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Liang KH, Yeh CT. A gene expression restriction network mediated by sense and antisense Alu sequences located on protein-coding messenger RNAs. BMC Genomics 2013; 14:325. [PMID: 23663499 PMCID: PMC3655826 DOI: 10.1186/1471-2164-14-325] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 05/07/2013] [Indexed: 01/08/2023] Open
Abstract
Background Alus are primate-specific retrotransposons which account for 10.6% of the human genome. A large number of protein-coding mRNAs are encoded with sense or antisense Alus in the un-translated regions. Results We postulated that mRNAs carrying Alus in the two opposite directions can generate double stranded RNAs, capable of regulating the levels of other Alu-carrying mRNAs post-transcriptionally. A gene expression profiling assay showed that the levels of antisense and sense Alus-carrying mRNAs were suppressed in a reversible manner by over-expression of exogenous sense and antisense Alus derived from mRNAs (Family-wise error rate P= 0.0483 and P < 0.0001 respectively). Screening through human mRNAs on the NCBI-RefSeq database, it was found that sense and antisense Alu-carrying transcripts were enriched in distinct cellular functions. Antisense Alu-carrying genes were particularly enriched in neurological and developmental processes, while sense Alu-carrying genes were enriched in immunological functions. Conclusions Taken together, we proposed a novel Alu-mediated regulation network capable of stabilizing Alu-carrying mRNA levels in different cell types and restricting the activated expression levels of protein-coding, Alu-carrying mRNAs.
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Affiliation(s)
- Kung-Hao Liang
- Liver Research Center, Chang Gung Memorial Hospital, and Molecular Medicine Research Center, Chang Gung University School of Medicine, Taipei, Taiwan
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202
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Hackett PB, Largaespada DA, Switzer KC, Cooper LJN. Evaluating risks of insertional mutagenesis by DNA transposons in gene therapy. Transl Res 2013; 161:265-83. [PMID: 23313630 PMCID: PMC3602164 DOI: 10.1016/j.trsl.2012.12.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 12/30/2022]
Abstract
Investigational therapy can be successfully undertaken using viral- and nonviral-mediated ex vivo gene transfer. Indeed, recent clinical trials have established the potential for genetically modified T cells to improve and restore health. Recently, the Sleeping Beauty (SB) transposon/transposase system has been applied in clinical trials to stably insert a chimeric antigen receptor (CAR) to redirect T-cell specificity. We discuss the context in which the SB system can be harnessed for gene therapy and describe the human application of SB-modified CAR(+) T cells. We have focused on theoretical issues relating to insertional mutagenesis in the context of human genomes that are naturally subjected to remobilization of transposons and the experimental evidence over the last decade of employing SB transposons for defining genes that induce cancer. These findings are put into the context of the use of SB transposons in the treatment of human disease.
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Affiliation(s)
- Perry B Hackett
- Department of Genetics Cell Biology and Development, Center for Genome Engineering and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA.
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203
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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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204
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Kaaij LJ, Hoogstrate SW, Berezikov E, Ketting RF. piRNA dynamics in divergent zebrafish strains reveal long-lasting maternal influence on zygotic piRNA profiles. RNA (NEW YORK, N.Y.) 2013; 19:345-356. [PMID: 23335638 PMCID: PMC3677245 DOI: 10.1261/rna.036400.112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/20/2012] [Indexed: 06/01/2023]
Abstract
Transposable elements (TEs) are mobile genetic elements that can have many deleterious effects on the fitness of their host. The germline-specific PIWI pathway guards the genome against TEs, deriving its specificity from sequence complementarity between PIWI-bound small RNAs (piRNAs) and the TEs. The piRNAs are derived from so-called piRNA clusters. Recent studies have demonstrated that the piRNA repertoire can be adjusted to accommodate recent TE invasions by capturing invading TEs in piRNA loci. Thus far, no information concerning piRNA divergence is available from vertebrates. We present piRNA analyses of two relatively divergent zebrafish strains. We find that significant differences in the piRNA populations have accumulated, most notably among active class I TEs. This divergence can be split into differences in piRNA abundance per element and differences in sense/antisense polarity ratios. In crosses between animals of the different strains, many of these differences are resolved in the progeny. However, some differences remain, often leaning to the maternally contributed piRNA population. These differences can be detected at least two generations later. Our data illustrate, for the first time, the fluidity of piRNA populations in vertebrates and how the established diversity is transmitted to future generations.
