scholarly journals Pipeline to detect the positional and directional relationship between transposable elements and adjacent genes in host genome

2021 ◽  
Vol 1 ◽  
pp. 1-None
Author(s):  
Caroline Meguerditchian ◽  
Ayse Ergun ◽  
Veronique Decroocq ◽  
Marie Lefebvre ◽  
Quynh-Trang Bui
Keyword(s):  
Transposable Elements ◽  
Host Genome

Interactions between Transposable Elements and the Host Genome

Mobile DNA II ◽  
2002 ◽  
pp. 1008-1023 ◽  
Author(s):  
Mariano Labrador ◽  
Victor G. Corces
Keyword(s):  
Transposable Elements ◽  
Host Genome

scholarly journals What is the impact of transposable elements on host genome variability?

1999 ◽  
Vol 266 (1429) ◽  
pp. 1677-1683 ◽  
Author(s):  
P. T. J. Emery ◽  
T. E. Robinson ◽  
R. Duddington ◽  
J. F. Y. Brookfield
Keyword(s):  
Transposable Elements ◽  
Host Genome ◽  
Genome Variability ◽  
The Impact

scholarly journals Pipeline to detect the relationship between transposable elements and adjacent genes in host genome

2021 ◽  
Author(s):  
Caroline Meguerditchian ◽  
Ayse Ergun ◽  
Veronique DECROOCQ ◽  
Marie LEFEBVRE ◽  
Quynh Trang Bui
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Transcriptional Activity ◽  
Potential Role ◽  
Host Genome ◽  
Signalling Pathways ◽  
Adjacent Gene ◽  
Replication Intermediates ◽  
The Relationship ◽  
Affect Gene Expression

Understanding the relationship between transposable elements (TEs) and their associated genes in the host genome is a key point to explore their potential role in genome evolution. Transposable elements can regulate and affect gene expression not only because of their mobility within the genome but also because of its transcriptional activity. Gene expression can be suppressed, decreased or increased and cellular signalling pathways can be activated through the act of the nearby TE expression itself or subsequent TE replication intermediates. We implemented a pipeline which is capable to reveal the relationship between TEs and adjacent gene distribution in the host genome. Our tool is freely available here : https://github.com/marieBvr/TEs_genes_relationship_pipeline

scholarly journals Impact of polymorphic transposable elements on transcription in lymphoblastoid cell lines from public data

2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Giovanni Spirito ◽  
Damiano Mangoni ◽  
Remo Sanges ◽  
Stefano Gustincich
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Cell Lines ◽  
Dna Sequences ◽  
Host Genome ◽  
Human Populations ◽  
Lymphoblastoid Cell Lines ◽  
Structural Variants ◽  
Public Data ◽  
The Impact

Abstract Background Transposable elements (TEs) are DNA sequences able to mobilize themselves and to increase their copy-number in the host genome. In the past, they have been considered mainly selfish DNA without evident functions. Nevertheless, currently they are believed to have been extensively involved in the evolution of primate genomes, especially from a regulatory perspective. Due to their recent activity they are also one of the primary sources of structural variants (SVs) in the human genome. By taking advantage of sequencing technologies and bioinformatics tools, recent surveys uncovered specific TE structural variants (TEVs) that gave rise to polymorphisms in human populations. When combined with RNA-seq data this information provides the opportunity to study the potential impact of TEs on gene expression in human. Results In this work, we assessed the effects of the presence of specific TEs in cis on the expression of flanking genes by producing associations between polymorphic TEs and flanking gene expression levels in human lymphoblastoid cell lines. By using public data from the 1000 Genome Project and the Geuvadis consortium, we exploited an expression quantitative trait loci (eQTL) approach integrated with additional bioinformatics data mining analyses. We uncovered human loci enriched for common, less common and rare TEVs and identified 323 significant TEV-cis-eQTL associations. SINE-R/VNTR/Alus (SVAs) resulted the TE class with the strongest effects on gene expression. We also unveiled differential functional enrichments on genes associated to TEVs, genes associated to TEV-cis-eQTLs and genes associated to the genomic regions mostly enriched in TEV-cis-eQTLs highlighting, at multiple levels, the impact of TEVs on the host genome. Finally, we also identified polymorphic TEs putatively embedded in transcriptional units, proposing a novel mechanism in which TEVs may mediate individual-specific traits. Conclusion We contributed to unveiling the effect of polymorphic TEs on transcription in lymphoblastoid cell lines.

