201
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The Fine LINE: Methylation Drawing the Cancer Landscape. BIOMED RESEARCH INTERNATIONAL 2015; 2015:131547. [PMID: 26448926 PMCID: PMC4584040 DOI: 10.1155/2015/131547] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 11/17/2014] [Accepted: 11/25/2014] [Indexed: 01/08/2023]
Abstract
LINE-1 (L1) is the most abundant mammalian transposable element that comprises nearly 20% of the genome, and nearly half of the mammalian genome has stemmed from L1-mediated mobilization. Expression and retrotransposition of L1 are suppressed by complex mechanisms, where the key role belongs to DNA methylation. Alterations in L1 methylation may lead to aberrant expression of L1 and have been described in numerous diseases. Accumulating evidence clearly indicates that loss of global DNA methylation observed in cancer development and progression is tightly associated with hypomethylation of L1 elements. Significant progress achieved in the last several years suggests that such parameters as L1 methylation status can be potentially utilized as clinical biomarkers for determination of the disease stage and in predicting the disease-free survival in cancer patients. In this paper, we summarize the current knowledge on L1 methylation, with specific emphasis given to success and challenges on the way of introduction of L1 into clinical practice.
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202
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Konkel MK, Walker JA, Hotard AB, Ranck MC, Fontenot CC, Storer J, Stewart C, Marth GT, Batzer MA. Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project. Genome Biol Evol 2015; 7:2608-22. [PMID: 26319576 PMCID: PMC4607524 DOI: 10.1093/gbe/evv167] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2015] [Indexed: 12/17/2022] Open
Abstract
The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic "young" Alu insertion events, absent from the human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths. All the sequenced Alu loci were derived from the AluY lineage with no evidence of retrotransposition activity involving older Alu families (e.g., AluJ and AluS). AluYa5 is currently the most active Alu subfamily in the human lineage, followed by AluYb8, and many others including three newly identified subfamilies we have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages.
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Affiliation(s)
- Miriam K Konkel
- Department of Biological Sciences, Louisiana State University
| | | | - Ashley B Hotard
- Department of Biological Sciences, Louisiana State University
| | - Megan C Ranck
- Department of Biological Sciences, Louisiana State University
| | | | - Jessica Storer
- Department of Biological Sciences, Louisiana State University Department of Molecular, Cellular and Developmental Biology, The Ohio State University
| | - Chip Stewart
- Department of Biology, Boston College Cancer Genome Computational Analysis, Cambridge, MA
| | - Gabor T Marth
- Department of Biology, Boston College Eccles Institute of Human Genetics, University of Utah
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University
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203
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Tsai CL, Williams GJ, Perry JJP, Tainer JA. An AAA+ ATPase Clamshell Targets Transposition. Cell 2015; 162:701-3. [PMID: 26276624 DOI: 10.1016/j.cell.2015.07.050] [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] [Indexed: 11/19/2022]
Abstract
DNA transposition plays key roles in genome diversity, pathogenesis, and evolution. Yet, structural and mechanistic information on transposition targeting and regulation is limited. Arias-Palomo and Berger now define the decameric organization of the AAA+ ATPase IstB, unveiling key insights into its targeting and regulation of IstA transposase activity.
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Affiliation(s)
- Chi-Lin Tsai
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gareth J Williams
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - J Jefferson P Perry
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
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204
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Jin Y, Tam OH, Paniagua E, Hammell M. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics 2015. [PMID: 26206304 DOI: 10.1093/bioinformatics/btv422] [Citation(s) in RCA: 320] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Most RNA-seq data analysis software packages are not designed to handle the complexities involved in properly apportioning short sequencing reads to highly repetitive regions of the genome. These regions are often occupied by transposable elements (TEs), which make up between 20 and 80% of eukaryotic genomes. They can contribute a substantial portion of transcriptomic and genomic sequence reads, but are typically ignored in most analyses. RESULTS Here, we present a method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. Our method shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR/NanoString-validated published datasets. AVAILABILITY AND IMPLEMENTATION The source code, associated GTF files for TE annotation, and testing data are freely available at http://hammelllab.labsites.cshl.edu/software. CONTACT mhammell@cshl.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ying Jin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Oliver H Tam
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Eric Paniagua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
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205
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Abstract
Alu element is the most successful transposon and it maintains a high level of content in primate genome. However, despite the fact that the expression level of independent Alu element is rather low under common condition, an increasing number of the observations for the Alu transcripts in cells and tissues have been reported recently. Alu transcripts play key roles in the network of gene expression regulation. The main functions of Alu transcript focus on gene regulation both at transcriptional and post-transcriptional levels. This review summarizes major functions of Alu transcripts on gene expression and highlights molecular mechanisms dependent on conserved sequence or secondary structure in order to unravel a relative ubiquitous way that Alu transcript uses to affect the whole genome.
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Affiliation(s)
- Li Zhang
- Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China.
| | - Ju-Gao Chen
- Department of Oncology, The Second Clinical Medical college (Shenzhen People׳s Hospital), Jinan University, Shenzhen, Guangdong, China
| | - Qi Zhao
- Laboratory of Fully Human Antibody Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China.
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206
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Miousse IR, Chalbot MCG, Lumen A, Ferguson A, Kavouras IG, Koturbash I. Response of transposable elements to environmental stressors. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2015; 765:19-39. [PMID: 26281766 PMCID: PMC4544780 DOI: 10.1016/j.mrrev.2015.05.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 12/21/2022]
Abstract
Transposable elements (TEs) comprise a group of repetitive sequences that bring positive, negative, as well as neutral effects to the host organism. Earlier considered as "junk DNA," TEs are now well-accepted driving forces of evolution and critical regulators of the expression of genetic information. Their activity is regulated by epigenetic mechanisms, including methylation of DNA and histone modifications. The loss of epigenetic control over TEs, exhibited as loss of DNA methylation and decondensation of the chromatin structure, may result in TEs reactivation, initiation of their insertional mutagenesis (retrotransposition) and has been reported in numerous human diseases, including cancer. Accumulating evidence suggests that these alterations are not the simple consequences of the disease, but often may drive the pathogenesis, as they can be detected early during disease development. Knowledge derived from the in vitro, in vivo, and epidemiological studies, clearly demonstrates that exposure to ubiquitous environmental stressors, many of which are carcinogens or suspected carcinogens, are capable of causing alterations in methylation and expression of TEs and initiate retrotransposition events. Evidence summarized in this review suggests that TEs are the sensitive endpoints for detection of effects caused by such environmental stressors, as ionizing radiation (terrestrial, space, and UV-radiation), air pollution (including particulate matter [PM]-derived and gaseous), persistent organic pollutants, and metals. Furthermore, the significance of these effects is characterized by their early appearance, persistence and presence in both, target organs and peripheral blood. Altogether, these findings suggest that TEs may potentially be introduced into safety and risk assessment and serve as biomarkers of exposure to environmental stressors. Furthermore, TEs also show significant potential to become invaluable surrogate biomarkers in clinic and possible targets for therapeutic modalities for disease treatment and prevention.
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Affiliation(s)
- Isabelle R Miousse
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Marie-Cecile G Chalbot
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Annie Lumen
- Division of Biochemical Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Alesia Ferguson
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Ilias G Kavouras
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Igor Koturbash
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
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207
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Sciamanna I, Gualtieri A, Piazza PF, Spadafora C. Regulatory roles of LINE-1-encoded reverse transcriptase in cancer onset and progression. Oncotarget 2015; 5:8039-51. [PMID: 25478632 PMCID: PMC4226666 DOI: 10.18632/oncotarget.2504] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
LINE-1 retrotransposons encode the reverse transcriptase (RT) enzyme, required for their own mobility, the expression of which is inhibited in differentiated tissues while being active in tumors. Experimental evidence indicate that the inhibition of LINE-1-derived RT restores differentiation in cancer cells, inhibits tumor progression and yields globally reprogrammed transcription profiles. Newly emerging data suggest that LINE-1-encoded RT modulates the biogenesis of miRNAs, by governing the balance between the production of regulatory double-stranded RNAs and RNA:DNA hybrid molecules, with a direct impact on global gene expression. Abnormally high RT activity unbalances the transcriptome in cancer cells, while RT inhibition restores ‘normal’ miRNA profiles and their regulatory networks. This RT-dependent mechanism can target the myriad of transcripts - both coding and non-coding, sense and antisense - in eukaryotic transcriptomes, with a profound impact on cell fates. LINE-1-encoded RT emerges therefore as a key regulator of a previously unrecognized mechanism in tumorigenesis
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208
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Jang S, Harshey RM. Repair of transposable phage Mu DNA insertions begins only when the E. coli replisome collides with the transpososome. Mol Microbiol 2015; 97:746-58. [PMID: 25983038 DOI: 10.1111/mmi.13061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/14/2015] [Indexed: 01/28/2023]
Abstract
We report a new cellular interaction between the infecting transposable phage Mu and the host Escherichia coli replication machinery during repair of Mu insertions, which involves filling-in of short target gaps on either side of the insertion, concomitant with degradation of extraneous long flanking DNA (FD) linked to Mu. Using the FD as a marker to follow repair, we find that after transposition into the chromosome, the unrepaired Mu is indefinitely stable until the replication fork arrives at the insertion site, whereupon the FD is rapidly degraded. When the fork runs into a Mu target gap, a double strand end (DSE) will result; we demonstrate fork-dependent DSEs proximal to Mu. These findings suggest that Pol III stalled at the transpososome is exploited for co-ordinated repair of both target gaps flanking Mu without replicating the intervening 37 kb of Mu, disassembling the stable transpososome in the process. This work is relevant to all transposable elements, including retroviral elements like HIV-1, which share with Mu the common problem of repair of their flanking target gaps.
