefly review the types of transposable elements present in the human genome and their mechanisms of mobility. We next highlight how advances in DNA sequencing and genomic technologies have enabled the discovery of novel retrotransposons in individual genomes. Finally, we discuss how L1-mediated retrotransposition events impact human genomes.
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Affiliation(s)
- Christine R Beck
- Department of Human Genetics, University of MIchigan Medical School, Ann Arbor, Michigan 48109-5618, USA.
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Zeimet AG, Fiegl H, Goebel G, Kopp F, Allasia C, Reimer D, Steppan I, Mueller-Holzner E, Ehrlich M, Marth C. DNA ploidy, nuclear size, proliferation index and DNA-hypomethylation in ovarian cancer. Gynecol Oncol 2011; 121:24-31. [PMID: 21251700 DOI: 10.1016/j.ygyno.2010.12.332] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 12/07/2010] [Accepted: 12/08/2010] [Indexed: 01/01/2023]
Abstract
OBJECTIVE The present study was undertaken to analyze the impact of epigenetic alterations with a main focus on nuclear area, aneuploidy, hyperploidy, and proliferation in 70 ovarian cancer specimens. METHODS Morphometric changes and somatic chromosomal ploidy status were assessed by Feulgen spectrophotometry. DNA-hypomethylation of LINE1 repeats was analyzed by means of MethyLight PCR, and methylation levels of satellite 2 (Sat2) and satellite alpha (Satα) DNA sequences in chromosome 1 were measured by Southern blot analysis. These parameters were analyzed with regard to correlations as well as to recurrence and survival. RESULTS We identified a significant association between LINE1 DNA-hypomethylation and patient age (p=0.029). Furthermore, LINE1 DNA-hypomethylation was positively correlated with the nuclear area (r=0.47; p<0.001) and the proliferation index (r=0.36; p<0.001). Univariate survival analysis showed that the nuclear area and LINE1 DNA-hypomethylation were prognostic factors for overall (p=0.015 and =0.006, respectively) and progression-free survival (p=0.020 and p=0.001 respectively), the percentage of aneuploidy only for overall survival (p=0.031). Subgroup survival analyses revealed that the prognostic value of these factors is strictly confined to mucinous cancers. In serous cancers no prognostic value could be pointed out for any analyzed parameter. Multivariate analysis of the entire cohort showed that the percentage of hyperploidy was an independent prognostic parameter for overall survival (p=0.003) and LINE1 DNA-hypomethylation for progression-free survival (p=0.03). In mucinous cancers nuclear area and LINE1 DNA-hypomethylation were found to be independent predictors of progression-free and overall survival. CONCLUSIONS In this study we identified the correlations between early cancer-associated genome DNA-hypomethylation, nuclear morphometric changes, somatic chromosomal ploidy status and the proliferation index. Prognostic relevance of nuclear area and LINE1 DNA-hypomethylation was revealed exclusively in mucinous ovarian cancers.
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MESH Headings
- Adenocarcinoma, Mucinous/genetics
- Adenocarcinoma, Mucinous/metabolism
- Adenocarcinoma, Mucinous/pathology
- Adenocarcinoma, Mucinous/surgery
- Adult
- Aged
- Aged, 80 and over
- Cell Growth Processes/physiology
- Cell Nucleus Size/physiology
- Chromosomes, Human, Pair 1
- Cystadenocarcinoma, Serous/genetics
- Cystadenocarcinoma, Serous/metabolism
- Cystadenocarcinoma, Serous/pathology
- Cystadenocarcinoma, Serous/surgery
- DNA Methylation
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Disease-Free Survival
- Female
- Genomic Instability
- Humans
- Long Interspersed Nucleotide Elements
- Middle Aged
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Ovarian Neoplasms/surgery
- Ploidies
- Young Adult
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Affiliation(s)
- Alain G Zeimet
- Department of Gynecology and Obstetrics, Informatics and Health Economics, Innsbruck Medical University, Innsbruck, Austria, Austria
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Abstract
Retrotransposons like L1 are silenced in somatic cells by a
variety of mechanisms acting at different levels. Protective
mechanisms include DNA methylation and packaging into inactive
chromatin to suppress transcription and prevent recombination,
potentially supported by cytidine deaminase editing of RNA.
