The impact of transposable elements on eukaryotic genomes: From genome size increase to genetic adaptation to stressful environments

Chénais, Benoı̂t; Caruso, Aurore; Hiard, Sophie; Casse, Nathalie

doi:10.1016/j.gene.2012.07.042

Cited by 280 publications

(266 citation statements)

References 155 publications

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“…As predicted by many workers on transposons and retrotransposons, a very high proportion of cis-regulatory changes have been found to derive from mobile elements [225]. As more vertebrate genomes sequences become available, the size of the mobile element-derived regulatory site repertoire has grown significantly.…”

Section: Evolution Of Regulatory Circuits By Mobile Elementsmentioning

confidence: 90%

How life changes itself: The Read–Write (RW) genome

Shapiro

2013

Physics of Life Reviews

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The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.

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Section: Evolution Of Regulatory Circuits By Mobile Elementsmentioning

confidence: 90%

How life changes itself: The Read–Write (RW) genome

Shapiro

2013

Physics of Life Reviews

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“…In several cases, they even appear to have provided ultimately a selective advantage. The effects of endogenous TEs encompass genome remodelling owing to DNA recombination and unequal crossover, changes in gene expression through transcription regulation and splicing variations, and even contribution to protein-coding sequences [15][16][17][18]. In the context of the latter, the present review will focus on the ERV class of TEs and address the process of endogenization of retroviruses, the co-optation of protein-coding genes from ERVs in diverse mammalian species and more specifically the diversion of retroviral gene functions to perform specialized tasks in the placenta.…”

Section: Introductionmentioning

confidence: 99%

Paleovirology of ‘ syncytins ’, retroviral env genes exapted for a role in placentation

Lavialle

Cornelis

Dupressoír

et al. 2013

Phil. Trans. R. Soc. B

342

307

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One contribution of 13 to a Theme Issue 'Paleovirology: insights from the genomic fossil record'. The development of the emerging field of 'paleovirology' allows biologists to reconstruct the evolutionary history of fossil endogenous retroviral sequences integrated within the genome of living organisms and has led to the retrieval of conserved, ancient retroviral genes 'exapted' by ancestral hosts to fulfil essential physiological roles, syncytin genes being undoubtedly among the most remarkable examples of such a phenomenon. Indeed, syncytins are 'new' genes encoding proteins derived from the envelope protein of endogenous retroviral elements that have been captured and domesticated on multiple occasions and independently in diverse mammalian species, through a process of convergent evolution. Knockout of syncytin genes in mice provided evidence for their absolute requirement for placenta development and embryo survival, via formation by cell-cell fusion of syncytial cell layers at the fetal-maternal interface. These genes of exogenous origin, acquired 'by chance' and yet still 'necessary' to carry out a basic function in placental mammals, may have been pivotal in the emergence of mammalian ancestors with a placenta from egg-laying animals via the capture of a founding retroviral env gene, subsequently replaced in the diverse mammalian lineages by new env-derived syncytin genes, each providing its host with a positive selective advantage.

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“…These mobile elements are ubiquitous in almost all organisms from different kingdoms and with different proportions depending on species (Chenais et al, 2012). TEs are not simply selfi sh DNA but rather important elements that contribute signifi cantly to genome evolution as well as its shape architecture (Feschotte & Pritham, 2007;Bire & Rouleux-Bonnin, 2012;Hirsch & Springer, 2017).…”

Section: Introductionmentioning

confidence: 99%