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Affiliation(s)
- Sooin Jang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Rasika M Harshey
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
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209
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Karimi A, Majidzadeh-A K, Madjd Z, Akbari A, Habibi L, Akrami SM. Effect of Copper Sulfate on Expression of Endogenous L1 Retrotransposons in HepG2 Cells (Hepatocellular Carcinoma). Biol Trace Elem Res 2015; 165:131-4. [PMID: 25663478 DOI: 10.1007/s12011-015-0256-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/25/2015] [Indexed: 12/26/2022]
Abstract
The long interspersed element-1 (LINE-1 or L1) constitutes approximately 17% of human genome. The expression of these elements is deregulated upon exposure to environmental exposures resulting to genomic instability and cancer promotion. The effect of copper as essential elements in regulation of L1 expression remained to be elucidated. Using non-cytotoxic concentrations of the copper, the expression of endogenous L1 was analyzed by qPCR after 6 days of copper pretreatment in human hepatocellular carcinoma cells (HepG2). The results indicated that the expression of active L1 elements are significantly downregulated at concentrations of 12.5, 25, and 50 μM (p < 0.005). Our data imply that low-level copper exposure may have a protective effect to suppress the induction of L1 activity and decrease incidence of cancer-associated L1 mutagenesis. If this achievement is confirmed by further studies, it can be applied in the long-term goals of cancer prevention.
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Affiliation(s)
- Abbas Karimi
- Tasnim Biotechnology Research Center (TBRC), Faculty of Medicine, AJA University of Medical Sciences, Etemadzadeh Ave., West Fatemi, Tehran, Iran
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210
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Naville M, Chalopin D, Casane D, Laurenti P, Volff JN. The coelacanth: Can a "living fossil" have active transposable elements in its genome? Mob Genet Elements 2015; 5:55-59. [PMID: 26442185 DOI: 10.1080/2159256x.2015.1052184] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 01/24/2023] Open
Abstract
The coelacanth has long been regarded as a "living fossil," with extant specimens looking very similar to fossils dating back to the Cretaceous period. The hypothesis of a slowly or even not evolving genome has been proposed to account for this apparent morphological stasis. While this assumption seems to be sustained by different evolutionary analyses on protein-coding genes, recent studies on transposable elements have provided more conflicting results. Indeed, the coelacanth genome contains many transposable elements and has been shaped by several major bursts of transposition during evolution. In addition, comparison of orthologous genomic regions from the genomes of the 2 extant coelacanth species L. chalumnae and L. menadoensis revealed multiple species-specific insertions, indicating transposable element recent activity and contribution to post-speciation genome divergence. These observations, which do not support the genome stasis hypothesis, challenge either the impact of transposable elements on organismal evolution or the status of the coelacanth as a "living fossil." Closer inspection of fossil and molecular data indicate that, even if coelacanths might evolve more slowly than some other lineages due to demographic and/or ecological factors, this variation is still in the range of a "non-fossil" vertebrate species.
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Affiliation(s)
- Magali Naville
- Equipe "Génomique des Poissons"; Institut de Génomique Fonctionnelle de Lyon (UMR5242); Ecole Normale Supérieure de Lyon ; Lyon, France
| | - Domitille Chalopin
- Equipe "Génomique des Poissons"; Institut de Génomique Fonctionnelle de Lyon (UMR5242); Ecole Normale Supérieure de Lyon ; Lyon, France
| | - Didier Casane
- Equipe "Réseaux de gènes, développement, évolution" Laboratoire Evolution, Génomes, Comportement, Ecologie (UMR9191); Université Paris-Diderot; UFR des Sciences du vivant ; Paris, France
| | - Patrick Laurenti
- Equipe "Réseaux de gènes, développement, évolution" Laboratoire Evolution, Génomes, Comportement, Ecologie (UMR9191); Université Paris-Diderot; UFR des Sciences du vivant ; Paris, France
| | - Jean-Nicolas Volff
- Equipe "Génomique des Poissons"; Institut de Génomique Fonctionnelle de Lyon (UMR5242); Ecole Normale Supérieure de Lyon ; Lyon, France
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211
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Lin X, Stenvang J, Rasmussen MH, Zhu S, Jensen NF, Tarpgaard LS, Yang G, Belling K, Andersen CL, Li J, Bolund L, Brünner N. The potential role of Alu Y in the development of resistance to SN38 (Irinotecan) or oxaliplatin in colorectal cancer. BMC Genomics 2015; 16:404. [PMID: 25997618 PMCID: PMC4440512 DOI: 10.1186/s12864-015-1552-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Accepted: 04/17/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Irinotecan (SN38) and oxaliplatin are chemotherapeutic agents used in the treatment of colorectal cancer. However, the frequent development of resistance to these drugs represents a considerable challenge in the clinic. Alus as retrotransposons comprise 11% of the human genome. Genomic toxicity induced by carcinogens or drugs can reactivate Alus by altering DNA methylation. Whether or not reactivation of Alus occurs in SN38 and oxaliplatin resistance remains unknown. RESULTS We applied reduced representation bisulfite sequencing (RRBS) to investigate the DNA methylome in SN38 or oxaliplatin resistant colorectal cancer cell line models. Moreover, we extended the RRBS analysis to tumor tissue from 14 patients with colorectal cancer who either did or did not benefit from capecitabine + oxaliplatin treatment. For the clinical samples, we applied a concept of 'DNA methylation entropy' to estimate the diversity of DNA methylation states of the identified resistance phenotype-associated methylation loci observed in the cell line models. We identified different loci being characteristic for the different resistant cell lines. Interestingly, 53% of the identified loci were Alu sequences- especially the Alu Y subfamily. Furthermore, we identified an enrichment of Alu Y sequences that likely results from increased integration of new copies of Alu Y sequence in the drug-resistant cell lines. In the clinical samples, SOX1 and other SOX gene family members were shown to display variable DNA methylation states in their gene regions. The Alu Y sequences showed remarkable variation in DNA methylation states across the clinical samples. CONCLUSION Our findings imply a crucial role of Alu Y in colorectal cancer drug resistance. Our study underscores the complexity of colorectal cancer aggravated by mobility of Alu elements and stresses the importance of personalized strategies, using a systematic and dynamic view, for effective cancer therapy.
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Affiliation(s)
- Xue Lin
- Department of Biomedicine, University of Aarhus, the Bartholin Building, DK-8000, Aarhus C, Denmark.
| | - Jan Stenvang
- Department of Veterinary Disease Biology, Section of Molecular Disease Biology, Faculty of Health and Medical Sciences, Copenhagen University, Strandboulevarden 49, Copenhagen, Denmark.
| | - Mads Heilskov Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgårdsvej 100, DK-8200, Aarhus N, Denmark.
| | - Shida Zhu
- BGI (Beijing Genomics Institute), Shenzhen, 518083, China.
| | - Niels Frank Jensen
- Department of Veterinary Disease Biology, Section of Molecular Disease Biology, Faculty of Health and Medical Sciences, Copenhagen University, Strandboulevarden 49, Copenhagen, Denmark.
| | - Line S Tarpgaard
- Department of Oncology, Odense University Hospital, Sdr. Boulevard 29, DK-5000, Odense C, Denmark.
| | - Guangxia Yang
- BGI (Beijing Genomics Institute), Shenzhen, 518083, China.
| | - Kirstine Belling
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800, Lyngby, Denmark.
| | - Claus Lindbjerg Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Brendstrupgårdsvej 100, DK-8200, Aarhus N, Denmark.
| | - Jian Li
- Department of Biomedicine, University of Aarhus, the Bartholin Building, DK-8000, Aarhus C, Denmark.
- BGI (Beijing Genomics Institute), Shenzhen, 518083, China.
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing, 210096, China.
| | - Lars Bolund
- Department of Biomedicine, University of Aarhus, the Bartholin Building, DK-8000, Aarhus C, Denmark.
- BGI (Beijing Genomics Institute), Shenzhen, 518083, China.
| | - Nils Brünner
- Department of Veterinary Disease Biology, Section of Molecular Disease Biology, Faculty of Health and Medical Sciences, Copenhagen University, Strandboulevarden 49, Copenhagen, Denmark.
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212
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Abstract
Transposable elements (TEs) are an important factor shaping eukaryotic genomes. Although a significant body of research has been conducted on the abundance of TEs in nuclear genomes, TEs in mitochondrial genomes remain elusive. In this study, we successfully assembled 28 complete yeast mitochondrial genomes and took advantage of the power of population genomics to determine mobile DNAs and their propensity. We have observed compelling evidence of GC clusters propagating within the mitochondrial genome and being horizontally transferred between species. These mitochondrial TEs experience rapid diversification by nucleotide substitution and, more importantly, undergo dynamic merger and shuffling to form new TEs. Given the hyper mobile and transformable nature of mitochondrial TEs, our findings open the door to a deeper understanding of eukaryotic mitochondrial genome evolution and the origin of nonautonomous TEs.