Furthermore, DNA strand breaks arising during attempted
retrotranspositions ought to activate cellular checkpoints, and L1
activation outside immunoprivileged sites may elicit immune
responses. A number of observations indicate that L1 sequences
nevertheless become reactivated in human cancer. Prominently,
methylation of L1 sequences is diminished in many cancer types and
full-length L1 RNAs become detectable, although strong expression
is restricted to germ cell cancers. L1 elements have been found to
be enriched at sites of illegitimate recombination in many
cancers. In theory, lack of L1 repression in cancer might cause
transcriptional deregulation, insertional mutations, DNA breaks,
and an increased frequency of recombinations, contributing to
genome disorganization, expression changes, and chromosomal
instability. There is however little evidence that such effects
occur at a gross scale in human cancers. Rather, as a rule, L1
repression is only partly alleviated. Unfortunately, many
techniques commonly used to investigate genetic and epigenetic
alterations in cancer cells are not well suited to detect subtle
effects elicited by partial reactivation of retroelements like L1
which are present as abundant, but heterogeneous copies.
Therefore, effects of L1 sequences exerted on the local chromatin
structure, on the transcriptional regulation of individual genes,
and on chromosome fragility need to be more closely investigated
in normal and cancer cells.
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Affiliation(s)
- Wolfgang A. Schulz
- Department of Urology, Heinrich Heine University, Mooreustrasse 5, 40225 Düsseldorf, Germany
- *Wolfgang A. Schulz:
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Ewing AD, Kazazian HH. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Res 2010; 20:1262-70. [PMID: 20488934 DOI: 10.1101/gr.106419.110] [Citation(s) in RCA: 224] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Using high-throughput sequencing, we devised a technique to determine the insertion sites of virtually all members of the human-specific L1 retrotransposon family in any human genome. Using diagnostic nucleotides, we were able to locate the approximately 800 L1Hs copies corresponding specifically to the pre-Ta, Ta-0, and Ta-1 L1Hs subfamilies, with over 90% of sequenced reads corresponding to human-specific elements. We find that any two individual genomes differ at an average of 285 sites with respect to L1 insertion presence or absence. In total, we assayed 25 individuals, 15 of which are unrelated, at 1139 sites, including 772 shared with the reference genome and 367 nonreference L1 insertions. We show that L1Hs profiles recapitulate genetic ancestry, and determine the chromosomal distribution of these elements. Using these data, we estimate that the rate of L1 retrotransposition in humans is between 1/95 and 1/270 births, and the number of dimorphic L1 elements in the human population with gene frequencies greater than 0.05 is between 3000 and 10,000.
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Affiliation(s)
- Adam D Ewing
- University of Pennsylvania Department of Genetics, Philadelphia, Pennsylvania 19104, USA
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Wolff EM, Byun HM, Han HF, Sharma S, Nichols PW, Siegmund KD, Yang AS, Jones PA, Liang G. Hypomethylation of a LINE-1 promoter activates an alternate transcript of the MET oncogene in bladders with cancer. PLoS Genet 2010; 6:e1000917. [PMID: 20421991 PMCID: PMC2858672 DOI: 10.1371/journal.pgen.1000917] [Citation(s) in RCA: 222] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Accepted: 03/19/2010] [Indexed: 12/31/2022] Open
Abstract
It was recently shown that a large portion of the human transcriptome can originate from within repetitive elements, leading to ectopic expression of protein-coding genes. However the mechanism of transcriptional activation of repetitive elements has not been definitively elucidated. For the first time, we directly demonstrate that hypomethylation of retrotransposons can cause altered gene expression in humans. We also reveal that active LINE-1s switch from a tetranucleosome to dinucleosome structure, acquiring H2A.Z- and nucleosome-free regions upstream of TSSs, previously shown only at active single-copy genes. Hypomethylation of a specific LINE-1 promoter was also found to induce an alternate transcript of the MET oncogene in bladder tumors and across the entire urothelium of tumor-bearing bladders. These data show that, in addition to contributing to chromosomal instability, hypomethylation of LINE-1s can alter the functional transcriptome and plays a role not only in human disease but also in disease predisposition. A surprisingly large portion of our transcriptome originates within repetitive elements, most commonly LINE-1s. However, the mechanism of activation has not been definitively shown. We directly demonstrate for the first time the causal relationship between DNA hypomethylation and transcriptional activation of LINE-1 promoters. Hypomethylation of specific LINE-1 promoters can alter the transcriptome, including activating an alternate transcript of the MET oncogene, not only in primary bladder tumors but also in premalignant urothelium across entire bladders with tumors. Our study has important implications for tumor biology, cancer detection, and treatment, and it also answers the long-standing question of whether hypomethylation of retrotransposons induces ectopic gene expression and influences disease susceptibility in humans, a phenomenon first described in agouti mice.
