The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation

Nicolau, Mélody; Picault, Nathalie; Moissiard, Guillaume

doi:10.3390/cells10112952

Cited by 18 publications

(13 citation statements)

References 275 publications

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“…The insertion of some short DNA transposons could influence the activities of nearby genes. We found the majority of retrotransposons contribute to ACRs in rice were LTR_Copia , it was reported some solo-LTRs tend to keep TF-specific CREs [ 70 ], indicating that functions of these LTRs in the regulation of gene expression can be mediated through distal interactions between CREs and TFs or trans -acting factors. Variation of TE-derived CREs could reflect differentiation of TE activities among different organisms during genome evolution.…”

Section: Discussionmentioning

confidence: 92%

Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (Oryza Sativa)

Zhang

2022

IJMS

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Growing evidence indicates that transposons or transposable elements (TEs)-derived accessible chromatin regions (ACRs) play essential roles in multiple biological processes by interacting with trans-acting factors. However, the function of TE-derived ACRs in the regulation of gene expression in the rice genome has not been well characterized. In this study, we examined the chromatin dynamics in six types of rice tissues and found that ~8% of ACRs were derived from TEs and exhibited distinct levels of accessibility and conservation as compared to those without TEs. TEs exhibited a TE subtype-dependent impact on ACR formation, which can be mediated by changes in the underlying DNA methylation levels. Moreover, we found that tissue-specific TE-derived ACRs might function in the tissue development through the modulation of nearby gene expression. Interestingly, many genes in domestication sweeps were found to overlap with TE-derived ACRs, suggesting their potential functions in the rice domestication. In addition, we found that the expression divergence of 1070 duplicate gene pairs were associated with TE-derived ACRs and had distinct distributions of TEs and ACRs around the transcription start sites (TSSs), which may experience different selection pressures. Thus, our study provides some insights into the biological implications of TE-derived ACRs in the rice genome. Our results imply that these ACRs are likely involved in the regulation of tissue development, rice domestication and functional divergence of duplicated genes.

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Section: Discussionmentioning

confidence: 92%

Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (Oryza Sativa)

Zhang

2022

IJMS

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“…Among several sources of modification in gene expression and novel isoform transcripts, TEs have been considered as fundamental suppliers of transcriptome plasticity, participating in gene networks and incorporating either regulatory sequences or protein domains into gene transcripts. The identification of chimeric transcripts is an important step to understanding transcriptome plasticity, since they may be triggered by ectopic conditions, such as cancer, oxidative stress, and heat shock (27, 90, 91), which may lead to both detrimental and advantageous outcomes (92). Therefore, uncovering the extent of chimeric transcripts between individual/cell/strain transcriptomes is a crucial first step to investigate potential exaptation/domestication events, or gene disruption and loss of function.…”

Section: Discussionmentioning

confidence: 99%

ChimeraTE: A pipeline to detect chimeric transcripts derived from genes and transposable elements

Oliveira

Fablet

Larue

et al. 2022

Preprint

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Transposable elements (TEs) are structural variants considered an important source of genetic diversity, which may arise in the transcriptome when TEs are transcribed in the same RNA molecule as genes, producing what we hereafter call chimeric transcripts. The presence of chimeric transcripts has been associated with adaptive traits in several species, but their identification remains hindered due to the lack of tools to detect them on a transcriptome-wide scale. Previous bioinformatics tools were developed to identify chimeric transcripts derived from TEs present in a reference genome. Nevertheless, different individuals/cells/strains might harbor different TE insertions generating such chimeric transcripts. Therefore, we have developed ChimeraTE, a pipeline that uses paired-end RNA-seq reads to identify chimeric transcripts with or without a reference genome, in a transcriptome-wide manner. ChimeraTE has two Modes: Mode 1 is a genome-guided approach that employs the canonical method of genome alignment, whereas Mode 2 identifies chimeric transcripts without a reference genome, being able to predict chimeras derived from fixed or polymorphic TEs. We have used both Modes with Illumina RNA-seq reads from ovarian tissues of Drosophila melanogaster wild-type strains, and found that ~3% of all genes generate chimeric transcripts. Approximately ~9% of all detected chimeras were absent from the D. melanogaster′s reference genome, corresponding to polymorphic insertions in the wild-type strains. ChimeraTE is the first pipeline with the ability to automatically uncover chimeric transcripts without a reference genome.

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“…TEs are an evolutionary force that contributes to the genetic diversity of organisms, especially when they are recruited to the host genome to become new genes; this domestication of TEs is a source of genetic innovation [ 10 , 11 ]. However, transposition activity can also contribute to the emergence of human diseases and the insertion of a TE into the genome has several direct or indirect consequences on the structure of the genome and the control of gene expression.…”

Section: Transposable Elements Of the Human Genomementioning

confidence: 99%

Transposable Elements and Human Diseases: Mechanisms and Implication in the Response to Environmental Pollutants

Chénais

2022

IJMS

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Transposable elements (TEs) are recognized as major players in genome plasticity and evolution. The high abundance of TEs in the human genome, especially the Alu and Long Interspersed Nuclear Element-1 (LINE-1) repeats, makes them responsible for the molecular origin of several diseases. This involves several molecular mechanisms that are presented in this review: insertional mutation, DNA recombination and chromosomal rearrangements, modification of gene expression, as well as alteration of epigenetic regulations. This literature review also presents some of the more recent and/or more classical examples of human diseases in which TEs are involved. Whether through insertion of LINE-1 or Alu elements that cause chromosomal rearrangements, or through epigenetic modifications, TEs are widely implicated in the origin of human cancers. Many other human diseases can have a molecular origin in TE-mediated chromosomal recombination or alteration of gene structure and/or expression. These diseases are very diverse and include hemoglobinopathies, metabolic and neurological diseases, and common diseases. Moreover, TEs can also have an impact on aging. Finally, the exposure of individuals to stresses and environmental contaminants seems to have a non-negligible impact on the epigenetic derepression and mobility of TEs, which can lead to the development of diseases. Thus, improving our knowledge of TEs may lead to new potential diagnostic markers of diseases.

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The Evolutionary Volte-Face of Transposable Elements: From Harmful Jumping Genes to Major Drivers of Genetic Innovation

Cited by 18 publications

References 275 publications

Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (Oryza Sativa)

Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (Oryza Sativa)

ChimeraTE: A pipeline to detect chimeric transcripts derived from genes and transposable elements

Transposable Elements and Human Diseases: Mechanisms and Implication in the Response to Environmental Pollutants

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