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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. Hedges32
Estimated H-index: 32
(University of Miami),
Victoria P. Belancio18
Estimated H-index: 18
(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.
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  • Citations (15)
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References204
Newest
Published on Nov 1, 2010in Genomics 2.91
Dae-Soo Kim16
Estimated H-index: 16
,
Jae Won Huh4
Estimated H-index: 4
+ 3 AuthorsKyu Tae Chang12
Estimated H-index: 12
Recent studies indicate major roles for transposable elements (TEs) in alternative splicing. In this study, we conducted genome-wide alternative splicing analyses focusing on new internal exon birth derived from TEs in human, mouse, and zebrafish genomes. We identified two different exon sets, TE-spliced exons and non-TE-spliced exons. The proportion of TE-spliced exons was nearly twice as high as the proportion of non-TE-spliced exons in the coding sequence (CDS) region. Detailed analysis of va...
5 Citations Source Cite
Published on Sep 1, 2010in Genome Research 10.10
Adam D. Ewing18
Estimated H-index: 18
(University of Pennsylvania),
Haig H. Kazazian88
Estimated H-index: 88
(University of Pennsylvania)
Using high-throughput sequencing, we devised a technique to determine the insertion sites of virtually all members of the human-specific L1 retrotransposon family in any human genome. Using diagnostic nucleotides, we were able to locate the approximately 800 L1Hs copies corresponding specifically to the pre-Ta, Ta-0, and Ta-1 L1Hs subfamilies, with over 90% of sequenced reads corresponding to human-specific elements. We find that any two individual genomes differ at an average of 285 sites with ...
205 Citations Source Cite
Published on Aug 1, 2010in Seminars in Cancer Biology 10.20
Victoria P. Belancio18
Estimated H-index: 18
(Tulane University),
Astrid M. Roy-Engel22
Estimated H-index: 22
(Tulane University),
Prescott L. Deininger48
Estimated H-index: 48
(Tulane University)
Genetic instability is one of the principal hallmarks and causative factors in cancer. Human transposable elements (TE) have been reported to cause human diseases, including several types of cancer through insertional mutagenesis of genes critical for preventing or driving malignant transformation. In addition to retrotransposition-associated mutagenesis, TEs have been found to contribute even more genomic rearrangements through non-allelic homologous recombination. TEs also have the potential t...
127 Citations Source Cite
Published on Aug 1, 2010in Seminars in Cancer Biology 10.20
Miriam K. Konkel22
Estimated H-index: 22
(Louisiana State University),
Mark A. Batzer83
Estimated H-index: 83
(Louisiana State University)
It is now commonly agreed that the human genome is not the stable entity originally presumed. Deletions, duplications, inversions, and insertions are common, and contribute significantly to genomic structural variations (SVs). Their collective impact generates much of the inter-individual genomic diversity observed among humans. Not only do these variations change the structure of the genome; they may also have functional implications, e.g. altered gene expression. Some SVs have been identified ...
116 Citations Source Cite
Published on Jul 1, 2010in Nucleic Acids Research 11.56
Victoria P. Belancio18
Estimated H-index: 18
(Tulane University),
Astrid M. Roy-Engel22
Estimated H-index: 22
(Tulane University)
+ 1 AuthorsPrescott L. Deininger48
Estimated H-index: 48
(Tulane University)
LINE-1 expression damages host DNA via insertions and endonuclease-dependent DNA double-strand breaks (DSBs) that are highly toxic and mutagenic. The predominant tissue of LINE-1 expression has been considered to be the germ line. We show that both full-length and processed L1 transcripts are widespread in human somatic tissues and transformed cells, with significant variation in both L1 expression and L1 mRNA processing. This is the first demonstration that RNA processing is a major regulator o...
128 Citations Source Cite
Published on Jul 1, 2010in Molecules and Cells 3.08
Dae-Soo Kim16
Estimated H-index: 16
(Korea Research Institute of Bioscience and Biotechnology),
Jae-Won Huh17
Estimated H-index: 17
(Korea Research Institute of Bioscience and Biotechnology)
+ 2 AuthorsKyu-Tae Chang23
Estimated H-index: 23
(Korea Research Institute of Bioscience and Biotechnology)
A dual coding event, which is the translation of different isoforms from a single gene, is one of the special patterns among the alternative splicing events. This is an important mechanism for the regulation of protein diversity in human and mouse genomes. Although the regulation for dual coding events has been characterized in a few genes, the individual mechanism remains unclear. Numerous studies have described the exonization of transposable elements, which is the splicing mediated insertion ...
2 Citations Source Cite
Published on Jun 7, 2010in Annual Review of Biochemistry 20.15
Michael R. Lieber78
Estimated H-index: 78
(University of Southern California)
Double-strand DNA breaks are common events in eukaryotic cells, and there are two major pathways for repairing them: homologous recombination (HR) and nonhomologous DNA end joining (NHEJ). The various causes of double-strand breaks (DSBs) result in a diverse chemistry of DNA ends that must be repaired. Across NHEJ evolution, the enzymes of the NHEJ pathway exhibit a remarkable degree of structural tolerance in the range of DNA end substrate configurations upon which they can act. In vertebrate c...