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Affiliation(s)
- Erika M. Wolff
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Hyang-Min Byun
- Department of Hematology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Han F. Han
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Pharmacology and Pharmaceutical Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Shikhar Sharma
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Peter W. Nichols
- Department of Pathology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Kimberly D. Siegmund
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Allen S. Yang
- Department of Hematology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Peter A. Jones
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Gangning Liang
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail:
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35
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Ryan FP. An alternative approach to medical genetics based on modern evolutionary biology. Part 2: retroviral symbiosis. J R Soc Med 2009; 102:324-31. [PMID: 19679734 DOI: 10.1258/jrsm.2009.090183] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Frank P Ryan
- Sheffield Primary Care Trust and Department of Animal and Plant Sciences, Sheffield University, Sheffield, UK.
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36
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St John J, Quinn TW. Recent CR1 non-LTR retrotransposon activity in coscoroba reveals an insertion site preference. BMC Genomics 2008; 9:567. [PMID: 19038033 PMCID: PMC2612034 DOI: 10.1186/1471-2164-9-567] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 11/27/2008] [Indexed: 11/17/2022] Open
Abstract
Background Chicken repeat 1 (CR1) is a taxonomically widespread non-LTR retrotransposon. Insertion site bias, or lack thereof, has not been demonstrated for CR1. Recent CR1 retrotranspositions were used to examine flanking regions for GC content and nucleotide bias at the insertion site. Results Elucidation of the exact octomer repeat sequence (TTCTGTGA) allowed for the identification of younger insertion events. The number of octomer repeats associated with a CR1 element increases after insertion with CR1s having one octomer being youngest. These young CR1s are flanked by regions of low GC content (38%). Furthermore, a bias for specific bases within the first four positions at the site of insertion was revealed. Conclusion This study focused on those loci where the insertion event has been most recent, as this would tend to minimize noise introduced by post-integration mutational events. Our data suggest that CR1 is not inserting into regions of higher GC content within the coscoroba genome; but rather, preferentially inserting into regions of lower GC content. Furthermore, there appears to be a base preference (TTCT) for the insertion site. The results of this study increase the current level of understanding regarding the elusive CR1 non-LTR retrotransposon.
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Affiliation(s)
- Judy St John
- Rocky Mountain Center for Conservation Genetics and Systematics, Division of Natural Sciences and Mathematics, University of Denver, Denver, Colorado, USA.
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37
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Le Rouzic A, Capy P. Population genetics models of competition between transposable element subfamilies. Genetics 2006; 174:785-93. [PMID: 16888345 PMCID: PMC1602078 DOI: 10.1534/genetics.105.052241] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Accepted: 07/24/2006] [Indexed: 11/18/2022] Open
Abstract
Transposable elements are one of the major components of genomes. Some copies are fully efficient; i.e., they are able to produce the proteins needed for their own transposition, and they can move and duplicate into the genome. Other copies are mutated. They may have lost their moving ability, their coding capacity, or both, thus becoming pseudogenes slowly eliminated from the genome through deletions and natural selection. Little is known about the dynamics of such mutant elements, particularly concerning their interactions with autonomous copies. To get a better understanding of the transposable elements' evolution after their initial invasion, we have designed a population genetics model of transposable elements dynamics including mutants or nonfunctional sequences. We have particularly focused on the case where these sequences are nonautonomous elements, known to be able to use the transposition machinery produced by the autonomous ones. The results show that such copies generally prevent the system from achieving a stable transposition-selection equilibrium and that nonautonomous elements can invade the system at the expense of autonomous ones. The resulting dynamics are mainly cyclic, which highlights the similarities existing between genomic selfish DNA sequences and host-parasite systems.