Transposable elements and host genome evolution

2000 ◽  
Vol 15 (3) ◽  
pp. 95-99 ◽  
Author(s):  
Margaret G Kidwell ◽  
Damon R Lisch
Keyword(s):  
Transposable Elements ◽  
Genome Evolution ◽  
Host Genome

scholarly journals Transposon Reactivation in the Germline May Be Useful for Both Transposons and Their Host Genomes

Cells ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 1172 ◽  
Author(s):  
Stéphanie Maupetit-Mehouas ◽  
Chantal Vaury
Keyword(s):  
Transposable Elements ◽  
Host Genome ◽  
Next Generation ◽  
Mutualistic Interactions ◽  
Transient Relaxation ◽  
The Relationship ◽  
Eukaryotic Genomes ◽  
Developmental Windows

Transposable elements (TEs) are long-term residents of eukaryotic genomes that make up a large portion of these genomes. They can be considered as perfectly fine members of genomes replicating with resident genes and being transmitted vertically to the next generation. However, unlike regular genes, TEs have the ability to send new copies to new sites. As such, they have been considered as parasitic members ensuring their own replication. In another view, TEs may also be considered as symbiotic sequences providing shared benefits after mutualistic interactions with their host genome. In this review, we recall the relationship between TEs and their host genome and discuss why transient relaxation of TE silencing within specific developmental windows may be useful for both.

scholarly journals Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Radka Symonová ◽  
Alexander Suh
Keyword(s):  
Transposable Elements ◽  
Genome Size ◽  
Fish Species ◽  
Teleost Fish ◽  
Class Ii ◽  
Nucleotide Composition ◽  
Host Genome ◽  
Fish Genome ◽  
Dna Transposons ◽  
Consensus Sequences

Abstract Background Teleost fish genome size has been repeatedly demonstrated to positively correlate with the proportion of transposable elements (TEs). This finding might have far-reaching implications for our understanding of the evolution of nucleotide composition across vertebrates. Genomes of fish and amphibians are GC homogenous, with non-teleost gars being the single exception identified to date, whereas birds and mammals are AT/GC heterogeneous. The exact reason for this phenomenon remains controversial. Since TEs make up significant proportions of genomes and can quickly accumulate across genomes, they can potentially influence the host genome with their own GC content (GC%). However, the GC% of fish TEs has so far been neglected. Results The genomic proportion of TEs indeed correlates with genome size, although not as linearly as previously shown with fewer genomes, and GC% negatively correlates with genome size in the 33 fish genome assemblies analysed here (excluding salmonids). GC% of fish TE consensus sequences positively correlates with the corresponding genomic GC% in 29 species tested. Likewise, the GC contents of the entire repetitive vs. non-repetitive genomic fractions correlate positively in 54 fish species in Ensembl. However, among these fish species, there is also a wide variation in GC% between the main groups of TEs. Class II DNA transposons, predominant TEs in fish genomes, are significantly GC-poorer than Class I retrotransposons. The AT/GC heterogeneous gar genome contains fewer Class II TEs, a situation similar to fugu with its extremely compact and also GC-enriched but AT/GC homogenous genome. Conclusion Our results reveal a previously overlooked correlation between GC% of fish genomes and their TEs. This applies to both TE consensus sequences as well as the entire repetitive genomic fraction. On the other hand, there is a wide variation in GC% across fish TE groups. These results raise the question whether GC% of TEs evolves independently of GC% of the host genome or whether it is driven by TE localization in the host genome. Answering these questions will help to understand how genomic GC% is shaped over time. Long-term accumulation of GC-poor(er) Class II DNA transposons might indeed have influenced AT/GC homogenization of fish genomes and requires further investigation.

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