Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly

Enriquez-Gasca, Rocio; Gould, Poppy A.; Rowe, Helen M.

doi:10.3390/v12101089

Cited by 30 publications

(23 citation statements)

References 155 publications

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“…To assess potential presence of transposable elements (TE) around eHBVs of interest ( Fig 3a ) we extracted the 5kb sequences flanking the eHBV coordinates from the respective genome assemblies, adjusting for reverse complementarity. These sequences were analysed for TE presence using HMMER [28] against the Dfam HMM profile library [29].…”

Section: Methodsmentioning

confidence: 99%

Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes

Lytras

Arriagada

Gifford

2020

Preprint

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Hepadnaviruses (family Hepadnaviviridae) are reverse-transcribing animal viruses that infect vertebrates. Vertebrate genomes contain DNA sequences derived from ancient hepadnaviruses, and these endogenous hepatitis B viruses (eHBVs) reveal aspects of the long-term coevolutionary relationship between hepadnaviruses and their vertebrate hosts. Here, we use a novel, data-oriented approach to recover and analyse the complete repertoire of eHBV elements in published animal genomes. We show that germline incorporation of hepadnaviruses is exclusive to a single vertebrate group (Sauria) and that the eHBVs contained in saurian genomes represent a far greater diversity of hepadnaviruses than previously recognised. Through in-depth characterisation of eHBV elements we establish the existence of four distinct subgroups within the genus Avihepadnavirus and trace their evolution through the Cenozoic Era. Furthermore, we provide a completely new perspective on hepadnavirus evolution by showing that the metahepadnaviruses (genus Metahepadnavirus) originated >300 million years ago in the Paleozoic Era, and has historically infected a broad range of vertebrates. We also show that eHBVs have been intra-genomically amplified in some saurian lineages, and that eHBVs located at approximately equivalent genomic loci have been acquired in entirely distinct germline integration events. These findings indicate that selective forces have favoured the accumulation of hepadnaviral sequences at specific loci in the saurian germline. Our investigation provides a range of new insights into the long-term evolutionary history of reverse-transcribing DNA viruses and demonstrates that germline incorporation of hepadnaviruses has played an important role in shaping the evolution of saurian genomes.

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Section: Methodsmentioning

confidence: 99%

Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes

Lytras

Arriagada

Gifford

2020

Preprint

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“…TEs have been viewed as genetic parasites that are especially dangerous during embryogenesis when transposition duplications are capable of entering the germline. However, TEs can act as a source of evolutionary innovation, by duplicating TF binding sites, rewiring gene regulatory networks, altering splicing patterns, and many other effects on the genome and cell ( Bourque et al, 2018 ), both beneficial and deleterious ( Enriquez-Gasca et al, 2020 ). During early embryonic development, the genome is reprogrammed back to a naïve state.…”

Section: Transposable Elements the Early Embryo And Naïve And Primementioning

confidence: 99%

Chromatin and Epigenetic Rearrangements in Embryonic Stem Cell Fate Transitions

Sun

et al. 2021

Front. Cell Dev. Biol.

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A major event in embryonic development is the rearrangement of epigenetic information as the somatic genome is reprogrammed for a new round of organismal development. Epigenetic data are held in chemical modifications on DNA and histones, and there are dramatic and dynamic changes in these marks during embryogenesis. However, the mechanisms behind this intricate process and how it is regulating and responding to embryonic development remain unclear. As embryos develop from totipotency to pluripotency, they pass through several distinct stages that can be captured permanently or transiently in vitro. Pluripotent naïve cells resemble the early epiblast, primed cells resemble the late epiblast, and blastomere-like cells have been isolated, although fully totipotent cells remain elusive. Experiments using these in vitro model systems have led to insights into chromatin changes in embryonic development, which has informed exploration of pre-implantation embryos. Intriguingly, human and mouse cells rely on different signaling and epigenetic pathways, and it remains a mystery why this variation exists. In this review, we will summarize the chromatin rearrangements in early embryonic development, drawing from genomic data from in vitro cell lines, and human and mouse embryos.

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“…In contrast, class I elements, or retrotransposons, replicate via an RNA intermediate, in a “copy and paste”-like fashion by reverse transcribing their RNA directly into the host DNA at a new genomic location. Previously disregarded as just being junk DNA, it is now evident that transposable elements played, and still play, an important role in shaping structure and function of our genome [ 4 , 5 ]. However, depending on the site of integration, retrotransposition events can also destabilize genome integrity and cause disease [ 6 , 7 , 8 ].…”

Section: Introductionmentioning

confidence: 99%

Recognize Yourself—Innate Sensing of Non-LTR Retrotransposons

Lagisquet

Zuber

Gramberg

2021

Viruses

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Although mobile genetic elements, or transposons, have played an important role in genome evolution, excess activity of mobile elements can have detrimental consequences. Already, the enhanced expression of transposons-derived nucleic acids can trigger autoimmune reactions that may result in severe autoinflammatory disorders. Thus, cells contain several layers of protective measures to restrict transposons and to sense the enhanced activity of these “intragenomic pathogens”. This review focuses on our current understanding of immunogenic patterns derived from the most active elements in humans, the retrotransposons long interspersed element (LINE)-1 and Alu. We describe the role of known pattern recognition receptors in nucleic acid sensing of LINE-1 and Alu and the possible consequences for autoimmune diseases.

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Host Gene Regulation by Transposable Elements: The New, the Old and the Ugly

Cited by 30 publications

References 155 publications

Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes

Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes

Chromatin and Epigenetic Rearrangements in Embryonic Stem Cell Fate Transitions

Recognize Yourself—Innate Sensing of Non-LTR Retrotransposons

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