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38
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Witherspoon DJ, Marchani EE, Watkins WS, Ostler CT, Wooding SP, Anders BA, Fowlkes JD, Boissinot S, Furano AV, Ray DA, Rogers AR, Batzer MA, Jorde LB. Human population genetic structure and diversity inferred from polymorphic L1(LINE-1) and Alu insertions. Hum Hered 2006; 62:30-46. [PMID: 17003565 DOI: 10.1159/000095851] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2006] [Accepted: 07/25/2006] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS The L1 retrotransposable element family is the most successful self-replicating genomic parasite of the human genome. L1 elements drive replication of Alu elements, and both have had far-reaching impacts on the human genome. We use L1 and Alu insertion polymorphisms to analyze human population structure. METHODS We genotyped 75 recent, polymorphic L1 insertions in 317 individuals from 21 populations in sub-Saharan Africa, East Asia, Europe and the Indian subcontinent. This is the first sample of L1 loci large enough to support detailed population genetic inference. We analyzed these data in parallel with a set of 100 polymorphic Alu insertion loci previously genotyped in the same individuals. RESULTS AND CONCLUSION The data sets yield congruent results that support the recent African origin model of human ancestry. A genetic clustering algorithm detects clusters of individuals corresponding to continental regions. The number of loci sampled is critical: with fewer than 50 typical loci, structure cannot be reliably discerned in these populations. The inclusion of geographically intermediate populations (from India) reduces the distinctness of clustering. Our results indicate that human genetic variation is neither perfectly correlated with geographic distance (purely clinal) nor independent of distance (purely clustered), but a combination of both: stepped clinal.
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Affiliation(s)
- D J Witherspoon
- Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, UT 84112-5330, USA.
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Lee J, Cordaux R, Han K, Wang J, Hedges DJ, Liang P, Batzer MA. Different evolutionary fates of recently integrated human and chimpanzee LINE-1 retrotransposons. Gene 2006; 390:18-27. [PMID: 17055192 PMCID: PMC1847406 DOI: 10.1016/j.gene.2006.08.029] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 08/05/2006] [Accepted: 08/25/2006] [Indexed: 11/21/2022]
Abstract
The long interspersed element-1 (LINE-1 or L1) is a highly successful retrotransposon in mammals. L1 elements have continued to actively propagate subsequent to the human-chimpanzee divergence, approximately 6 million years ago, resulting in species-specific inserts. Here, we report a detailed characterization of chimpanzee-specific L1 subfamily diversity and a comparison with their human-specific counterparts. Our results indicate that L1 elements have experienced different evolutionary fates in humans and chimpanzees within the past approximately 6 million years. Although the species-specific L1 copy numbers are on the same order in both species (1200-2000 copies), the number of retrotransposition-competent elements appears to be much higher in the human genome than in the chimpanzee genome. Also, while human L1 subfamilies belong to the same lineage, we identified two lineages of recently integrated L1 subfamilies in the chimpanzee genome. The two lineages seem to have coexisted for several million years, but only one shows evidence of expansion within the past three million years. These differential evolutionary paths may be the result of random variation, or the product of competition between L1 subfamily lineages. Our results suggest that the coexistence of several L1 subfamily lineages within a species may be resolved in a very short evolutionary period of time, perhaps in just a few million years. Therefore, the chimpanzee genome constitutes an excellent model in which to analyze the evolutionary dynamics of L1 retrotransposons.
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Affiliation(s)
- Jungnam Lee
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Richard Cordaux
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Kyudong Han
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Jianxin Wang
- Department of Cancer Genetics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Dale J. Hedges
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
| | - Ping Liang
- Department of Cancer Genetics, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
| | - Mark A. Batzer
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
- * Corresponding author. Tel.: +1 225 578 7102; fax: +1 225 578 7113. E-mail address: (M.A. Batzer)
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40
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Schulz WA, Steinhoff C, Florl AR. Methylation of endogenous human retroelements in health and disease. Curr Top Microbiol Immunol 2006; 310:211-50. [PMID: 16909913 DOI: 10.1007/3-540-31181-5_11] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Retroelements constitute approximately 45% of the human genome. Long interspersed nuclear element (LINE) autonomous retrotransposons are predominantly represented by LINE-1, nonautonomous small interspersed nuclear elements (SINEs) are primarily represented by ALUs, and LTR retrotransposons by several families of human endogenous retroviruses (HERVs). The vast majority of LINE and HERV elements are densely methylated in normal somatic cells and contained in inactive chromatin. Methylation and chromatin structure together ensure a stable equilibrium between retroelements and their host. Hypomethylation and expression in developing germ cells opens a "window of opportunity" for retrotransposition and recombination that contribute to human evolution, but also inherited disease. In somatic cells, the presence of retroelements may be exploited to organize the genome into active and inactive regions, to separate domains and functional regions within one chromatin domain, to suppress transcriptional noise, and to regulate transcript stability. Retroelements, particularly ALUs, may also fulfill physiological roles during responses to stress and infections. Reactivation and hypomethylation of LINEs and HERVs may be important in the pathophysiology of cancer and various autoimmune diseases, contributing to chromosomal instability and chronically aberrant immune responses. The emerging insights into the pathophysiological importance of endogenous retroelements accentuate the gaps in our knowledge of how these elements are controlled in normal developing and mature cells.
