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Restless Genomes: Humans as a Model Organism for Understanding Host-Retrotransposable Element Dynamics
Published on Jan 1, 2011in Advances in Genetics 4.69
· DOI :10.1016/B978-0-12-380860-8.00006-9
Dale J. Hedges31
Estimated H-index: 31
(University of Miami),
Victoria P. Belancio17
Estimated H-index: 17
(Tulane University)
Abstract
Since their initial discovery in maize, there have been various attempts to categorize the relationship between transposable elements (TEs) and their host organisms. These have ranged from TEs being selfish parasites to their role as essential, functional components of organismal biology. Research over the past several decades has, in many respects, only served to complicate the issue even further. On the one hand, investigators have amassed substantial evidence concerning the negative effects that TE-mutagenic activity can have on host genomes and organismal fitness. On the other hand, we find an increasing number of examples, across several taxa, of TEs being incorporated into functional biological roles for their host organism. Some 45% of our own genomes are comprised of TE copies. While many of these copies are dormant, having lost their ability to mobilize, several lineages continue to actively proliferate in modern human populations. With its complement of ancestral and active TEs, the human genome exhibits key aspects of the host–TE dynamic that has played out since early on in organismal evolution. In this review, we examine what insights the particularly well-characterized human system can provide regarding the nature of the host–TE interaction.
  • References (204)
  • Cited By (15)
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References204
Published on Mar 1, 1992in Oncogene 6.85
Bratthauer Gl1
Estimated H-index: 1
,
Fanning Tg1
Estimated H-index: 1
84 Citations
Published on Jan 1, 2002
Alan M. Lambowitz1
Estimated H-index: 1
,
Martin Gellert1
Estimated H-index: 1
+ 3 AuthorsPhoebe A. Rice35
Estimated H-index: 35
This new edition of the bestselling series on movable genetic elements highlights the many exciting advances in the field over the last decade, including conservative site-specific recombination, programmed rearrangements, DNA-only transposons, and LTR, and non-LTR retrotransposons. Virtually all organisms contain multiple mobile DNAs that can move from place to place, and in some organisms, mobile DNA elements make up a significant portion of the genome. Mobile DNA III provides a comprehensive ...
1,222 Citations Source Cite
Published on Feb 1, 2000in Nature 41.58
Sha Mi1
Estimated H-index: 1
(Genetics Institute, Inc.),
Xinhua Lee1
Estimated H-index: 1
(Genetics Institute, Inc.)
+ 9 AuthorsSteve Howes1
Estimated H-index: 1
(Genetics Institute, Inc.)
Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis
981 Citations Source Cite
Published on Jan 1, 2007
Michael Lynch88
Estimated H-index: 88
The Origin of Eukaryotes Genome Size and Organismal Complexity The Human Genome Why Population Size Matters Three Keys to Chromosomal Integrity The Nucleotide-composition Landscape Mobile Genetic Elements Genomic Expansion by Gene Duplication Genes in Pieces Transcription and Regulatory-region Complexity Expansion and Contraction of Organelle Genomes Sex Chromosome Evolution Genomfart
851 Citations
Published on May 2, 2006in Cancer Cell International 3.96
S. Mehdi Belgnaoui10
Estimated H-index: 10
(Eastern Virginia Medical School),
Roger G. Gosden36
Estimated H-index: 36
(Cornell University)
+ 1 AuthorsAbdelali Haoudi10
Estimated H-index: 10
(Eastern Virginia Medical School)
Background Long interspersed nuclear elements (LINEs), Alu and endogenous retroviruses (ERVs) make up some 45% of human DNA. LINE-1 also called L1, is the most common family of non-LTR retrotransposons in the human genome and comprises about 17% of the genome. L1 elements require the integration into chromosomal target sites using L1-encoded endonuclease which creates staggering DNA breaks allowing the newly transposed L1 copies to integrate into the genome. L1 expression and retrotransposition ...