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213
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Ma B, Li T, Xiang Z, He N. MnTEdb, a collective resource for mulberry transposable elements. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav004. [PMID: 25725060 PMCID: PMC4343074 DOI: 10.1093/database/bav004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mulberry has been used as an economically important food crop for the domesticated silkworm for thousands of years, resulting in one of the oldest and well-known plant-herbivore interactions. The genome of Morus notabilis has now been sequenced and there is an opportunity to mine the transposable element (TE) data. To better understand the roles of TEs in structural, functional and evolutionary dynamics of the mulberry genome, a specific, comprehensive and user-friendly web-based database, MnTEdb, was constructed. It was built based on a detailed and accurate identification of all TEs in mulberry. A total of 5925 TEs belonging to 13 superfamilies and 1062 families were deposited in this database. MnTEdb enables users to search, browse and download the mulberry TE sequences. Meanwhile, data mining tools, including BLAST, GetORF, HMMER, Sequence Extractor and JBrowse were also integrated into MnTEdb. MnTEdb will assist researchers to efficiently take advantage of our newly annotated TEs, which facilitate their studies in the origin, amplification and evolution of TEs, as well as the comparative analysis among the different species. Database URL:http://morus.swu.edu.cn/mntedb/
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Affiliation(s)
- Bi Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Tian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Ningjia He
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
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214
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Stapley J, Santure AW, Dennis SR. Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species. Mol Ecol 2015; 24:2241-52. [PMID: 25611725 DOI: 10.1111/mec.13089] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/17/2015] [Accepted: 01/19/2015] [Indexed: 12/11/2022]
Abstract
Rapid adaptation of invasive species to novel habitats has puzzled evolutionary biologists for decades, especially as this often occurs in the face of limited genetic variability. Although some ecological traits common to invasive species have been identified, little is known about the possible genomic/genetic mechanisms that may underlie their success. A common scenario in many introductions is that small founder population sizes will often lead to reduced genetic diversity, but that invading populations experience large environmental perturbations, such as changes in habitat and environmental stress. Although sudden and intense stress is usually considered in a negative context, these perturbations may actually facilitate rapid adaptation by affecting genome structure, organization and function via interactions with transposable elements (TEs), especially in populations with low genetic diversity. Stress-induced changes in TE activity can alter gene action and can promote structural variation that may facilitate the rapid adaptation observed in new environments. We focus here on the adaptive potential of TEs in relation to invasive species and highlight their role as powerful mutational forces that can rapidly create genetic diversity. We hypothesize that activity of transposable elements can explain rapid adaptation despite low genetic variation (the genetic paradox of invasive species), and provide a framework under which this hypothesis can be tested using recently developed and emerging genomic technologies.
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Affiliation(s)
- Jessica Stapley
- Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield, S10 2TN, UK
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215
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Longo MS, Brown JD, Zhang C, O'Neill MJ, O'Neill RJ. Identification of a recently active mammalian SINE derived from ribosomal RNA. Genome Biol Evol 2015; 7:775-88. [PMID: 25637222 PMCID: PMC4994717 DOI: 10.1093/gbe/evv015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Complex eukaryotic genomes are riddled with repeated sequences whose derivation does not coincide with phylogenetic history and thus is often unknown. Among such sequences, the capacity for transcriptional activity coupled with the adaptive use of reverse transcription can lead to a diverse group of genomic elements across taxa, otherwise known as selfish elements or mobile elements. Short interspersed nuclear elements (SINEs) are nonautonomous mobile elements found in eukaryotic genomes, typically derived from cellular RNAs such as tRNAs, 7SL or 5S rRNA. Here, we identify and characterize a previously unknown SINE derived from the 3'-end of the large ribosomal subunit (LSU or 28S rDNA) and transcribed via RNA polymerase III. This new element, SINE28, is represented in low-copy numbers in the human reference genome assembly, wherein we have identified 27 discrete loci. Phylogenetic analysis indicates these elements have been transpositionally active within primate lineages as recently as 6 MYA while modern humans still carry transcriptionally active copies. Moreover, we have identified SINE28s in all currently available assembled mammalian genome sequences. Phylogenetic comparisons indicate that these elements are frequently rederived from the highly conserved LSU rRNA sequences in a lineage-specific manner. We propose that this element has not been previously recognized as a SINE given its high identity to the canonical LSU, and that SINE28 likely represents one of possibly many unidentified, active transposable elements within mammalian genomes.
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Affiliation(s)
- Mark S Longo
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut
| | - Judy D Brown
- Department of Allied Health Sciences and Institute for Systems Genomics, University of Connecticut
| | - Chu Zhang
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut
| | - Michael J O'Neill
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut
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216
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Startek M, Szafranski P, Gambin T, Campbell IM, Hixson P, Shaw CA, Stankiewicz P, Gambin A. Genome-wide analyses of LINE-LINE-mediated nonallelic homologous recombination. Nucleic Acids Res 2015; 43:2188-98. [PMID: 25613453 PMCID: PMC4344489 DOI: 10.1093/nar/gku1394] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Nonallelic homologous recombination (NAHR), occurring between low-copy repeats (LCRs) >10 kb in size and sharing >97% DNA sequence identity, is responsible for the majority of recurrent genomic rearrangements in the human genome. Recent studies have shown that transposable elements (TEs) can also mediate recurrent deletions and translocations, indicating the features of substrates that mediate NAHR may be significantly less stringent than previously believed. Using >4 kb length and >95% sequence identity criteria, we analyzed of the genome-wide distribution of long interspersed element (LINE) retrotransposon and their potential to mediate NAHR. We identified 17 005 directly oriented LINE pairs located <10 Mbp from each other as potential NAHR substrates, placing 82.8% of the human genome at risk of LINE-LINE-mediated instability. Cross-referencing these regions with CNVs in the Baylor College of Medicine clinical chromosomal microarray database of 36 285 patients, we identified 516 CNVs potentially mediated by LINEs. Using long-range PCR of five different genomic regions in a total of 44 patients, we confirmed that the CNV breakpoints in each patient map within the LINE elements. To additionally assess the scale of LINE-LINE/NAHR phenomenon in the human genome, we tested DNA samples from six healthy individuals on a custom aCGH microarray targeting LINE elements predicted to mediate CNVs and identified 25 LINE-LINE rearrangements. Our data indicate that LINE-LINE-mediated NAHR is widespread and under-recognized, and is an important mechanism of structural rearrangement contributing to human genomic variability.
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Affiliation(s)
- Michał Startek
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Ian M Campbell
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Patricia Hixson
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Anna Gambin
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, 2 Banacha street, 02-097 Warsaw, Poland Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawińskiego street, 02-106 Warsaw, Poland
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217
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Mustafa H, David M, Brudno M. Assembly and characterization of novel Alu inserts detected from next-generation sequencing data. Mob Genet Elements 2014; 4:1-7. [PMID: 26442170 DOI: 10.4161/21592543.2014.969584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 08/06/2014] [Accepted: 09/01/2014] [Indexed: 12/30/2022] Open
Abstract
Repetitive elements generally, and Alu inserts specifically are a large contributor to the recent evolution of the human genome. By assembling the sequences of novel Alu inserts using their respective subfamily consensus sequences as references, we found an exponential decay in the Alu subfamily call enrichment with increased number of sequence variants (Pearson correlation [Formula: see text], [Formula: see text]). By mapping the sequences of these inserts to a human reference genome, we infer the reference Alu sources of a subset of the novel Alus, of which 85% were previously shown to be active. We also evaluate relationships between the loci of the novel inserts and their inferred sources.
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Affiliation(s)
- Harun Mustafa
- Department of Computer Science; University of Toronto ; Toronto, Canada
| | - Matei David
- Department of Computer Science; University of Toronto ; Toronto, Canada
| | - Michael Brudno
- Department of Computer Science; University of Toronto ; Toronto, Canada ; Centre for Computational Medicine; Hospital for Sick Children ; Toronto, Canada
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218
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Naville M, Chalopin D, Volff JN. Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths. PLoS One 2014; 9:e114382. [PMID: 25470617 PMCID: PMC4255032 DOI: 10.1371/journal.pone.0114382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/10/2014] [Indexed: 01/29/2023] Open
Abstract
Coelacanths are lobe-finned fish represented by two extant species, Latimeria chalumnae in South Africa and Comoros and L. menadoensis in Indonesia. Due to their intermediate phylogenetic position between ray-finned fish and tetrapods in the vertebrate lineage, they are of great interest from an evolutionary point of view. In addition, extant specimens look similar to 300 million-year-old fossils; because of their apparent slowly evolving morphology, coelacanths have been often described as « living fossils ». As an underlying cause of such a morphological stasis, several authors have proposed a slow evolution of the coelacanth genome. Accordingly, sequencing of the L. chalumnae genome has revealed a globally low substitution rate for protein-coding regions compared to other vertebrates. However, genome and gene evolution can also be influenced by transposable elements, which form a major and dynamic part of vertebrate genomes through their ability to move, duplicate and recombine. In this work, we have searched for evidence of transposition activity in coelacanth genomes through the comparative analysis of orthologous genomic regions from both Latimeria species. Comparison of 5.7 Mb (0.2%) of the L. chalumnae genome with orthologous Bacterial Artificial Chromosome clones from L. menadoensis allowed the identification of 27 species-specific transposable element insertions, with a strong relative contribution of CR1 non-LTR retrotransposons. Species-specific homologous recombination between the long terminal repeats of a new coelacanth endogenous retrovirus was also detected. Our analysis suggests that transposon activity is responsible for at least 0.6% of genome divergence between both Latimeria species. Taken together, this study demonstrates that coelacanth genomes are not evolutionary inert: they contain recently active transposable elements, which have significantly contributed to post-speciation genome divergence in Latimeria.
