Host–transposon interactions: conflict, cooperation, and cooption

Cosby, Rachel; Chang, Ni-Chen; Feschotte, Cédric

doi:10.1101/gad.327312.119

Cited by 237 publications

(239 citation statements)

References 224 publications

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“…Nowadays, there is a considerable amount of evidence against the junk DNA hypothesis. With few known exceptions, eukaryotic genomes are densely wrapped with TEs [4] that contribute to their adaptation and evolution [5].…”

Section: Introductionmentioning

confidence: 99%

“What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Moschetti

Palazzo

Lorusso

et al. 2020

Biology

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Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes. Besides their most intuitive role as insertional mutagens, TEs can modify the transcriptional pattern of host genes by juxtaposing new cis-regulatory sequences. A key element of TE biology is that they carry transcriptional control elements that fine-tune the transcription of their own genes, but that can also perturb the transcriptional activity of neighboring host genes. From this perspective, the transposition-mediated modulation of gene expression is an important issue for the short-term adaptation of physiological functions to the environmental changes, and for long-term evolutionary changes. Here, we review the current literature concerning the regulatory and structural elements operating in cis provided by TEs in Drosophila. Furthermore, we highlight that, besides their influence on both TEs and host genes expression, they can affect the chromatin structure and epigenetic status as well as both the chromosome's structure and stability. It emerges that Drosophila is a good model organism to study the effect of TE-linked regulatory sequences, and it could help future studies on TE-host interactions in any complex eukaryotic genome.

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Section: Introductionmentioning

confidence: 99%

“What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Moschetti

Palazzo

Lorusso

et al. 2020

Biology

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“…There are examples of both models in the literature, however it is unclear which model is the most common in nature. In a recent review, Cosby et al examined in great details the literature on this topic and they proposed that the arms race model may not be the most prevalent one [53], but that instead, strategies that would allow TEs to persist and multiply without jeopardizing the fitness of the host have been overlooked. In this context the stability of sub-optimal base composition may provide an example of self-regulation of nLTR-RTs to maintain a harmonious relationship with their hosts.…”

Section: Resultsmentioning

confidence: 99%

Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons

Ruggiero

Boissinot

2020

Mobile DNA

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Background: Non-LTR retrotransposons often exhibit base composition that is markedly different from the nucleotide content of their host's gene. For instance, the mammalian L1 element is AT-rich with a strong A bias on the positive strand, which results in a reduced transcription. It is plausible that the A-richness of mammalian L1 is a self-regulatory mechanism reflecting a trade-off between transposition efficiency and the deleterious effect of L1 on its host. We examined if the A-richness of L1 is a general feature of non-LTR retrotransposons or if different clades of elements have evolved different nucleotide content. We also investigated if elements belonging to the same clade evolved towards different base composition in different genomes or if elements from different clades evolved towards similar base composition in the same genome. Results: We found that non-LTR retrotransposons differ in base composition among clades within the same host but also that elements belonging to the same clade differ in base composition among hosts. We showed that nucleotide content remains constant within the same host over extended period of evolutionary time, despite mutational patterns that should drive nucleotide content away from the observed base composition. Conclusions:Our results suggest that base composition is evolving under selection and may be reflective of the long-term co-evolution between non-LTR retrotransposons and their host. Finally, the coexistence of elements with drastically different base composition suggests that these elements may be using different strategies to persist and multiply in the genome of their host.

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“…In some cases, these pathways may be part of evolving “arms‐races” between TEs and their “hosts”, such as the piRNA pathway and KRAB‐ZNF transcription factors (reviewed in ref. [104]). In the study of such pathways, or in cases of recent horizontal transfers of TEs into a new species, it may be helpful to continue to assume the “TE vs host” perspective.…”

Section: Moving Beyond the “Tes Versus Host” Way Of Thinkingmentioning

confidence: 99%

What Doesn't Kill You Makes You Stronger: Transposons as Dual Players in Chromatin Regulation and Genomic Variation

2020

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Transposable elements (TEs) are sequences currently or historically mobile, and are present across all eukaryotic genomes. A growing interest in understanding the regulation and function of TEs has revealed seemingly dichotomous roles for these elements in evolution, development, and disease. On the one hand, many gene regulatory networks owe their organization to the spread of cis‐elements and DNA binding sites through TE mobilization during evolution. On the other hand, the uncontrolled activity of transposons can generate mutations and contribute to disease, including cancer, while their increased expression may also trigger immune pathways that result in inflammation or senescence. Interestingly, TEs have recently been found to have novel essential functions during mammalian development. Here, the function and regulation of TEs are discussed, with a focus on LINE1 in mammals. It is proposed that LINE1 is a beneficial endogenous dual regulator of gene expression and genomic diversity during mammalian development, and that both of these functions may be detrimental if deregulated in disease contexts.

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Host–transposon interactions: conflict, cooperation, and cooption

Cited by 237 publications

References 224 publications

“What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

“What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons

What Doesn't Kill You Makes You Stronger: Transposons as Dual Players in Chromatin Regulation and Genomic Variation

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