126 Citations Source Cite
Published on Jan 1, 2012in Frontiers in Bioscience 2.35
Kristine J. Kines11
Estimated H-index: 11
,
Victoria P. Belancio17
Estimated H-index: 17
(Tulane University)
Historically the accumulated mass of mammalian transposable elements (TEs), particularly those located within gene boundaries, was viewed as a genetic burden potentially detrimental to the genomic landscape. This notion has been strengthened by the discovery that transposable sequences can alter the architecture of the transcriptome, not only through insertion, but also long after the integration process is completed. Insertions previously considered harmless are now known to impact the expressi...
25 Citations Source Cite
Published on Oct 1, 1990in The EMBO Journal 10.56
Yue Xiong5
Estimated H-index: 5
(University of Rochester),
Thomas H. Eickbush47
Estimated H-index: 47
(University of Rochester)
Abstract To study the evolutionary relationship of reverse transcriptase (RT) containing genetic elements, a phylogenetic tree of 82 retroelements from animals, plants, protozoans and bacteria was constructed. The tree was based on seven amino acid domains totalling 178 residues identified in all RTs. We have also identified these seven domains in the RNA-directed RNA polymerases from various plus-strand RNA viruses. The sequence similarity of these RNA polymerases to RT suggests that these two ...
1,060 Citations Source Cite
Published on Aug 1, 2001in Genome Biology 13.21
Natalia Volfovsky15
Estimated H-index: 15
,
Brian J. Haas64
Estimated H-index: 64
,
Steven L. Salzberg118
Estimated H-index: 118
Background A computational system for analysis of the repetitive structure of genomic sequences is described. The method uses suffix trees to organize and search the input sequences; this data structure has been used previously for efficient computation of exact and degenerate repeats.
118 Citations Source Cite
Published on Jan 1, 2005
Casey M. Bergman30
Estimated H-index: 30
,
Olivier Andrieu4
Estimated H-index: 4
+ 3 AuthorsDominique Anxolabéhère21
Estimated H-index: 21
7 Citations
Cited By15
Published on Sep 15, 2011
Astrid M. Roy-Engel21
Estimated H-index: 21
(Tulane University),
Victoria P. Belancio17
Estimated H-index: 17
(Tulane University)
Retrotransposition is a ‘copy-and-paste’ mechanism whereby a retrotransposable element is copied from one genomic location and inserted into another genomic location, using a ribonucleic acid intermediate. The consequences of the retrotransposon-associated alterations of the genomic landscape range from silent events to changes contributing to species-specific and individual differences as well as a broad spectrum of diseases. Retrotransposon-induced genetic variation can lead to inactivation or...
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Published on Jun 17, 2014in Nucleic Acids Research 11.56
Jiali Zhuang5
Estimated H-index: 5
,
Jie Wang15
Estimated H-index: 15
+ 1 AuthorsZhiping Weng84
Estimated H-index: 84
Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the population level can provide crucial insights into the processes and mechanisms of genome evolution. Pooling genomic materials from multiple individuals followed by high-throughput sequencing is an efficient way of characterizing genomic polymorphisms in a population. Here we describe a novel method named TEMP, specifically designed to det...
55 Citations Source Cite
Published on Aug 1, 2014in Toxicology Letters 3.17
Abbas Karimi5
Estimated H-index: 5
(Iran University of Medical Sciences),
Zahra Madjd20
Estimated H-index: 20
(Iran University of Medical Sciences)
+ 1 AuthorsSeyed Mohammad Akrami13
Estimated H-index: 13
(Tehran University of Medical Sciences)
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 As 2 O 3 on L1 retrotransposition alteration in human hepatocellular carcinoma cells (H...