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Affiliation(s)
- Magali Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Domitille Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail:
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219
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Lee HE, Eo J, Kim HS. Composition and evolutionary importance of transposable elements in humans and primates. Genes Genomics 2014. [DOI: 10.1007/s13258-014-0249-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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220
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Lexa M, Steflova P, Martinek T, Vorlickova M, Vyskot B, Kejnovsky E. Guanine quadruplexes are formed by specific regions of human transposable elements. BMC Genomics 2014; 15:1032. [PMID: 25431265 PMCID: PMC4407331 DOI: 10.1186/1471-2164-15-1032] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/29/2014] [Indexed: 11/23/2022] Open
Abstract
Background Transposable elements form a significant proportion of eukaryotic genomes. Recently, Lexa et al. (Nucleic Acids Res 42:968-978, 2014) reported that plant long terminal repeat (LTR) retrotransposons often contain potential quadruplex sequences (PQSs) in their LTRs and experimentally confirmed their ability to adopt four-stranded DNA conformations. Results Here, we searched for PQSs in human retrotransposons and found that PQSs are specifically localized in the 3’-UTR of LINE-1 elements, in LTRs of HERV elements and are strongly accumulated in specific regions of SVA elements. Circular dichroism spectroscopy confirmed that most PQSs had adopted monomolecular or bimolecular guanine quadruplex structures. Evolutionarily young SVA elements contained more PQSs than older elements and their propensity to form quadruplex DNA was higher. Full-length L1 elements contained more PQSs than truncated elements; the highest proportion of PQSs was found inside transpositionally active L1 elements (PA2 and HS families). Conclusions Conservation of quadruplexes at specific positions of transposable elements implies their importance in their life cycle. The increasing quadruplex presence in evolutionarily young LINE-1 and SVA families makes these elements important contributors toward present genome-wide quadruplex distribution. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1032) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno, Czech Republic.
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221
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Kim YJ, Han K. Endogenous retrovirus-mediated genomic variations in chimpanzees. Mob Genet Elements 2014; 4:1-4. [PMID: 26442175 PMCID: PMC4588550 DOI: 10.4161/2159256x.2014.990792] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 11/18/2014] [Accepted: 11/19/2014] [Indexed: 11/19/2022] Open
Abstract
Transposable elements (TEs) have played a significant role in the evolution of host genome by triggering genomic rearrangements. TEs have been studied in various research fields, ranging from population genomics to personalized medicines. Human-specific TEs and TEs existing in the human genome have been well studied. Unlike them, non-human primate-specific TEs remain shrouded in mystery. However, the study of TE-mediated genomic or genetic variations through comparative genomics is essential to understand mechanisms which TEs utilize to modify species-specific genome architecture and to cause species-specific diseases, Therefore, we have studied chimpanzee-specific TEs as well as human-specific TEs. At first, we identified human-specific HERV-K integrated into the human genome after the divergence of human and chimpanzee. Then, for a comparative study of HERV-Ks and non-human ERVs, we extracted chimpanzee-specific endogenous retroviruses (PtERVs) from the chimpanzee genome. We identified 256 chimpanzee-specific PtERVs and characterized them, focusing on their estimated evolutionary age, polymorphism level in chimpanzee populations, and potential impact on the difference between the human and chimpanzee genomes.
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Affiliation(s)
- Yun-Ji Kim
- Department of Nanobiomedical Science; Global Research Center for Regenerative Medicine; Dankook University; Cheonan, Republic of Korea
- DKU-Theragen Institute for NGS Analysis (DTiNa); Cheonan, Republic of Korea
| | - Kyudong Han
- Department of Nanobiomedical Science; Global Research Center for Regenerative Medicine; Dankook University; Cheonan, Republic of Korea
- DKU-Theragen Institute for NGS Analysis (DTiNa); Cheonan, Republic of Korea
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222
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Lee KJ, Conley AB, Lunyak VV, Jordan IK. Do human transposable element small RNAs serve primarily as genome defenders or genome regulators? Mob Genet Elements 2014; 2:19-25. [PMID: 22754749 PMCID: PMC3383446 DOI: 10.4161/mge.19031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
It is currently thought that small RNA (sRNA) based repression mechanisms are primarily employed to mitigate the mutagenic threat posed by the activity of transposable elements (TEs). This can be achieved by the sRNA guided processing of TE transcripts via Dicer-dependent (e.g., siRNA) or Dicer-independent (e.g., piRNA) mechanisms. For example, potentially active human L1 elements are silenced by mRNA cleavage induced by element encoded siRNAs, leading to a negative correlation between element mRNA and siRNA levels. On the other hand, there is emerging evidence that TE derived sRNAs can also be used to regulate the host genome. Here, we evaluated these two hypotheses for human TEs by comparing the levels of TE derived mRNA and TE sRNA across six tissues. The genome defense hypothesis predicts a negative correlation between TE mRNA and TE sRNA levels, whereas the genome regulatory hypothesis predicts a positive correlation. On average, TE mRNA and TE sRNA levels are positively correlated across human tissues. These correlations are higher than seen for human genes or for randomly permuted control data sets. Overall, Alu subfamilies show the highest positive correlations of element mRNA and sRNA levels across tissues, although a few of the youngest, and potentially most active, Alu subfamilies do show negative correlations. Thus, Alu derived sRNAs may be related to both genome regulation and genome defense. These results are inconsistent with a simple model whereby TE derived sRNAs reduce levels of standing TE mRNA via transcript cleavage, and suggest that human cells efficiently process TE transcripts into sRNA based on the available message levels. This may point to a widespread role for processed TE transcripts in genome regulation or to alternative roles of TE-to-sRNA processing including the mitigation of TE transcript cytotoxicity.
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223
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Upton KR, Baillie JK, Faulkner GJ. Is somatic retrotransposition a parasitic or symbiotic phenomenon? Mob Genet Elements 2014; 1:279-282. [PMID: 22545239 PMCID: PMC3337137 DOI: 10.4161/mge.18422] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The extraordinary evolutionary success of transposable elements (TEs) invites us to question the nature of the co-evolutionary dynamics between TE and host. Although sometimes assumed to be wholly parasitic, TEs have penetrated and spread throughout eukaryotic genomes at a rate unparalleled by other parasites. This near-ubiquity, occurring despite the potentially deleterious effects of insertional mutagenesis, raises the possibility that a counterbalancing benefit exists for the host. Such a benefit may act at the population level to generate genomic diversity within a species and hence greater adaptability under new selective pressures, or at the level of primary gain for the individual. Recent studies have highlighted the occurrence of retrotransposition events in the germline and discovered a surprisingly high rate of mobilization in somatic cells. Here we examine the available evidence for somatic retrotransposition and discuss how this phenomenon may confer a selective advantage upon an individual or species.
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Affiliation(s)
- Kyle R Upton
- Division of Genetics and Genomics; The Roslin Institute and Royal (Dick) School of Veterinary Studies; University of Edinburgh; Easter Bush, UK
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224
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Kim BD. Foldback intercoil DNA and the mechanism of DNA transposition. Genomics Inform 2014; 12:80-6. [PMID: 25317106 PMCID: PMC4196379 DOI: 10.5808/gi.2014.12.3.80] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 11/20/2022] Open
Abstract
Foldback intercoil (FBI) DNA is formed by the folding back at one point of a non-helical parallel track of double-stranded DNA at as sharp as 180° and the intertwining of two double helixes within each other's major groove to form an intercoil with a diameter of 2.2 nm. FBI DNA has been suggested to mediate intra-molecular homologous recombination of a deletion and inversion. Inter-molecular homologous recombination, known as site-specific insertion, on the other hand, is mediated by the direct perpendicular approach of the FBI DNA tip, as the attP site, onto the target DNA, as the attB site. Transposition of DNA transposons involves the pairing of terminal inverted repeats and 5-7-bp tandem target duplication. FBI DNA configuration effectively explains simple as well as replicative transposition, along with the involvement of an enhancer element. The majority of diverse retrotransposable elements that employ a target site duplication mechanism is also suggested to follow the FBI DNA-mediated perpendicular insertion of the paired intercoil ends by non-homologous end-joining, together with gap filling. A genome-wide perspective of transposable elements in light of FBI DNA is discussed.
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Affiliation(s)
- Byung-Dong Kim
- Department of Plant Science, Seoul National University, Seoul 151-921, Korea. ; The Korean Academy of Science and Technology, Seongnam 463-808, Korea
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225
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Ayarpadikannan S, Kim HS. The impact of transposable elements in genome evolution and genetic instability and their implications in various diseases. Genomics Inform 2014; 12:98-104. [PMID: 25317108 PMCID: PMC4196381 DOI: 10.5808/gi.2014.12.3.98] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 08/14/2014] [Accepted: 08/18/2014] [Indexed: 12/15/2022] Open
Abstract
Approximately 45% of the human genome is comprised of transposable elements (TEs). Results from the Human Genome Project have emphasized the biological importance of TEs. Many studies have revealed that TEs are not simply "junk" DNA, but rather, they play various roles in processes, including genome evolution, gene expression regulation, genetic instability, and cancer disposition. The effects of TE insertion in the genome varies from negligible to disease conditions. For the past two decades, many studies have shown that TEs are the causative factors of various genetic disorders and cancer. TEs are a subject of interest worldwide, not only in terms of their clinical aspects but also in basic research, such as evolutionary tracking. Although active TEs contribute to genetic instability and disease states, non-long terminal repeat transposons are well studied, and their roles in these processes have been confirmed. In this review, we will give an overview of the importance of TEs in studying genome evolution and genetic instability, and we suggest that further in-depth studies on the mechanisms related to these phenomena will be useful for both evolutionary tracking and clinical diagnostics.
