Regulatory activities of transposable elements: from conflicts to benefits

Chuong, Edward B.; Elde, Nels C.; Feschotte, Cédric

doi:10.1038/nrg.2016.139

Cited by 1,133 publications

(1,279 citation statements)

References 187 publications

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“…While very few LINE-1s are actively mobile, mobility can result in human disease and is a significant source of genome variation (45). LINE-1 retrotransposition is initiated by a DNA nick targeted to a consensus 5′-TTTT/A-3′ site, and the 3′ end of the nick then anneals to the polyA at the 3′ end of the LINE-1 mRNA which serves as a template for DNA synthesis [reviewed in (46)].…”

Section: Discussionmentioning

confidence: 99%

Initiation of homologous recombination at DNA nicks

Maizels

Davis

2018

Nucleic Acids Research

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Discontinuities in only a single strand of the DNA duplex occur frequently, as a result of DNA damage or as intermediates in essential nuclear processes and DNA repair. Nicks are the simplest of these lesions: they carry clean ends bearing 3′-hydroxyl groups that can undergo ligation or prime new DNA synthesis. In contrast, single-strand breaks also interrupt only one DNA strand, but they carry damaged ends that require clean-up before subsequent steps in repair. Despite their apparent simplicity, nicks can have significant consequences for genome stability. The availability of enzymes that can introduce a nick almost anywhere in a large genome now makes it possible to systematically analyze repair of nicks. Recent experiments demonstrate that nicks can initiate recombination via pathways distinct from those active at double-strand breaks (DSBs). Recombination at targeted DNA nicks can be very efficient, and because nicks are intrinsically less mutagenic than DSBs, nick-initiated gene correction is useful for genome engineering and gene therapy. This review revisits some physiological examples of recombination at nicks, and outlines experiments that have demonstrated that nicks initiate homology-directed repair by distinctive pathways, emphasizing research that has contributed to our current mechanistic understanding of recombination at nicks in mammalian cells.

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Section: Discussionmentioning

confidence: 99%

Initiation of homologous recombination at DNA nicks

Maizels

Davis

2018

Nucleic Acids Research

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“…Despite this intricate mechanism designed for the purpose of tackling TE expansion, repeats have been consistently overcoming barriers to their transposition and spreading throughout genomes and populations (Haig 2016). This host-parasite coevolution is reminiscent of an arms race (Jacobs et al 2014); it is also conceivable, however, that repeat expansion is successful partly due to the co-option of TEs within host regulatory networks (Chuong et al 2016(Chuong et al , 2017Shapiro 2016). Perhaps there is simply insufficient evolutionary pressure to completely suppress TE expansion, or host organisms might have managed to strike the delicate balance between overspending host energy on absolute restriction of TEs from the genome and underspending such that TEs become detrimental to the host's existence.…”

Section: Discussionmentioning

confidence: 99%

Two modes of targeting transposable elements by piRNA pathway in human testis

Gainetdinov

Skvortsova

Kondratieva

et al. 2017

RNA

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PIWI proteins and their partner small RNAs, termed piRNAs, are known to control transposable elements (TEs) in the germline. Here, we provide evidence that in humans this control is exerted in two different modes. On the one hand, production of piRNAs specifically targeting evolutionarily youngest TEs (L1HS, L1PA2-L1PA6, LTR12C, SVA) is present both at prenatal and postnatal stages of spermatogenesis and is performed without involvement of piRNA clusters. On the other hand, at postnatal stages, piRNAs deriving from pachytene clusters target "older" TEs and thus complement cluster-independent piRNA production to achieve relevant targeting of virtually all TEs expressed in postnatal testis. We also find that converging transcription of antisense-oriented genes contributes to the origin of genic postnatal prepachytene clusters. Finally, while a fraction of pachytene piRNAs was previously shown to arise from long intergenic noncoding RNAs (lincRNAs, i.e., pachytene piRNA cluster primary transcripts), we ascertain that these are a specific set of lincRNAs that both possess distinguishing epigenetic features and are expressed exclusively in testis.

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“…Transposable elements (TEs) can drive evolution by controlling gene expression and through mutagenic transposition [1,2]. TEs were first described in maize by Barbara McClintock who named them controlling elements, because of their capacity to regulate gene expression [3].…”

Section: Introductionmentioning

confidence: 99%

Genetic and epigenetic variation of transposable elements in Arabidopsis

Underwood

Henderson

Martienssen

2017

Current Opinion in Plant Biology

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Transposable elements are mobile genetic elements that are prevalent in plant genomes and are silenced by epigenetic modification. Different epigenetic modification pathways play distinct roles in the control of transposable element transcription, replication and recombination. The Arabidopsis genome contains families of all of the major transposable element classes, which are differentially enriched in particular genomic regions. Whole genome sequencing and DNA methylation profiling of hundreds of natural Arabidopsis accessions has revealed that transposable elements exhibit significant intraspecific genetic and epigenetic variation, and that genetic variation often underlies epigenetic variation. Together, epigenetic modification and the forces of selection define the scope within which transposable elements can contribute to, and control, genome evolution.

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Regulatory activities of transposable elements: from conflicts to benefits

Cited by 1,133 publications

References 187 publications

Initiation of homologous recombination at DNA nicks

Initiation of homologous recombination at DNA nicks

Two modes of targeting transposable elements by piRNA pathway in human testis

Genetic and epigenetic variation of transposable elements in Arabidopsis

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