9 Citations Source Cite
Published on Nov 1, 2012in Cell 31.40
Fan Zhang4
Estimated H-index: 4
(University of Massachusetts Medical School),
Jie Wang15
Estimated H-index: 15
(University of Massachusetts Medical School)
+ 9 AuthorsPhillip D. Zamore80
Estimated H-index: 80
(University of Massachusetts Medical School)
Summary piRNAs silence transposons during germline development. In Drosophila , transcripts from heterochromatic clusters are processed into primary piRNAs in the perinuclear nuage. The nuclear DEAD box protein UAP56 has been previously implicated in mRNA splicing and export, whereas the DEAD box protein Vasa has an established role in piRNA production and localizes to nuage with the piRNA binding PIWI proteins Ago3 and Aub. We show that UAP56 colocalizes with the cluster-associated HP1 variant ...
112 Citations Source Cite
Published on Oct 1, 2013in Journal of Human Genetics 2.94
Sérgio U. Dani4
Estimated H-index: 4
,
Winfried März + 1 AuthorsGerhard Franz Walter7
Estimated H-index: 7
The core aspects of the biology and evolution of sexual reproduction are reviewed with a focus on the diploid, sexually reproducing, outbreeding, polymorphic, unspecialized, altricial and cultural human species. Human mate choice and pair bonding are viewed as central to individuals’ lives and to the evolution of the species, and genetic assistance in reproduction is viewed as a universal human right. Pairomics is defined as an emerging branch of the omics science devoted to the study of mate ch...
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Published on Nov 1, 2013in Developmental Cell 9.62
Andreas W. Thomae9
Estimated H-index: 9
(Ludwig Maximilian University of Munich),
Georg O.M. Schade1
Estimated H-index: 1
(Max Planck Society)
+ 5 AuthorsAxel Imhof46
Estimated H-index: 46
(Ludwig Maximilian University of Munich)
Summary Speciation involves the reproductive isolation of natural populations due to the sterility or lethality of their hybrids. However, the molecular basis of hybrid lethality and the evolutionary driving forces that provoke it remain largely elusive. The hybrid male rescue ( Hmr ) and the lethal hybrid rescue ( Lhr ) genes serve as a model to study speciation in Drosophilids because their interaction causes lethality in male hybrid offspring. Here, we show that HMR and LHR form a centromeric...
28 Citations Source Cite
Published on Jun 1, 2015in Biological Trace Element Research 2.36
Abbas Karimi5
Estimated H-index: 5
(Tehran University of Medical Sciences),
Keivan Majidzadeh-A5
Estimated H-index: 5
(Aja University of Medical Sciences)
+ 3 AuthorsSeyed Mohammad Akrami13
Estimated H-index: 13
(Tehran University of Medical Sciences)
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 hepatocellul...
5 Citations Source Cite
Published on Apr 1, 2013in Epigenomics 4.98
Richard G. Hunter23
Estimated H-index: 23
,
Bruce S. McEwen192
Estimated H-index: 192
The brain is the central organ of the body's response to and perception of stress. Both the juvenile and the adult brain show a significant capacity for lasting physiological, structural and behavioral plasticity as a consequence of stress exposure. The hypothesis that epigenetic mechanisms might lie behind the lasting effects of stress upon the brain has proven a fruitful one. In this review, we examine the growing literature showing that stress has a direct impact on epigenetic marks at all li...
72 Citations Source Cite
Published on Aug 1, 2013in Cancer Letters 6.49
Yuping Mei3
Estimated H-index: 3
(University of Maryland, Baltimore),
David Clark8
Estimated H-index: 8
(University of Maryland, Baltimore),
Li Mao54
Estimated H-index: 54
(University of Maryland Marlene and Stewart Greenebaum Cancer Center)
Piwi-interacting RNAs (piRNAs), a newly identified class of small non-coding RNAs, direct the Piwi-dependent transposon silencing, heterochromatin modification and germ cell maintenance. Owing to our limited knowledge regarding their biogenesis, piRNAs are considered as the most mysterious class of small regulatory RNAs, particularly in pathogenesis such as tumorigenesis. Recently, several lines of evidence have emerged to suggest that piRNAs may be dis-regulated and play crucial roles in tumori...
49 Citations Source Cite
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