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Affiliation(s)
- W A Schulz
- Urologische Klinik, Heinrich Heine Universität, Düsseldorf, Germany.
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41
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Khan H, Smit A, Boissinot S. Molecular evolution and tempo of amplification of human LINE-1 retrotransposons since the origin of primates. Genome Res 2005; 16:78-87. [PMID: 16344559 PMCID: PMC1356131 DOI: 10.1101/gr.4001406] [Citation(s) in RCA: 253] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We investigated the evolution of the families of LINE-1 (L1) retrotransposons that have amplified in the human lineage since the origin of primates. We identified two phases in the evolution of L1. From approximately 70 million years ago (Mya) until approximately 40 Mya, three distinct L1 lineages were simultaneously active in the genome of ancestral primates. In contrast, during the last 40 million years (Myr), i.e., during the evolution of anthropoid primates, a single lineage of families has evolved and amplified. We found that novel (i.e., unrelated) regulatory regions (5'UTR) have been frequently recruited during the evolution of L1, whereas the two open-reading frames (ORF1 and ORF2) have remained relatively conserved. We found that L1 families coexisted and formed independently evolving L1 lineages only when they had different 5'UTRs. We propose that L1 families with different 5'UTR can coexist because they don't rely on the same host-encoded factors for their transcription and therefore do not compete with each other. The most prolific L1 families (families L1PA8 to L1PA3) amplified between 40 and 12 Mya. This period of high activity corresponds to an episode of adaptive evolution in a segment of ORF1. The correlation between the high activity of L1 families and adaptive evolution could result from the coevolution of L1 and a host-encoded repressor of L1 activity.
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Affiliation(s)
- Hameed Khan
- Department of Biology, Queens College, the City University of New York, Flushing, New York 11367, USA
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42
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Roman-Gomez J, Jimenez-Velasco A, Agirre X, Cervantes F, Sanchez J, Garate L, Barrios M, Castillejo JA, Navarro G, Colomer D, Prosper F, Heiniger A, Torres A. Promoter hypomethylation of the LINE-1 retrotransposable elements activates sense/antisense transcription and marks the progression of chronic myeloid leukemia. Oncogene 2005; 24:7213-23. [PMID: 16170379 DOI: 10.1038/sj.onc.1208866] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Revised: 04/20/2005] [Accepted: 05/20/2005] [Indexed: 01/05/2023]
Abstract
Aberrant genome-wide hypomethylation is thought to be related to tumorigenesis by promoting genomic instability. Since DNA methylation is considered an important mechanism for the silencing of retroelements, hypomethylation in human tumors may lead to their reactivation. However, the role of DNA hypomethylation in chronic myeloid leukemia (CML) remains to be elucidated. In this study, the methylation status of the LINE-1 (L1) retrotransposon promoter was analysed in CML samples from the chronic-phase (CP, n=140) and the blast crisis (BC, n=47). L1 hypomethylation was significantly more frequent in BC (74.5%) than in CP (38%) (P<0.0001). Furthermore, L1 hypomethylation led to activation of both ORF1 sense transcription (P<0.0001) and c-MET gene antisense transcription (P<0.0001), and was significantly associated with high levels of BCR-ABL (P=0.02) and DNMT3b4 (P=0.001) transcripts. Interestingly, in CP-CML, extensive L1 hypomethylation was associated with poorer prognosis in terms of cytogenetic response to interferon (P=0.004) or imatinib (P=0.034) and progression-free survival (P=0.005). The above results strongly suggest that activation of both sense and antisense transcriptions by aberrant promoter hypomethylation of the L1 elements plays a role in the progression and clinical behavior of the CML.
