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 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.

scholarly journals The Genomic Ecosystem of Transposable Elements in Maize

2019 ◽  
Author(s):  
Michelle C. Stitzer ◽  
Sarah N. Anderson ◽  
Nathan M. Springer ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Flowering Plant ◽  
Genome Wide ◽  
Family Level ◽  
Genomic Environment ◽  
Single Category ◽  
The Impact

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017

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 The impact of transposable elements on mammalian development

Development ◽  
2016 ◽  
Vol 143 (22) ◽  
pp. 4101-4114 ◽  
Author(s):  
Jose L. Garcia-Perez ◽  
Thomas J. Widmann ◽  
Ian R. Adams
Keyword(s):  
Transposable Elements ◽  
Mammalian Development ◽  
The Impact

scholarly journals The impact of transposable elements on tomato diversity

2020 ◽  
Author(s):  
Marisol Domínguez ◽  
Elise Dugas ◽  
Médine Benchouaia ◽  
Basile Leduque ◽  
José Jimenez-Gomez ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Agronomic Traits ◽  
Association Studies ◽  
Low Frequency ◽  
Genome Wide Association Studies ◽  
Environmental Response ◽  
Whole Genome Resequencing ◽  
Wild Accessions ◽  
Genetic Pool ◽  
The Impact

ABSTRACTTomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leveraged whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identified 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and disproportionately located within or adjacent to genes involved in environmental response. In addition, we show that genic TE insertions tend to have strong transcriptional effects and can notably lead to the generation of multiple transcript isoforms. We also uncovered through genome-wide association studies (GWAS) ~180 TIPs associated with extreme variations in major agronomic traits or secondary metabolites. Importantly, these TIPs tend to affect loci that are distinct from those tagged by SNPs. Collectively, our findings suggest a unique and important role for TE mobilization in tomato diversification, with important implications for future breeding.

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 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

scholarly journals Transposable elements in the genome of the lichen-forming fungus Umbilicaria pustulata, and their distribution in different climate zones along elevation

2021 ◽  
Author(s):  
Francesco Dal Grande ◽  
Veronique Jamilloux ◽  
Nathalie Choisne ◽  
Anjuli Calchera ◽  
Malte Petersen ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Phenotypic Diversity ◽  
Elevation Gradients ◽  
Climate Niche ◽  
Fungal Evolution ◽  
Specific Distribution ◽  
Fungal Adaptation ◽  
The Impact ◽  
Insertion Frequency

Background: Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Accumulating evidence suggests that TEs may not be randomly distributed in the genome. Drift and natural selection are important forces shaping TE distribution and accumulation, acting directly on the TE element or indirectly on the host species. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold-temperate. We trace the occurrence of the newly identified TEs in populations along three replicated elevation gradients using a Pool-Seq approach, to identify TE insertions of potential adaptive significance. Results: We found that TEs cover 21.26 % of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. Out of a total of 182 TE copies we identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. Conclusions: This pioneering study into the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution. Particularly, it may serve as a foundation for assessing the impact of TE dynamics on fungal adaptation to the abiotic environment, and the impact of TE activity on the evolution and maintenance of a symbiotic lifestyle.

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