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Affiliation(s)
- Selvam Ayarpadikannan
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Korea
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226
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Ianc B, Ochis C, Persch R, Popescu O, Damert A. Hominoid composite non-LTR retrotransposons-variety, assembly, evolution, and structural determinants of mobilization. Mol Biol Evol 2014; 31:2847-64. [PMID: 25216663 DOI: 10.1093/molbev/mst256] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
SVA (SINE-R-VNTR-Alu) elements constitute the youngest family of composite non-LTR retrotransposons in hominoid primates. The sequence of their assembly, however, remains unclear. Recently, a second family of VNTR-containing composites, LAVA (L1-Alu-VNTR-Alu), has been identified in gibbons. We now report the existence of two additional VNTR composite families, PVA (PTGR2-VNTR-Alu) and FVA (FRAM-VNTR-Alu), in the genome of Nomascus leucogenys. Like LAVA, they share the 5'-Alu-like region and VNTR with SVA, but differ at their 3'-ends. The 3'-end of PVA comprises part of the PTGR2 gene, whereas FVA is characterized by the presence of a partial FRAM element in its 3'-domain. Splicing could be identified as the mechanism of acquisition of the variant 3'-ends in all four families of VNTR composites. SVAs have been shown to be mobilized by the L1 protein machinery in trans. A critical role in this process has been ascribed to their 5'-hexameric repeat/ Alu-like region. The Alu-like region displays specific features in each of the VNTR composite families/subfamilies with characteristic deletions found in the evolutionary younger subfamilies. Using reciprocal exchanges between SVA_E and PVA/FVA elements, we demonstrate that the structure, not the presence of the (CCCTCT)n/ Alu-like region determines mobilization capacity. Combination of LAVA and SVA_E domains does not yield any active elements-suggesting the use of different combinations of host factors for the two major groups of VNTR composites. Finally, we demonstrate that the LAVA 3'-L1ME5 fragment attenuates mobilization capacity.
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Affiliation(s)
- Bianca Ianc
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University, Cluj-Napoca, Romania
| | - Cornelia Ochis
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University, Cluj-Napoca, Romania
| | | | - Octavian Popescu
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University, Cluj-Napoca, Romania Institute of Biology, Romanian Academy, Bucharest, Romania
| | - Annette Damert
- Institute for Interdisciplinary Research in Bio-Nano-Sciences, Molecular Biology Center, Babes-Bolyai-University, Cluj-Napoca, Romania
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227
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Naveira H, Bello X, Abal-Fabeiro JL, Maside X. Evidence for the persistence of an active endogenous retrovirus (ERVE) in humans. Genetica 2014; 142:451-60. [PMID: 25192754 DOI: 10.1007/s10709-014-9789-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 08/26/2014] [Indexed: 02/02/2023]
Abstract
Transposable elements (TEs) account for nearly half (44 %) of the human genome. However, their overall activity has been steadily declining over the past 35-50 million years, so that <0.05 % of TEs are presumably still "alive" (potentially transposable) in human populations. All the active elements are retrotransposons, either autonomous (LINE-1 and possibly the endogenous retrovirus ERVK), or non-autonomous (Alu and SVA, whose transposition is dependent on the LINE-1 enzymatic machinery). Here we show that a lineage of the endogenous retrovirus ERVE was recently engaged in ectopic recombination events and may have at least one potentially fully functional representative, initially reported as a novel retrovirus isolated from blood cells of a Chinese patient with chronic myeloid leukemia, which bears signals of positive selection on its envelope region. Altogether, there is strong evidence that ERVE should be included in the short list of potentially active TEs, and we give clues on how to identify human specific insertions of this element that are likely to be segregating in some of our populations.
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MESH Headings
- Animals
- Base Sequence
- Endogenous Retroviruses/classification
- Endogenous Retroviruses/genetics
- Evolution, Molecular
- Gene Products, env/chemistry
- Gene Products, env/genetics
- Genome, Human/genetics
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Models, Molecular
- Molecular Sequence Data
- Phylogeny
- Protein Structure, Tertiary
- Retroelements/genetics
- Selection, Genetic
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Horacio Naveira
- Grupo de Investigación en Bioloxía Evolutiva, Departamento de Bioloxía Celular e Molecular, Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, 15071, A Coruña, Spain,
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228
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Retrotransposons in pluripotent cells: Impact and new roles in cellular plasticity. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:417-26. [PMID: 25042909 DOI: 10.1016/j.bbagrm.2014.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/08/2014] [Accepted: 07/10/2014] [Indexed: 12/27/2022]
Abstract
Transposable Elements are pieces of DNA able to mobilize from one location to another within genomes. Although they constitute more than 50% of the human genome, they have been classified as selfish DNA, with the only mission to spread within genomes and generate more copies of themselves that will ensure their presence over generations. Despite their remarkable prevalence, only a minor group of transposable elements remain active in the human genome and can sporadically be associated with the generation of a genetic disorder due to their ongoing mobility. Most of the transposable elements identified in the human genome corresponded to fixed insertions that no longer move in genomes. As selfish DNA, transposable element insertions accumulate in cell types where genetic information can be passed to the next generation. Indeed, work from different laboratories has demonstrated that the main heritable load of TE accumulation in humans occurs during early embryogenesis. Thus, active transposable elements have a clear impact on our pluripotent genome. However, recent findings suggest that the main proportion of fixed non-mobile transposable elements might also have emerging roles in cellular plasticity. In this concise review, we provide an overview of the impact of currently active transposable elements in our pluripotent genome and further discuss new roles of transposable elements (active or not) in regulating pluripotency. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
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229
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An Z, Tang Z, Ma B, Mason AS, Guo Y, Yin J, Gao C, Wei L, Li J, Fu D. Transposon variation by order during allopolyploidisation between Brassica oleracea and Brassica rapa. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:825-35. [PMID: 24176077 DOI: 10.1111/plb.12121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 09/23/2013] [Indexed: 05/02/2023]
Abstract
Although many studies have shown that transposable element (TE) activation is induced by hybridisation and polyploidisation in plants, much less is known on how different types of TE respond to hybridisation, and the impact of TE-associated sequences on gene function. We investigated the frequency and regularity of putative transposon activation for different types of TE, and determined the impact of TE-associated sequence variation on the genome during allopolyploidisation. We designed different types of TE primers and adopted the Inter-Retrotransposon Amplified Polymorphism (IRAP) method to detect variation in TE-associated sequences during the process of allopolyploidisation between Brassica rapa (AA) and Brassica oleracea (CC), and in successive generations of self-pollinated progeny. In addition, fragments with TE insertions were used to perform Blast2GO analysis to characterise the putative functions of the fragments with TE insertions. Ninety-two primers amplifying 548 loci were used to detect variation in sequences associated with four different orders of TE sequences. TEs could be classed in ascending frequency into LTR-REs, TIRs, LINEs, SINEs and unknown TEs. The frequency of novel variation (putative activation) detected for the four orders of TEs was highest from the F1 to F2 generations, and lowest from the F2 to F3 generations. Functional annotation of sequences with TE insertions showed that genes with TE insertions were mainly involved in metabolic processes and binding, and preferentially functioned in organelles. TE variation in our study severely disturbed the genetic compositions of the different generations, resulting in inconsistencies in genetic clustering. Different types of TE showed different patterns of variation during the process of allopolyploidisation.
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Affiliation(s)
- Z An
- Engineering Research Center of South Upland Agriculture of Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China; Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
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Karimi A, Madjd Z, Habibi L, Akrami SM. Exposure of hepatocellular carcinoma cells to low-level As₂O₃ causes an extra toxicity pathway via L1 retrotransposition induction. Toxicol Lett 2014; 229:111-7. [PMID: 24960058 DOI: 10.1016/j.toxlet.2014.05.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 11/17/2022]
Abstract
Various mechanisms have been proposed for toxicity and carcinogenesis pattern of arsenic, a naturally occurring metalloid. The extent to which the long interspersed element-1 (LINE-1) retrotransposon, an ubiquitous retroelement with autonomous mobility, can be influenced upon exposure to low-level arsenic remains to be elucidated. The aim of this study was to evaluate the possible effect of low-level As2O3 on L1 retrotransposition alteration in human hepatocellular carcinoma cells (HepG2). L1 retrotransposition in HepG2 cells was performed by the in vitro retrotransposition assay using an EGFP-tagged L1RP. Following determination of non-cytotoxic concentrations of arsenic by a MTT assay, the cells were transfected with pL1RP-EGFP and then exposed to 0.25, 0.50 and 0.75 μM of As2O3. The amount of EGFP and its copy number in retrotransposed cells were evaluated by FACS and qPCR analysis in treated vs. control cells, respectively. Significant increase in retrotransposition frequency was found after 12 days exposure to 0.50 and 0.75 μM of As2O3 by FACS analysis (P<0.05). Obtained results were further confirmed by real time PCR, which showed significant induction of retrotransposition in all mentioned concentrations. Our findings indicate that low-level long-term As2O3 exposure may pave activation of L1 retrotransposon.