1,368 Citations Source Cite
Published on Jun 1, 2010in Cell 31.40
Cheng Ran Lisa Huang7
Estimated H-index: 7
(Johns Hopkins University School of Medicine),
Anna M. Schneider3
Estimated H-index: 3
(Johns Hopkins University School of Medicine)
+ 11 AuthorsTao Wang20
Estimated H-index: 20
(Johns Hopkins University School of Medicine)
Characterizing structural variants in the human genome is of great importance, but a genome wide analysis to detect interspersed repeats has not been done. Thus, the degree to which mobile DNAs contribute to genetic diversity, heritable disease, and oncogenesis remains speculative. We perform transposon insertion profiling by microarray (TIP-chip) to map human L1(Ta) retrotransposons (LINE-1 s) genome-wide. This identified numerous novel human L1(Ta) insertional polymorphisms with highly variant...
185 Citations Source Cite
Published on Jun 1, 2010in Cell 31.40
Rebecca C. Iskow13
Estimated H-index: 13
(Emory University),
Michael T. McCabe13
Estimated H-index: 13
(University of Maryland, Baltimore)
+ 6 AuthorsScott E. Devine16
Estimated H-index: 16
Summary Two abundant classes of mobile elements, namely Alu and L1 elements, continue to generate new retrotransposon insertions in human genomes. Estimates suggest that these elements have generated millions of new germline insertions in individual human genomes worldwide. Unfortunately, current technologies are not capable of detecting most of these young insertions, and the true extent of germline mutagenesis by endogenous human retrotransposons has been difficult to examine. Here, we describ...
385 Citations Source Cite
Published on Jun 1, 2010in Cell 31.40
Christine R. Beck16
Estimated H-index: 16
(University of Michigan),
Pamela Collier3
Estimated H-index: 3
(University of Leicester)
+ 5 AuthorsJohn V. Moran47
Estimated H-index: 47
(University of Michigan)
Summary Highly active (i.e., "hot") long interspersed element-1 (LINE-1 or L1) sequences comprise the bulk of retrotransposition activity in the human genome; however, the abundance of hot L1s in the human population remains largely unexplored. Here, we used a fosmid-based, paired-end DNA sequencing strategy to identify 68 full-length L1s that are differentially present among individuals but are absent from the human genome reference sequence. The majority of these L1s were highly active in a cu...
319 Citations Source Cite
Cited By15
Newest
Published on Dec 1, 2018in Nature Communications 12.35
Karen H. Y. Wong1
Estimated H-index: 1
(University of California, San Francisco),
Michal Levy-Sakin10
Estimated H-index: 10
(University of California, San Francisco),
Pui-Yan Kwok67
Estimated H-index: 67
(University of California, San Francisco)
The human reference genome is used extensively in modern biological research. However, a single consensus representation is inadequate to provide a universal reference structure because it is a haplotype among many in the human population. Using 10× Genomics (10×G) “Linked-Read” technology, we perform whole genome sequencing (WGS) and de novo assembly on 17 individuals across five populations. We identify 1842 breakpoint-resolved non-reference unique insertions (NUIs) that, in aggregate, add up ...
4 Citations Source Cite
Published on Apr 1, 2018in Trends in Molecular Medicine 11.02
Patrick Küry25
Estimated H-index: 25
(University of Düsseldorf),
Avindra Nath33
Estimated H-index: 33
(National Institutes of Health)
+ 6 AuthorsHervé Perron6
Estimated H-index: 6
(University of Lyon)
The causes of multiple sclerosis and amyotrophic lateral sclerosis have long remained elusive. A new category of pathogenic components, normally dormant within human genomes, has been identified: human endogenous retroviruses (HERVs). These represent ∼8% of the human genome, and environmental factors have reproducibly been shown to trigger their expression. The resulting production of envelope (Env) proteins from HERV-W and HERV-K appears to engage pathophysiological pathways leading to the path...
23 Citations Source Cite
Published on Dec 1, 2017in BMC Research Notes
Hilda P. Navarrete (Autonomous University of Baja California), Linda H. Soler (Autonomous University of Baja California)+ 1 AuthorsMarco A. Ramos7
Estimated H-index: 7
(Autonomous University of Baja California)
Objective Presently, non-LTR retrotransposons are the most active mobile elements in the human genome. Among these, Alu elements are highly represented in the modern population. Worldwide, distribution of Alu polymorphisms (insertion/deletion; I/D) shows variability between different populations. Two Alu insertion loci, ACE and PR, are significant biomarkers that have served in several genotype–phenotype association studies. In Mexico, studies concerning the frequency of these biomarkers have be...
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Published on Nov 1, 2017in Progress in Biophysics & Molecular Biology 3.43
William B. Miller3
Estimated H-index: 3
An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological a...
6 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-A9
Estimated H-index: 9
(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 Aug 1, 2014in Toxicology Letters 3.17
Abbas Karimi3
Estimated H-index: 3
(Iran University of Medical Sciences),
Zahra Madjd21
Estimated H-index: 21
(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 Jun 17, 2014in Nucleic Acids Research 11.56
Jiali Zhuang5
Estimated H-index: 5
,
Jie Wang15
Estimated H-index: 15
+ 1 AuthorsZhiping Weng86
Estimated H-index: 86
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...
61 Citations Source Cite
Published on Nov 1, 2013in Developmental Cell 9.62
Andreas W. Thomae9
Estimated H-index: 9
(Ludwig Maximilian University of Munich),
Georg O.M. Schade2
Estimated H-index: 2
(Max Planck Society)
+ 5 AuthorsAxel Imhof49
Estimated H-index: 49
(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...
32 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 Walter8
Estimated H-index: 8
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 Aug 1, 2013in Cancer Letters 6.49
Yuping Mei4
Estimated H-index: 4
(University of Maryland, Baltimore),
David J. Clark19
Estimated H-index: 19
(University of Maryland, Baltimore),
Li Mao8
Estimated H-index: 8
(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...
52 Citations Source Cite