Characterization and distribution of repetitive elements in association with genes in the human genome

Liang, Kai-Chiang; Tseng, Joseph T.; Tsai, Shaw-Jenq; Sun, Han

doi:10.1016/j.compbiolchem.2015.02.007

Cited by 13 publications

(10 citation statements)

References 49 publications

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“…Growing evidence supports that repetitive intronic elements, such as the long interspersed elements (LINEs) and the short interspersed elements (SINEs) contained in several introns of both PII- and PI-SVMP genes ( Table 1 ) can influence genome stability and gene expression (reviewed in [ 75 ]). Thus, these interspersed repeats may alter genome recombination structure and rates, through a number of mechanisms, including replication slippage and unequal crossover [ 76 , 77 ], potentially impacting regulation of gene expression [ 78 ], recombination events leading to tandem duplication of segments of the genome [ 79 , 80 ], gene conversion [ 81 ], and chromosomal organization [ 79 ].…”

Section: Resultsmentioning

confidence: 99%

Insights into the Evolution of a Snake Venom Multi-Gene Family from the Genomic Organization of Echis ocellatus SVMP Genes

Sanz

Calvete

2016

Toxins

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The molecular events underlying the evolution of the Snake Venom Metalloproteinase (SVMP) family from an A Disintegrin And Metalloproteinase (ADAM) ancestor remain poorly understood. Comparative genomics may provide decisive information to reconstruct the evolutionary history of this multi-locus toxin family. Here, we report the genomic organization of Echis ocellatus genes encoding SVMPs from the PII and PI classes. Comparisons between them and between these genes and the genomic structures of Anolis carolinensis ADAM28 and E. ocellatus PIII-SVMP EOC00089 suggest that insertions and deletions of intronic regions played key roles along the evolutionary pathway that shaped the current diversity within the multi-locus SVMP gene family. In particular, our data suggest that emergence of EOC00028-like PI-SVMP from an ancestral PII(e/d)-type SVMP involved splicing site mutations that abolished both the 3′ splice AG acceptor site of intron 12* and the 5′ splice GT donor site of intron 13*, and resulted in the intronization of exon 13* and the consequent destruction of the structural integrity of the PII-SVMP characteristic disintegrin domain.

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Section: Resultsmentioning

confidence: 99%

Insights into the Evolution of a Snake Venom Multi-Gene Family from the Genomic Organization of Echis ocellatus SVMP Genes

Sanz

Calvete

2016

Toxins

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“…Different combinations of repetitive elements can shape the function of particular genes, 136 and the open/close status of the chromatin may also condition TE distribution. Because this last feature may be dependent on gene type, we further questioned whether the patterns of TEs linked to ME/CFS DM promoters depended on downstream encoded gene types, here classified as protein coding, short noncoding, long noncoding, or pseudogenes.…”

Section: Genomic Location Associations Between Me/cfs Dna Differentiamentioning

confidence: 99%

“…The significance of particular sets of TEs remain enigmatic; however, initiatives such as the GBRED database and its web interface (http://www.binfo.ncku.edu.tw/GBRED/ index.html 136 ), designed to provide detailed information of repetitive elements associated with particular genes, will eventually permit unveiling of their functional role.…”

Section: April 2019mentioning

confidence: 99%

Epigenetic Components of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Uncover Potential Transposable Element Activation