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Affiliation(s)
- Abbas Karimi
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine (FATiM), Iran University of Medical Sciences, Tehran, Iran; Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Madjd
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine (FATiM), Iran University of Medical Sciences, Tehran, Iran; Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran, Iran; Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Laleh Habibi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Akrami
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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231
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Robinson KM, Dunning Hotopp JC. Mobile elements and viral integrations prompt considerations for bacterial DNA integration as a novel carcinogen. Cancer Lett 2014; 352:137-44. [PMID: 24956175 DOI: 10.1016/j.canlet.2014.05.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 04/30/2014] [Accepted: 05/01/2014] [Indexed: 12/11/2022]
Abstract
Insertional mutagenesis has been repeatedly demonstrated in cancer genomes and has a role in oncogenesis. Mobile genetic elements can induce cancer development by random insertion into cancer related genes or by inducing translocations. L1s are typically implicated in cancers of an epithelial cell origin, while Alu elements have been implicated in leukemia as well as epithelial cell cancers. Likewise, viral infections have a significant role in cancer development predominantly through integration into the human genome and mutating or deregulating cancer related genes. Human papilloma virus is the best-known example of viral integrations contributing to carcinogenesis. However, hepatitis B virus, Epstein-Barr virus, and Merkel cell polyomavirus also integrate into the human genome and disrupt cancer related genes. Thus far, the role of microbes in cancer has primarily been attributed to mutations induced through chronic inflammation or toxins, as is the case with Helicobacter pylori and enterotoxigenic Bacteroides fragilis. We hypothesize that like mobile elements and viral DNA, bacterial and parasitic DNA may also integrate into the human somatic genome and be oncogenic. Until recently it was believed that bacterial DNA could not integrate into the human genome, but new evidence demonstrates that bacterial insertional mutagenesis may occur in cancer cells. Although this work does not show causation between bacterial insertions and cancer, it prompts more research in this area. Promising new sequencing technologies may reduce the risk of artifactual chimeric sequences, thus diminishing some of the challenges of identifying novel insertions in the somatic human genome.
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Affiliation(s)
- Kelly M Robinson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA; Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.
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232
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Bailly-Bechet M, Haudry A, Lerat E. “One code to find them all”: a perl tool to conveniently parse RepeatMasker output files. Mob DNA 2014. [PMCID: PMC4021974 DOI: 10.1186/1759-8753-5-13] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Of the different bioinformatic methods used to recover transposable elements (TEs) in genome sequences, one of the most commonly used procedures is the homology-based method proposed by the RepeatMasker program. RepeatMasker generates several output files, including the .out file, which provides annotations for all detected repeats in a query sequence. However, a remaining challenge consists of identifying the different copies of TEs that correspond to the identified hits. This step is essential for any evolutionary/comparative analysis of the different copies within a family. Different possibilities can lead to multiple hits corresponding to a unique copy of an element, such as the presence of large deletions/insertions or undetermined bases, and distinct consensus corresponding to a single full-length sequence (like for long terminal repeat (LTR)-retrotransposons). These possibilities must be taken into account to determine the exact number of TE copies. Results We have developed a perl tool that parses the RepeatMasker .out file to better determine the number and positions of TE copies in the query sequence, in addition to computing quantitative information for the different families. To determine the accuracy of the program, we tested it on several RepeatMasker .out files corresponding to two organisms (Drosophila melanogaster and Homo sapiens) for which the TE content has already been largely described and which present great differences in genome size, TE content, and TE families. Conclusions Our tool provides access to detailed information concerning the TE content in a genome at the family level from the .out file of RepeatMasker. This information includes the exact position and orientation of each copy, its proportion in the query sequence, and its quality compared to the reference element. In addition, our tool allows a user to directly retrieve the sequence of each copy and obtain the same detailed information at the family level when a local library with incomplete TE class/subclass information was used with RepeatMasker. We hope that this tool will be helpful for people working on the distribution and evolution of TEs within genomes.
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233
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Vlaikou AM, Manolakos E, Noutsopoulos D, Markopoulos G, Liehr T, Vetro A, Ziegler M, Weise A, Kreskowski K, Papoulidis I, Thomaidis L, Syrrou M. An Interstitial 4q31.21q31.22 Microdeletion Associated with Developmental Delay: Case Report and Literature Review. Cytogenet Genome Res 2014; 142:227-38. [DOI: 10.1159/000361001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2014] [Indexed: 11/19/2022] Open
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234
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Kurnosov AA, Ustiugova SV, Pogorelyĭ MV, Komkov AI, Bolotin DA, Khodosevich KV, Mamedov IZ, Lebedev IB. [A novel approach to identification of somatic retroelements' insertions in human genome]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2014; 39:466-76. [PMID: 24707728 DOI: 10.1134/s1068162013040110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The activity of retroelements is one of the factors leading to genetic variability of the modern humans. Insertions of retroelements may result in alteration of gene expression and functional diversity between cells. In recent years an increasing amount of data indicating an elevated level of retroelements' mobilisation in some human and animal tissues has been reported. Therefore, the development of a system for the detection of somatic retroposition events is required. Here we describe a novel approach to the whole-genome identification of somatic retroelemts' insertions in human genome. The developed approach was applied for the comparisons of somatic mosaicism levels in two tissues of the investigated individual. A total of 3410 insertions of retroelements belonging to AluYa5 subfamily were identified.
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235
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Polymorphic L1 retrotransposons are frequently in strong linkage disequilibrium with neighboring SNPs. Gene 2014; 541:55-9. [PMID: 24614499 DOI: 10.1016/j.gene.2014.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Revised: 03/03/2014] [Accepted: 03/06/2014] [Indexed: 11/22/2022]
Abstract
L1 retrotransposons have been the major driver of structural variation of the human genome. L1 insertion polymorphism (LIP)-mediated genomic variation can alter the transcriptome and contribute to the divergence of human phenotypes. To assess this possibility, a genome-wide association study (GWAS) including LIPs is required. Toward this ultimate goal, the present study examined linkage disequilibrium between six LIPs and their neighboring single nucleotide polymorphisms (SNPs). Genomic PCR and sequencing of L1-plus and -minus alleles from different donors revealed that all six LIPs were in strong linkage disequilibrium with at least one SNP. In addition, comparison of syntenic regions containing the identified SNP nucleotides was performed among modern humans (L1-plus and -minus alleles), archaic humans and non-human primates, revealing two different evolutionary schemes that might have resulted in the observed strong SNP-LIP linkage disequilibria. This study provides an experimental framework and guidance for a future SNP-LIP integrative GWAS.
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236
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Heras SR, Macias S, Cáceres JF, Garcia-Perez JL. Control of mammalian retrotransposons by cellular RNA processing activities. Mob Genet Elements 2014; 4:e28439. [PMID: 25346866 PMCID: PMC4203495 DOI: 10.4161/mge.28439] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 03/02/2014] [Accepted: 03/05/2014] [Indexed: 01/27/2023] Open
Abstract
Retrotransposons make up roughly 50% of the mammalian genome and have played an important role in genome evolution. A small fraction of non-LTR retrotransposons, LINE-1 and SINE elements, is currently active in the human genome. These elements move in our genome using an intermediate RNA and a reverse transcriptase activity by a copy and paste mechanism. Their ongoing mobilization can impact the human genome leading to several human disorders. However, how the cell controls the activity of these elements minimizing their mutagenic effect is not fully understood. Recent studies have highlighted that the intermediate RNA of retrotransposons is a target of different mechanisms that limit the mobilization of endogenous retrotransposons in mammals. Here, we provide an overview of recent discoveries that show how RNA processing events can act to control the activity of mammalian retrotransposons and discuss several arising questions that remain to be answered.
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Affiliation(s)
- Sara R Heras
- GENYO; Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government; Granada, Spain
| | - Sara Macias
- Medical Research Council Human Genetics Unit; Institute of Genetics and Molecular Medicine; University of Edinburgh; Western General Hospital; Edinburgh, UK
| | - Javier F Cáceres
- Medical Research Council Human Genetics Unit; Institute of Genetics and Molecular Medicine; University of Edinburgh; Western General Hospital; Edinburgh, UK
| | - Jose L Garcia-Perez
- GENYO; Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government; Granada, Spain
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237
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Soliai MM, Meyer SE, Udall JA, Elzinga DE, Hermansen RA, Bodily PM, Hart AA, Coleman CE. De novo genome assembly of the fungal plant pathogen Pyrenophora semeniperda. PLoS One 2014; 9:e87045. [PMID: 24475219 PMCID: PMC3903604 DOI: 10.1371/journal.pone.0087045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/18/2013] [Indexed: 12/31/2022] Open
Abstract
Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen that has a wide host range within the Poaceae. One of its hosts is cheatgrass (Bromus tectorum), a species exotic to the United States that has invaded natural ecosystems of the Intermountain West. As a natural pathogen of cheatgrass, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing seeds within the seed bank; however, few genetic resources exist for the fungus. Here, the genome of P. semeniperda isolate assembled from sequence reads of 454 pyrosequencing is presented. The total assembly is 32.5 Mb and includes 11,453 gene models encoding putative proteins larger than 24 amino acids. The models represent a variety of putative genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, extensive rearrangements, including inter- and intrachromosomal rearrangements, were found when the P. semeniperda genome was compared to P. tritici-repentis, a related fungal species.