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MESH Headings
- Adult
- Antineoplastic Agents/therapeutic use
- Benzamides
- Blast Crisis/genetics
- Blast Crisis/pathology
- CpG Islands
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Disease Progression
- Female
- Humans
- Imatinib Mesylate
- Interferons/therapeutic use
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/mortality
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy
- Leukemia, Myeloid, Chronic-Phase/genetics
- Leukemia, Myeloid, Chronic-Phase/pathology
- Leukemia, Myeloid, Chronic-Phase/therapy
- Long Interspersed Nucleotide Elements/genetics
- Male
- Middle Aged
- Multivariate Analysis
- Open Reading Frames
- Piperazines/therapeutic use
- Promoter Regions, Genetic
- Proto-Oncogene Proteins c-abl/metabolism
- Proto-Oncogene Proteins c-met/metabolism
- Pyrimidines/therapeutic use
- Regression Analysis
- Retroelements/genetics
- Transcription, Genetic/drug effects
- Treatment Outcome
- DNA Methyltransferase 3B
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Affiliation(s)
- Jose Roman-Gomez
- Hematology Department, Reina Sofia Hospital, Avda. Menendez Pidal s/n. 14004, Cordoba, Spain.
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43
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Boissinot S, Furano AV. The recent evolution of human L1 retrotransposons. Cytogenet Genome Res 2005; 110:402-6. [PMID: 16093692 DOI: 10.1159/000084972] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2003] [Accepted: 11/07/2003] [Indexed: 11/19/2022] Open
Abstract
L1 elements are the most successful retrotransposons in mammals and are responsible for at least 30% of human DNA. Far from being indolent genomic parasites, L1 elements have evolved and amplified rapidly during human evolution. Indeed during just the last 25 million years (MY) five distinct L1 families have emerged and generated tens of thousands of copies. The most recently evolved human specific L1 family is currently active and L1 copies have been accumulating in the human genome at about the same rate per generation as the currently active L1 families in Old World rats and mice. At times during the last 25 MY L1 activity constituted a significant enough genetic load to be subject to negative selection. During these same times, and in apparent response to the host, L1 underwent adaptive evolution. Understanding the molecular basis for these evolutionary changes should help illuminate one of the least understood but most important aspects of L1 biology, namely the extent and nature of the interaction between L1 and its host.
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Affiliation(s)
- S Boissinot
- Department of Biology, Queens College, CUNY, Flushing, NY 11367-1597, USA.
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44
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Han K, Sen SK, Wang J, Callinan PA, Lee J, Cordaux R, Liang P, Batzer MA. Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages. Nucleic Acids Res 2005; 33:4040-52. [PMID: 16034026 PMCID: PMC1179734 DOI: 10.1093/nar/gki718] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Long INterspersed Elements (LINE-1s or L1s) are abundant non-LTR retrotransposons in mammalian genomes that are capable of insertional mutagenesis. They have been associated with target site deletions upon insertion in cell culture studies of retrotransposition. Here, we report 50 deletion events in the human and chimpanzee genomes directly linked to the insertion of L1 elements, resulting in the loss of approximately 18 kb of sequence from the human genome and approximately 15 kb from the chimpanzee genome. Our data suggest that during the primate radiation, L1 insertions may have deleted up to 7.5 Mb of target genomic sequences. While the results of our in vivo analysis differ from those of previous cell culture assays of L1 insertion-mediated deletions in terms of the size and rate of sequence deletion, evolutionary factors can reconcile the differences. We report a pattern of genomic deletion sizes similar to those created during the retrotransposition of Alu elements. Our study provides support for the existence of different mechanisms for small and large L1-mediated deletions, and we present a model for the correlation of L1 element size and the corresponding deletion size. In addition, we show that internal rearrangements can modify L1 structure during retrotransposition events associated with large deletions.