Almenar-Pérez

Ovejero

Sánchez-Fito

et al. 2019

Clinical Therapeutics

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Purpose: Studies to determine epigenetic changes associated with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) remain scarce; however, current evidence clearly shows that methylation patterns of genomic DNA and noncoding RNA profiles of immune cells differ between patients and healthy subjects, suggesting an active role of these epigenetic mechanisms in the disease. The present study compares and contrasts the available ME/CFS epigenetic data in an effort to evidence overlapping pathways capable of explaining at least some of the dysfunctional immune parameters linked to this disease. Methods: A systematic search of the literature evaluating the ME/CFS epigenome landscape was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria. Differential DNA methylation and noncoding RNA differential expression patterns associated with ME/CFS were used to screen for the presence of transposable elements using the Dfam browser, a search program nurtured with the Repbase repetitive sequence database and the RepeatMasker annotation tool. Findings: Unexpectedly, particular associations of transposable elements and ME/CFS epigenetic hallmarks were uncovered. A model for the disease emerged involving transcriptional induction of endogenous dormant transposons and structured cellular RNA interactions, triggering the activation of the innate immune system without a concomitant active infection. Implications: Repetitive sequence filters (ie, RepeatMasker) should be avoided when analyzing transcriptomic data to assess the potential participation of repetitive sequences ("junk repetitive DNA"), representing >45% of the human genome, in the onset and evolution of ME/CFS. In addition, transposable element screenings aimed at designing cost-effective, focused empirical assays that can confirm or disprove the suspected involvement of transposon transcriptional activation in this disease, following the pilot strategy presented here, will require databases gathering large ME/CFS epigenetic datasets.

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“…This carrier is comprised of TAP-1 and TAP-2 subunits and is essential in antigen processing and highly conserved among various eukaryotic species ( Zhao et al 2006 , Murata et al 2009 ). Some genes may be associated with repetitive DNA in different species genomes and may involve various functions, such as genome stability, gene expression regulation, chromatin formation, and as miRNAs ( Roberts et al 2014 , Liang et al 2015 ). This association of genes with repetitive DNA has been found in some species of lizards, fish, and mammals ( Valente et al 2011 , Pokorná et al 2011 , Terencio et al 2015 ), and is also evident for analyzed species in this study.…”

Section: Discussionmentioning

confidence: 99%

Differential repetitive DNA composition in the centromeric region of chromosomes of Amazonian lizard species in the family Teiidae

Carvalho

Carmo

Neves

et al. 2016

CCG

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Differences in heterochromatin distribution patterns and its composition were observed in Amazonian teiid species. Studies have shown repetitive DNA harbors heterochromatic blocks which are located in centromeric and telomeric regions in Ameiva ameiva (Linnaeus, 1758), Kentropyx calcarata (Spix, 1825), Kentropyx pelviceps (Cope, 1868), and Tupinambis teguixin (Linnaeus, 1758). In Cnemidophorus sp.1, repetitive DNA has multiple signals along all chromosomes. The aim of this study was to characterize moderately and highly repetitive DNA sequences by Cot1-DNA from Ameiva ameiva and Cnemidophorus sp.1 genomes through cloning and DNA sequencing, as well as mapping them chromosomally to better understand its organization and genome dynamics. The results of sequencing of DNA libraries obtained by Cot1-DNA showed that different microsatellites, transposons, retrotransposons, and some gene families also comprise the fraction of repetitive DNA in the teiid species. FISH using Cot1-DNA probes isolated from both Ameiva ameiva and Cnemidophorus sp.1 showed these sequences mainly located in heterochromatic centromeric, and telomeric regions in Ameiva ameiva, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin chromosomes, indicating they play structural and functional roles in the genome of these species. In Cnemidophorus sp.1, Cot1-DNA probe isolated from Ameiva ameiva had multiple interstitial signals on chromosomes, whereas mapping of Cot1-DNA isolated from the Ameiva ameiva and Cnemidophorus sp.1 highlighted centromeric regions of some chromosomes. Thus, the data obtained showed that many repetitive DNA classes are part of the genome of Ameiva ameiva, Cnemidophorus sp.1, Kentroyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin, and these sequences are shared among the analyzed teiid species, but they were not always allocated at the same chromosome position.

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Characterization and distribution of repetitive elements in association with genes in the human genome

Cited by 13 publications

References 49 publications

Insights into the Evolution of a Snake Venom Multi-Gene Family from the Genomic Organization of Echis ocellatus SVMP Genes

Insights into the Evolution of a Snake Venom Multi-Gene Family from the Genomic Organization of Echis ocellatus SVMP Genes

Epigenetic Components of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Uncover Potential Transposable Element Activation

Differential repetitive DNA composition in the centromeric region of chromosomes of Amazonian lizard species in the family Teiidae

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