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Affiliation(s)
- Marcus M. Soliai
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Susan E. Meyer
- USDA Forest Service, Rocky Mountain Research Station, Shrub Sciences Laboratory, Provo, Utah, United States of America
| | - Joshua A. Udall
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - David E. Elzinga
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Russell A. Hermansen
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Paul M. Bodily
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Aaron A. Hart
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Craig E. Coleman
- Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
- * E-mail:
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238
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Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes. Proc Natl Acad Sci U S A 2014; 111:1676-83. [PMID: 24398522 DOI: 10.1073/pnas.1321818111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
TET/JBP dioxygenases oxidize methylpyrimidines in nucleic acids and are implicated in generation of epigenetic marks and potential intermediates for DNA demethylation. We show that TET/JBP genes are lineage-specifically expanded in all major clades of basidiomycete fungi, with the majority of copies predicted to encode catalytically active proteins. This pattern differs starkly from the situation in most other organisms that possess just a single or a few copies of the TET/JBP family. In most basidiomycetes, TET/JBP genes are frequently linked to a unique class of transposons, KDZ (Kyakuja, Dileera, and Zisupton) and appear to have dispersed across chromosomes along with them. Several of these elements typically encode additional proteins, including a divergent version of the HMG domain. Analysis of their transposases shows that they contain a previously uncharacterized version of the RNase H fold with multiple distinctive Zn-chelating motifs and a unique insert, which are predicted to play roles in structural stabilization and target sequence recognition, respectively. We reconstruct the complex evolutionary history of TET/JBPs and associated transposons as involving multiple rounds of expansion with concomitant lineage sorting and loss, along with several capture events of TET/JBP genes by different transposon clades. On a few occasions, these TET/JBP genes were also laterally transferred to certain Ascomycota, Glomeromycota, Viridiplantae, and Amoebozoa. One such is an inactive version, calnexin-independence factor 1 (Cif1), from Schizosaccharomyces pombe, which has been implicated in inducing an epigenetically transmitted prion state. We argue that this unique transposon-TET/JBP association is likely to play important roles in speciation during evolution and epigenetic regulation.
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239
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Douville RN, Nath A. Human endogenous retroviruses and the nervous system. HANDBOOK OF CLINICAL NEUROLOGY 2014; 123:465-85. [PMID: 25015500 DOI: 10.1016/b978-0-444-53488-0.00022-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Renée N Douville
- Department of Microbiology, University of Winnipeg, Winnipeg, Manitoba, Canada
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD, USA.
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240
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Ahmed M, Liang P. Study of Modern Human Evolution via Comparative Analysis with the Neanderthal Genome. Genomics Inform 2013; 11:230-8. [PMID: 24465235 PMCID: PMC3897851 DOI: 10.5808/gi.2013.11.4.230] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 11/20/2013] [Accepted: 11/21/2013] [Indexed: 12/11/2022] Open
Abstract
Many other human species appeared in evolution in the last 6 million years that have not been able to survive to modern times and are broadly known as archaic humans, as opposed to the extant modern humans. It has always been considered fascinating to compare the modern human genome with that of archaic humans to identify modern human-specific sequence variants and figure out those that made modern humans different from their predecessors or cousin species. Neanderthals are the latest humans to become extinct, and many factors made them the best representatives of archaic humans. Even though a number of comparisons have been made sporadically between Neanderthals and modern humans, mostly following a candidate gene approach, the major breakthrough took place with the sequencing of the Neanderthal genome. The initial genome-wide comparison, based on the first draft of the Neanderthal genome, has generated some interesting inferences regarding variations in functional elements that are not shared by the two species and the debated admixture question. However, there are certain other genetic elements that were not included or included at a smaller scale in those studies, and they should be compared comprehensively to better understand the molecular make-up of modern humans and their phenotypic characteristics. Besides briefly discussing the important outcomes of the comparative analyses made so far between modern humans and Neanderthals, we propose that future comparative studies may include retrotransposons, pseudogenes, and conserved non-coding regions, all of which might have played significant roles during the evolution of modern humans.
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Affiliation(s)
- Musaddeque Ahmed
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
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241
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Carreira PE, Richardson SR, Faulkner GJ. L1 retrotransposons, cancer stem cells and oncogenesis. FEBS J 2013; 281:63-73. [PMID: 24286172 PMCID: PMC4160015 DOI: 10.1111/febs.12601] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/28/2013] [Accepted: 11/11/2013] [Indexed: 12/17/2022]
Abstract
Retrotransposons have played a central role in human genome evolution. The accumulation of heritable L1, Alu and SVA retrotransposon insertions continues to generate structural variation within and between populations, and can result in spontaneous genetic disease. Recent works have reported somatic L1 retrotransposition in tumours, which in some cases may contribute to oncogenesis. Intriguingly, L1 mobilization appears to occur almost exclusively in cancers of epithelial cell origin. In this review, we discuss how L1 retrotransposition could potentially trigger neoplastic transformation, based on the established correlation between L1 activity and cellular plasticity, and the proven capacity of L1-mediated insertional mutagenesis to decisively alter gene expression and functional output.
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Affiliation(s)
- Patricia E Carreira
- Cancer Biology Program, Mater Medical Research Institute, South Brisbane, Australia
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242
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Ahmed M, Li W, Liang P. Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements. Mob DNA 2013; 4:25. [PMID: 24216009 PMCID: PMC3831846 DOI: 10.1186/1759-8753-4-25] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/09/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alu elements are the most abundant mobile elements in the human genome, with over 1 million copies and constituting more than 10% of the genome. The majority of these Alu elements were inserted into the primate genome 35 to 60 million years ago, but certain subfamilies of Alu elements are relatively very new and suspected to be still evolving. We attempted to trace the source/master copies of all human-specific members of the Alu Yb lineage using a computational approach by clustering similar Yb elements and constructing an evolutionary relation among the members of a cluster. RESULTS We discovered that one copy of Yb8 at 10p14 is the source of several active Yb8 copies, which retrotransposed to generate 712 copies or 54% of all human-specific Yb8 elements. We detected eight other Yb8 elements that had generated ten or more copies, potentially acting as 'stealth drivers'. One Yb8 element at 14q32.31 seemed to act as the source copy for all Yb9 elements tested, having producing 13 active Yb9 elements, and subsequently generated a total of 131 full-length copies. We identified and characterized three new subclasses of Yb elements: Yb8a1, Yb10 and Yb11. Their copy numbers in the reference genome are 75, 8 and 16. We analysed personal genome data from the 1000 Genome Project and detected an additional 6 Yb8a1, 3 Yb10 and 15 Yb11 copies outside the reference genome. Our analysis indicates that the Yb8a1 subfamily has a similar age to Yb9 (1.93 million years and 2.15 million years, respectively), while Yb10 and Yb11 evolved only 1.4 and 0.71 million years ago, suggesting a linear evolutionary path from Yb8a1 to Yb10 and then to Yb11. Our preliminary data indicate that members in Yb10 and Yb11 are mostly polymorphic, indicating their young age. CONCLUSIONS Our findings suggest that the Yb lineage is still evolving with new subfamilies being formed. Due to their very young age and the high rate of being polymorphic, insertions from these young subfamilies are very useful genetic markers for studying human population genetics and migration patterns, and the trend for mobile element insertions in the human genome.
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Affiliation(s)
| | | | - Ping Liang
- Department of Biological Sciences, Brock University, St Catharines, Ontario L2S 3A1, Canada.
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243
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Tufarelli C, Cruickshanks HA, Meehan RR. LINE-1 activation and epigenetic silencing of suppressor genes in cancer: Causally related events? Mob Genet Elements 2013; 3:e26832. [PMID: 24251074 DOI: 10.4161/mge.26832] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/11/2013] [Accepted: 10/15/2013] [Indexed: 01/11/2023] Open
Abstract
The ability of active retrotransposon elements to move within the host genome and alter gene expression with subsequent phenotypic variation led to their initial discovery. In recent years it has become apparent that these elements can also modulate host gene expression independently of their transposition activity. Many retrotransposons maintain endogenous promoter motifs that can potentially drive expression of adjacent DNA modules. Similarly to transposition dependent dysregulation, these proto-promoters can progress disease states when active. Indeed aberrant activation of retrotransposon derived promoters in cancer can lead to transcription of oncogenic isoforms of cellular genes. Here we propose that activation of promoters of transposable elements in cancer can also drive transcription of long non-coding RNAs whose expression leads to silencing of linked tumor suppressor genes. Such transcription driven by aberrantly active transposable elements in cancer can lead to a characteristic reprogramming of epigenetic profiles, thus extending the potential molecular mechanisms whereby retrotransposons can directly contribute to cancer development and subsequent progression.
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Affiliation(s)
- Cristina Tufarelli
- School of Medicine; University of Nottingham; Royal Derby Hospital Centre; Derby, England UK ; Centre for Genetics and Genomics; University of Nottingham; Nottingham, England UK
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244
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Robinson KM, Sieber KB, Dunning Hotopp JC. A review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer. PLoS Genet 2013; 9:e1003877. [PMID: 24146634 PMCID: PMC3798261 DOI: 10.1371/journal.pgen.1003877] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Lateral gene transfer (LGT) from bacteria to animals occurs more frequently than was appreciated prior to the advent of genome sequencing. In 2007, LGT from bacterial Wolbachia endosymbionts was detected in ∼33% of the sequenced arthropod genomes using a bioinformatic approach. Today, Wolbachia/host LGT is thought to be widespread and many other cases of bacteria-animal LGT have been described. In insects, LGT may be more frequently associated with endosymbionts that colonize germ cells and germ stem cells, like Wolbachia endosymbionts. We speculate that LGT may occur from bacteria to a wide variety of eukaryotes, but only becomes vertically inherited when it occurs in germ cells. As such, LGT may happen routinely in somatic cells but never become inherited or fixed in the population. Lack of inheritance of such mutations greatly decreases our ability to detect them. In this review, we propose that such noninherited bacterial DNA integration into chromosomes in human somatic cells could induce mutations leading to cancer or autoimmune diseases in a manner analogous to mobile elements and viral integrations.