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Affiliation(s)
| | | | - Jianxin Wang
- Department of Cancer Genetics, Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, NY 14263, USA
| | | | | | | | - Ping Liang
- Department of Cancer Genetics, Roswell Park Cancer InstituteElm and Carlton Streets, Buffalo, NY 14263, USA
| | - Mark A. Batzer
- To whom correspondence should be addressed. Tel: +1 225 578 7102; Fax: +1 225 578 7113;
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45
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Chen JM, Stenson PD, Cooper DN, Férec C. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet 2005; 117:411-27. [PMID: 15983781 DOI: 10.1007/s00439-005-1321-0] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Accepted: 04/04/2005] [Indexed: 10/25/2022]
Abstract
Diverse long interspersed element-1 (LINE-1 or L1)-dependent mutational mechanisms have been extensively studied with respect to L1 and Alu elements engineered for retrotransposition in cultured cells and/or in genome-wide analyses. To what extent the in vitro studies can be held to accurately reflect in vivo events in the human genome, however, remains to be clarified. We have attempted to address this question by means of a systematic analysis of recent L1-mediated retrotranspositional events that have caused human genetic disease, with a view to providing a more complete picture of how L1-mediated retrotransposition impacts upon the architecture of the human genome. A total of 48 such mutations were identified, including those described as L1-mediated retrotransposons, as well as insertions reported to contain a poly(A) tail: 26 were L1 trans-driven Alu insertions, 15 were direct L1 insertions, four were L1 trans-driven SVA insertions, and three were associated with simple poly(A) insertions. The systematic study of these lesions, when combined with previous in vitro and genome-wide analyses, has strengthened several important conclusions regarding L1-mediated retrotransposition in humans: (a) approximately 25% of L1 insertions are associated with the 3' transduction of adjacent genomic sequences, (b) approximately 25% of the new L1 inserts are full-length, (c) poly(A) tail length correlates inversely with the age of the element, and (d) the length of target site duplication in vivo is rarely longer than 20 bp. Our analysis also suggests that some 10% of L1-mediated retrotranspositional events are associated with significant genomic deletions in humans. Finally, the identification of independent retrotranspositional events that have integrated at the same genomic locations provides new insight into the L1-mediated insertional process in humans.
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Affiliation(s)
- Jian-Min Chen
- INSERM U613-Génétique Moléculaire et Génétique Epidémiologique, Etablissement Français du Sang-Bretagne, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, 29220, France.
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46
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Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. Natural genetic variation caused by transposable elements in humans. Genetics 2005; 168:933-51. [PMID: 15514065 PMCID: PMC1448813 DOI: 10.1534/genetics.104.031757] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Transposons and transposon-like repetitive elements collectively occupy 44% of the human genome sequence. In an effort to measure the levels of genetic variation that are caused by human transposons, we have developed a new method to broadly detect transposon insertion polymorphisms of all kinds in humans. We began by identifying 606,093 insertion and deletion (indel) polymorphisms in the genomes of diverse humans. We then screened these polymorphisms to detect indels that were caused by de novo transposon insertions. Our method was highly efficient and led to the identification of 605 nonredundant transposon insertion polymorphisms in 36 diverse humans. We estimate that this represents 25-35% of approximately 2075 common transposon polymorphisms in human populations. Because we identified all transposon insertion polymorphisms with a single method, we could evaluate the relative levels of variation that were caused by each transposon class. The average human in our study was estimated to harbor 1283 Alu insertion polymorphisms, 180 L1 polymorphisms, 56 SVA polymorphisms, and 17 polymorphisms related to other forms of mobilized DNA. Overall, our study provides significant steps toward (i) measuring the genetic variation that is caused by transposon insertions in humans and (ii) identifying the transposon copies that produce this variation.