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205
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Morin A, Bardot B, Simeonova I, Lejour V, Bouarich-Bourimi R, Toledo F. Of mice and men: fuzzy tandem repeats and divergent p53 transcriptional repertoires. Transcription 2013; 4:67-71. [PMID: 23412358 DOI: 10.4161/trns.23772] [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: 11/19/2022] Open
Abstract
The clinical importance of tumor suppressor p53 makes it one of the most studied transcription factors. A comparison of mammalian p53 transcriptional repertoires may help identify fundamental principles in genome evolution and better understand cancer processes. Here we summarize mechanisms underlying the divergence of mammalian p53 transcriptional repertoires, with an emphasis on the rapid evolution of fuzzy tandem repeats containing p53 response elements.
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206
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Cui X, Jin P, Cui X, Gu L, Lu Z, Xue Y, Wei L, Qi J, Song X, Luo M, An G, Cao X. Control of transposon activity by a histone H3K4 demethylase in rice. Proc Natl Acad Sci U S A 2013; 110:1953-8. [PMID: 23319643 PMCID: PMC3562835 DOI: 10.1073/pnas.1217020110] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) are ubiquitously present in plant genomes and often account for significant fractions of the nuclear DNA. For example, roughly 40% of the rice genome consists of TEs, many of which are retrotransposons, including 14% LTR- and ∼1% non-LTR retrotransposons. Despite their wide distribution and abundance, very few TEs have been found to be transpositional, indicating that TE activities may be tightly controlled by the host genome to minimize the potentially mutagenic effects associated with active transposition. Consistent with this notion, a growing body of evidence suggests that epigenetic silencing pathways such as DNA methylation, RNA interference, and H3K9me2 function collectively to repress TE activity at the transcriptional and posttranscriptional levels. It is not yet clear, however, whether the removal of histone modifications associated with active transcription is also involved in TE silencing. Here, we show that the rice protein JMJ703 is an active H3K4-specific demethylase required for TEs silencing. Impaired JMJ703 activity led to elevated levels of H3K4me3, the misregulation of numerous endogenous genes, and the transpositional reactivation of two families of non-LTR retrotransposons. Interestingly, loss of JMJ703 did not affect TEs (such as Tos17) previously found to be silenced by other epigenetic pathways. These results indicate that the removal of active histone modifications is involved in TE silencing and that different subsets of TEs may be regulated by distinct epigenetic pathways.
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Affiliation(s)
- Xiekui Cui
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ping Jin
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
- Department of Life Science, Pohang University of Science and Technology, Pohang 790-784, Korea; and
| | - Xia Cui
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lianfeng Gu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhike Lu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongming Xue
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Liya Wei
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Jianfei Qi
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ming Luo
- Commonwealth Scientific and Industrial Research Organization Plant Industry, Canberra, ACT 2601, Australia
| | - Gynheung An
- Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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207
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Abstract
What good are transposable elements (TEs)? Although their activity can be harmful to host genomes and can cause disease, they nevertheless represent an important source of genetic variation that has helped shape genomes. In this review, we examine the impact of TEs, collectively referred to as the mobilome, on the transcriptome. We explore how TEs—particularly retrotransposons—contribute to transcript diversity and consider their potential significance as a source of small RNAs that regulate host gene transcription. We also discuss a critical role for the mobilome in engineering transcriptional networks, permitting coordinated gene expression, and facilitating the evolution of novel physiological processes.
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Affiliation(s)
- Michael Cowley
- Department of Medical & Molecular Genetics, King's College London, London, United Kingdom
| | - Rebecca J. Oakey
- Department of Medical & Molecular Genetics, King's College London, London, United Kingdom
- * E-mail:
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208
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Xing J, Witherspoon DJ, Jorde LB. Mobile element biology: new possibilities with high-throughput sequencing. Trends Genet 2013; 29:280-9. [PMID: 23312846 DOI: 10.1016/j.tig.2012.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/20/2012] [Accepted: 12/11/2012] [Indexed: 12/29/2022]
Abstract
Mobile elements comprise more than half of the human genome, but until recently their large-scale detection was time consuming and challenging. With the development of new high-throughput sequencing (HTS) technologies, the complete spectrum of mobile element variation in humans can now be identified and analyzed. Thousands of new mobile element insertions (MEIs) have been discovered, yielding new insights into mobile element biology, evolution, and genomic variation. Here, we review several high-throughput methods, with an emphasis on techniques that specifically target MEIs in humans. We highlight recent applications of these methods in evolutionary studies and in the analysis of somatic alterations in human normal and tumor tissues.