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Affiliation(s)
- Kelly M. Robinson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Karsten B. Sieber
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Julie C. Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryand, United States of America
- * E-mail:
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245
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David M, Mustafa H, Brudno M. Detecting Alu insertions from high-throughput sequencing data. Nucleic Acids Res 2013; 41:e169. [PMID: 23921633 PMCID: PMC3783187 DOI: 10.1093/nar/gkt612] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing technologies have allowed for the cataloguing of variation in personal human genomes. In this manuscript, we present alu-detect, a tool that combines read-pair and split-read information to detect novel Alus and their precise breakpoints directly from either whole-genome or whole-exome sequencing data while also identifying insertions directly in the vicinity of existing Alus. To set the parameters of our method, we use simulation of a faux reference, which allows us to compute the precision and recall of various parameter settings using real sequencing data. Applying our method to 100 bp paired Illumina data from seven individuals, including two trios, we detected on average 1519 novel Alus per sample. Based on the faux-reference simulation, we estimate that our method has 97% precision and 85% recall. We identify 808 novel Alus not previously described in other studies. We also demonstrate the use of alu-detect to study the local sequence and global location preferences for novel Alu insertions.
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Affiliation(s)
- Matei David
- Department of Computer Science, University of Toronto, 10 King's College Road, Toronto, ON M5S 3G4, Canada and Centre for Computational Medicine, Genetics and Genome Biology Program, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
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246
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Shukla R, Upton K, Muñoz-Lopez M, Gerhardt D, Fisher M, Nguyen T, Brennan P, Baillie J, Collino A, Ghisletti S, Sinha S, Iannelli F, Radaelli E, Dos Santos A, Rapoud D, Guettier C, Samuel D, Natoli G, Carninci P, Ciccarelli F, Garcia-Perez J, Faivre J, Faulkner G. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 2013; 153:101-11. [PMID: 23540693 PMCID: PMC3898742 DOI: 10.1016/j.cell.2013.02.032] [Citation(s) in RCA: 280] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 12/21/2012] [Accepted: 02/19/2013] [Indexed: 01/31/2023]
Abstract
LINE-1 (L1) retrotransposons are mobile genetic elements comprising ~17% of the human genome. New L1 insertions can profoundly alter gene function and cause disease, though their significance in cancer remains unclear. Here, we applied enhanced retrotransposon capture sequencing (RC-seq) to 19 hepatocellular carcinoma (HCC) genomes and elucidated two archetypal L1-mediated mechanisms enabling tumorigenesis. In the first example, 4/19 (21.1%) donors presented germline retrotransposition events in the tumor suppressor mutated in colorectal cancers (MCC). MCC expression was ablated in each case, enabling oncogenic β-catenin/Wnt signaling. In the second example, suppression of tumorigenicity 18 (ST18) was activated by a tumor-specific L1 insertion. Experimental assays confirmed that the L1 interrupted a negative feedback loop by blocking ST18 repression of its enhancer. ST18 was also frequently amplified in HCC nodules from Mdr2(-/-) mice, supporting its assignment as a candidate liver oncogene. These proof-of-principle results substantiate L1-mediated retrotransposition as an important etiological factor in HCC.
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Affiliation(s)
- Ruchi Shukla
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Kyle R. Upton
- Cancer Biology Program, Mater Medical Research Institute, South Brisbane QLD 4101, Australia
| | - Martin Muñoz-Lopez
- Department of Human DNA Variability, Pfizer-University of Granada and Andalusian Government Center for Genomics and Oncology (GENYO), 18007 Granada, Spain
| | - Daniel J. Gerhardt
- Cancer Biology Program, Mater Medical Research Institute, South Brisbane QLD 4101, Australia
| | - Malcolm E. Fisher
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Thu Nguyen
- Cancer Biology Program, Mater Medical Research Institute, South Brisbane QLD 4101, Australia
| | - Paul M. Brennan
- Edinburgh Cancer Research Centre, The University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XR, UK
| | - J. Kenneth Baillie
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
| | - Agnese Collino
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
| | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
| | - Shruti Sinha
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
| | - Fabio Iannelli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
| | - Enrico Radaelli
- DIVET, School of Veterinary Medicine, University of Milan, Via Celoria, 20133 Milan, Italy
| | - Alexandre Dos Santos
- INSERM U785, Centre Hépatobiliaire, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Delphine Rapoud
- INSERM U785, Centre Hépatobiliaire, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Catherine Guettier
- INSERM U785, Centre Hépatobiliaire, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Didier Samuel
- INSERM U785, Centre Hépatobiliaire, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
| | - Piero Carninci
- RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-chô, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Francesca D. Ciccarelli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, 20139 Milan, Italy
| | - Jose Luis Garcia-Perez
- Department of Human DNA Variability, Pfizer-University of Granada and Andalusian Government Center for Genomics and Oncology (GENYO), 18007 Granada, Spain
| | - Jamila Faivre
- INSERM U785, Centre Hépatobiliaire, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Geoffrey J. Faulkner
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush EH25 9RG, UK
- Cancer Biology Program, Mater Medical Research Institute, South Brisbane QLD 4101, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane QLD 4072, Australia
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247
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Wei L, Xiao M, An Z, Ma B, Mason AS, Qian W, Li J, Fu D. New insights into nested long terminal repeat retrotransposons in Brassica species. MOLECULAR PLANT 2013; 6:470-482. [PMID: 22930733 DOI: 10.1093/mp/sss081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Long terminal repeat (LTR) retrotransposons, one of the foremost types of transposons, continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation. Many LTR-TEs preferentially insert within other LTR-TEs, but the cause and evolutionary significance of these nested LTR-TEs are not well understood. In this study, a total of 1.52Gb of Brassica sequence containing 2020 bacterial artificial chromosomes (BACs) was scanned, and six bacterial artificial chromosome (BAC) clones with extremely nested LTR-TEs (LTR-TEs density: 7.24/kb) were selected for further analysis. The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions, with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5-23Mya. LTR-TEs also preferably inserted into TA-rich repeat regions. Gene prediction by Genescan identified 207 genes in the 0.84Mb of total BAC sequences. Only a few genes (3/207) could be matched to the Brassica expressed sequence tag (EST) database, indicating that most genes were inactive after retrotransposon insertion. Five of the six BACs were putatively centromeric. Hence, nested LTR-TEs in centromere regions are rapidly duplicated, repeatedly inserted, and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences. Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions, and that these nested LTR-TEs play a role in the formation of centromeres.
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Affiliation(s)
- Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
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248
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Koonin EV. Elaborate security TRAINing to fight against expression of genomic junk. Cell Cycle 2013; 12:553-4. [PMID: 23370394 DOI: 10.4161/cc.23717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A new study shows that the expression of two classes of repetitive elements in the mouse genome is controlled through two complementary mechanisms: DNA methylation and p53-mediated transcription suppression.¹ When both lines of defense fail, expression of the repeats yields large quantities of double-stranded RNA, triggering interferon response that leads to caspase-dependent cell death. These notable findings highlight two fundamental trends: tight coupling of defense and cell death mechanisms that appears to be universal in cellular life and the exploitation of the expression of "junk" DNA as a signal triggering "altruistic" cell suicide.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
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249
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Kim YJ, Lee J, Han K. Transposable Elements: No More 'Junk DNA'. Genomics Inform 2012; 10:226-33. [PMID: 23346034 PMCID: PMC3543922 DOI: 10.5808/gi.2012.10.4.226] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 11/16/2012] [Accepted: 11/17/2012] [Indexed: 01/03/2023] Open
Abstract
Since the advent of whole-genome sequencing, transposable elements (TEs), just thought to be 'junk' DNA, have been noticed because of their numerous copies in various eukaryotic genomes. Many studies about TEs have been conducted to discover their functions in their host genomes. Based on the results of those studies, it has been generally accepted that they have a function to cause genomic and genetic variations. However, their infinite functions are not fully elucidated. Through various mechanisms, including de novo TE insertions, TE insertion-mediated deletions, and recombination events, they manipulate their host genomes. In this review, we focus on Alu, L1, human endogenous retrovirus, and short interspersed element/variable number of tandem repeats/Alu (SVA) elements and discuss how they have affected primate genomes, especially the human and chimpanzee genomes, since their divergence.
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Affiliation(s)
- Yun-Ji Kim
- Department of Nanobiomedical Science, WCU Research Center, Dankook University, Cheonan 330-714, Korea
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250
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Hayes M, Pyon YS, Li J. A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data. PLoS One 2012; 7:e52881. [PMID: 23300804 PMCID: PMC3531386 DOI: 10.1371/journal.pone.0052881] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/22/2012] [Indexed: 01/08/2023] Open
Abstract
Structural variation (SV) has been reported to be associated with numerous diseases such as cancer. With the advent of next generation sequencing (NGS) technologies, various types of SV can be potentially identified. We propose a model based clustering approach utilizing a set of features defined for each type of SV events. Our method, termed SVMiner, not only provides a probability score for each candidate, but also predicts the heterozygosity of genomic deletions. Extensive experiments on genome-wide deep sequencing data have demonstrated that SVMiner is robust against the variability of a single cluster feature, and it significantly outperforms several commonly used SV detection programs. SVMiner can be downloaded from http://cbc.case.edu/svminer/.
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Affiliation(s)
- Matthew Hayes
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Yoon Soo Pyon
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Jing Li
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, United States of America
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