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Affiliation(s)
- E Andrew Bennett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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47
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Duvernell DD, Pryor SR, Adams SM. Teleost fish genomes contain a diverse array of L1 retrotransposon lineages that exhibit a low copy number and high rate of turnover. J Mol Evol 2005; 59:298-308. [PMID: 15553085 DOI: 10.1007/s00239-004-2625-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Retrotransposable elements exhibit a wide range of variation in population dynamics, abundance, and lineage diversity among host genomes across taxa. This range of diversity is illustrated by a single well-defined constituent monophyletic clade of L1 non-LTR retrotransposons that is shared between mammalian and teleost fish genomes. Despite the clear phylogenetic relationships that exist between mammalian and teleost L1 sequences, these elements exhibit markedly different dynamics within their respective taxa. While mammalian genomes typically contain a single, abundant lineage of L1 elements that traces millions of years of evolution, the zebraflsh genome was recently shown to exhibit a high diversity of ancient lineages coexisting at a very low copy number and apparently exhibiting a high rate of turnover. In the present study, a combination of degenerate PCR, lineage-specific PCR, and genomic Southern blot analysis is utilized to demonstrate high L1 lineage diversity, low copy number, and a high proportion of polymorphic inserts in the genomes of the killifish species, Fundulus heteroclitus. Additional species surveyed by degenerate PCR include Cyprinodon variegatus, Rivulus marmoratus, and Menidia beryllina. These results further support the generality of the differences that exist in host-element dynamics between teleost fish and mammalian genomes with regard to L1 retrotransposons.
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Affiliation(s)
- David D Duvernell
- Department of Biological Sciences, Southern Illinois University, Edwardsville, IL 62026, USA.
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48
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Nelson PN, Hooley P, Roden D, Davari Ejtehadi H, Rylance P, Warren P, Martin J, Murray PG. Human endogenous retroviruses: transposable elements with potential? Clin Exp Immunol 2004; 138:1-9. [PMID: 15373898 PMCID: PMC1809191 DOI: 10.1111/j.1365-2249.2004.02592.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2004] [Indexed: 12/20/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are a significant component of a wider family of retroelements that constitute part of the human genome. These viruses, perhaps representative of previous exogenous retroviral infection, have been integrated and passed through successive generations within the germ line. The retention of HERVs and isolated elements, such as long-terminal repeats, could have the potential to harm. In this review we describe HERVs within the context of the family of known transposable elements and survey these viruses in terms of superantigens and molecular mimics. It is entirely possible that these mechanisms provide the potential for undesired immune responses.
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Affiliation(s)
- P N Nelson
- Research Institute in Healthcare Science, University of Wolverhampton, UK.
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49
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Farley AH, Luning Prak ET, Kazazian HH. More active human L1 retrotransposons produce longer insertions. Nucleic Acids Res 2004; 32:502-10. [PMID: 14742665 PMCID: PMC373329 DOI: 10.1093/nar/gkh202] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Revised: 09/18/2003] [Accepted: 12/10/2003] [Indexed: 11/13/2022] Open
Abstract
The vast majority of L1 insertions are 5' truncated and thus inactive. Yet, the mechanism of 5' truncation is unknown. To examine whether the frequency of L1 retrotransposition is directly correlated with the length of genomic L1 insertions, we used a cell culture assay to measure retrotransposition frequency and a PCR-based assay to measure L1 insertion length. We tested five full-length human L1 elements that retrotranspose at different frequencies: LRE3, L1(RP), L1.3, L1.2A and L1.2B. Our data suggest that L1 insertion length correlates with L1 retrotransposition frequency for insertions >1 kb in length. For two elements, L1(RP) and L1.2A, we found that swapping the reverse transcriptase domains had little effect. Instead, we found that genomic insertion length and retrotransposition frequency are substantially affected by amino acid substitutions at positions 363, 1220 and 1259 in ORF2. We suggest that the region containing residues 1220 and 1259 may be important in the binding of ORF2p to L1 RNA to facilitate reverse transcription.
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Affiliation(s)
- Alexander H Farley
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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50
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Ostertag EM, Goodier JL, Zhang Y, Kazazian HH. SVA elements are nonautonomous retrotransposons that cause disease in humans. Am J Hum Genet 2003; 73:1444-51. [PMID: 14628287 PMCID: PMC1180407 DOI: 10.1086/380207] [Citation(s) in RCA: 253] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Accepted: 09/24/2003] [Indexed: 11/04/2022] Open
Abstract
L1 elements are the only active autonomous retrotransposons in the human genome. The nonautonomous Alu elements, as well as processed pseudogenes, are retrotransposed by the L1 retrotransposition proteins working in trans. Here, we describe another repetitive sequence in the human genome, the SVA element. Our analysis reveals that SVA elements are currently active in the human genome. SVA elements, like Alus and L1s, occasionally insert into genes and cause disease. Furthermore, SVA elements are probably mobilized in trans by active L1 elements.
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Affiliation(s)
- Eric M Ostertag
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6145, USA
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