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Affiliation(s)
- Jinchuan Xing
- Department of Genetics, Human Genetic Institute of New Jersey, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
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209
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Deng Z, Wang Z, Lieberman PM. Telomeres and viruses: common themes of genome maintenance. Front Oncol 2012; 2:201. [PMID: 23293769 PMCID: PMC3533235 DOI: 10.3389/fonc.2012.00201] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 12/08/2012] [Indexed: 12/14/2022] Open
Abstract
Genome maintenance mechanisms actively suppress genetic instability associated with cancer and aging. Some viruses provoke genetic instability by subverting the host's control of genome maintenance. Viruses have their own specialized strategies for genome maintenance, which can mimic and modify host cell processes. Here, we review some of the common features of genome maintenance utilized by viruses and host chromosomes, with a particular focus on terminal repeat (TR) elements. The TRs of cellular chromosomes, better known as telomeres, have well-established roles in cellular chromosome stability. Cellular telomeres are themselves maintained by viral-like mechanisms, including self-propagation by reverse transcription, recombination, and retrotransposition. Viral TR elements, like cellular telomeres, are essential for viral genome stability and propagation. We review the structure and function of viral repeat elements and discuss how they may share telomere-like structures and genome protection functions. We consider how viral infections modulate telomere regulatory factors for viral repurposing and can alter normal host telomere structure and chromosome stability. Understanding the common strategies of viral and cellular genome maintenance may provide new insights into viral-host interactions and the mechanisms driving genetic instability in cancer.
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Affiliation(s)
- Zhong Deng
- The Wistar Institute Philadelphia, PA, USA
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210
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Dridi S. Alu mobile elements: from junk DNA to genomic gems. SCIENTIFICA 2012; 2012:545328. [PMID: 24278713 PMCID: PMC3820591 DOI: 10.6064/2012/545328] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 11/06/2012] [Indexed: 06/02/2023]
Abstract
Alus, the short interspersed repeated sequences (SINEs), are retrotransposons that litter the human genomes and have long been considered junk DNA. However, recent findings that these mobile elements are transcribed, both as distinct RNA polymerase III transcripts and as a part of RNA polymerase II transcripts, suggest biological functions and refute the notion that Alus are biologically unimportant. Indeed, Alu RNAs have been shown to control mRNA processing at several levels, to have complex regulatory functions such as transcriptional repression and modulating alternative splicing and to cause a host of human genetic diseases. Alu RNAs embedded in Pol II transcripts can promote evolution and proteome diversity, which further indicates that these mobile retroelements are in fact genomic gems rather than genomic junks.
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Affiliation(s)
- Sami Dridi
- Nutrition Research Institute, The University of North Carolina at Chapel Hill, 500 Laureate Way, Kannapolis, NC 28081, USA
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211
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Transposable elements and human cancer: a causal relationship? Biochim Biophys Acta Rev Cancer 2012; 1835:28-35. [PMID: 22982062 DOI: 10.1016/j.bbcan.2012.09.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 08/30/2012] [Accepted: 09/04/2012] [Indexed: 12/18/2022]
Abstract
Transposable elements are present in almost all genomes including that of humans. These mobile DNA sequences are capable of invading genomes and their impact on genome evolution is substantial as they contribute to the genetic diversity of organisms. The mobility of transposable elements can cause deleterious mutations, gene disruption and chromosome rearrangements that may lead to several pathologies including cancer. This mini-review aims to give a brief overview of the relationship that transposons and retrotransposons may have in the genetic cause of human cancer onset, or conversely creating protection against cancer. Finally, the cause of TE mobility may also be the cancer cell environment itself.
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212
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Abstract
In this issue of Genome Biology, Nellåker et al. show massive purging of deleterious transposable element variants, through negative selection, in 18 mouse strains.
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Affiliation(s)
- Rita Rebollo
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
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