Origin and evolution of SINEs in eukaryotic genomes

Крамеров, Д. А.; Vassetzky, Nikita S.

doi:10.1038/hdy.2011.43

Cited by 149 publications

(155 citation statements)

References 77 publications

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“…Thus, modularity, or the clustering of epistatic interactions, is considered to be a determining feature of virus-like evolutionary systems and has also been proposed to be important for transposable element evolution (38). Recent work has shown that bacterial mobile DNA elements can acquire discrete functional modules (39), and numerous examples of the acquisition of novel modules by retrotransposons are also known (14,40,41). The exchange of modules between mobile elements produces structural variants of transposons with a potential evolutionary advantage and may yield novel transposon families (38,39).…”

Section: Rnh Domain Of Ta11 L1-like Retrotransposons Is Homologous Tomentioning

confidence: 99%

Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution

Smyshlyaev

Voigt

Блинов

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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Although a variety of non-LTR retrotransposons of the L1 superfamily have been found in plant genomes over recent decades, their diversity, distribution, and evolution have yet to be analyzed in depth. Here, we perform comprehensive comparative and evolutionary analyses of L1 retrotransposons from 29 genomes of land plants covering a wide range of taxa. We identify numerous L1 elements in these genomes and detect a striking diversity of their domain composition. We show that all known land plant L1 retrotransposons can be grouped into five major families based on their phylogenetic relationships and domain composition. Moreover, we trace the putative evolution timeline that created the current variants and reveal that evolutionary events included losses and acquisitions of diverse putative RNA-binding domains and the acquisition of an Archaea-like ribonuclease H (RNH) domain. We also show that the latter RNH domain is autonomously active in vitro and speculate that retrotransposons may play a role in the horizontal transfer of RNH between plants, Archaea, and bacteria. The acquisition of an Archaea-like RNH domain by plant L1 retrotransposons negates the hypothesis that RNH domains in non-LTR retrotransposons have a single origin and provides evidence that acquisition happened at least twice. Together, our data indicate that the evolution of the investigated retrotransposons can be mainly characterized by repeated events of domain rearrangements and identify modular evolution as a major trend in the evolution of plant L1 retrotransposons. E ver since the discovery of the first transposon by Barbara McClintock in 1948 in maize, plants have provided a prime model system to study transposition. Both DNA transposons and retrotransposons are abundant in plants (1) and play a major role in driving genetic diversity and evolution of these organisms. Interestingly, non-LTR retrotransposons, the class of retrotransposons that is most represented in mammals, are found less abundantly in plants (2-5). More recently, however, a variety of non-LTR retrotransposons has been discovered in plants, and they were classified to three non-LTR retrotransposon superfamilies: retrotransposable element (RTE), Dualen, and L1 (6-8).The L1 superfamily is perhaps the best-studied plant non-LTR retrotransposon group, members of which have been identified in most plants. Among other species, they occur in corn [Zea mays (Cin4)], thale cress [Arabidopsis thaliana (Ta11-1)], and the alga Chlorella vulgaris (Zepp) (9-11).In general, plant L1 retrotransposons carry two ORFs. The protein encoded by ORF1 (ORF1p) usually contains an RNA recognition motif (RRM) (12)(13)(14). Similarly, human L1 ORF1p, which presumably acts as an RNA chaperone (15), also contains an RRM that was shown to bind single-stranded nucleic acids in cooperation with the ORF1p C-terminal domain (14). The second ORF (ORF2) of plant L1 retrotransposons encodes a polyprotein (ORF2p) that exhibits apurinic/apyrimidinic endonuclease (APE) and reverse transcriptase (RT) activities....

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Section: Rnh Domain Of Ta11 L1-like Retrotransposons Is Homologous Tomentioning

confidence: 99%

Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution

Smyshlyaev

Voigt

Блинов

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

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“…They present common sequence features such as a 5 0 -terminal head deriving from a tRNAs, 7SL RNA or 5S rRNA, an internal RNA Polymerase III promoter, a central body and a 3 0 -terminal tail consisting of simple repeats. 38 The mouse genome contains 2 major families of SINEs named B1 and B2. 39 SINE B1 are derived from 7SL RNAs.…”

Section: Biological Function Of As Uchl1mentioning

confidence: 99%

SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation

Zucchelli

Cotella

Takahashi³

et al. 2015

RNA Biology

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“…The explosive nature of multiplication of SINEs and the fact that they all are located predominantly in intergenic areas, pseudogenes, and noncoding regions of genes suggest that their bursts of amplification were genetic catastrophes associated with massive loss of those genomes in which SINEs inserted within essential genes (2, 9, 10) and presumably contributed to the diversity of mammalian species. In fact, integration of new SINE copies into coding or regulatory sequences has the potential to disturb gene expression (11).…”

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confidence: 99%

p53 cooperates with DNA methylation and a suicidal interferon response to maintain epigenetic silencing of repeats and noncoding RNAs

Leonova

Brodsky

Lipchick

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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Large parts of mammalian genomes are transcriptionally inactive and enriched with various classes of interspersed and tandem repeats. Here we show that the tumor suppressor protein p53 cooperates with DNA methylation to maintain silencing of a large portion of the mouse genome. Massive transcription of major classes of short, interspersed nuclear elements (SINEs) B1 and B2, both strands of near-centromeric satellite DNAs consisting of tandem repeats, and multiple species of noncoding RNAs was observed in p53-deficient but not in p53 wild-type mouse fibroblasts treated with the DNA demethylating agent 5-aza-2'-deoxycytidine. The abundance of these transcripts exceeded the level of β-actin mRNA by more than 150-fold. Accumulation of these transcripts, which are capable of forming double-stranded RNA (dsRNA), was accompanied by a strong, endogenous, apoptosis-inducing type I IFN response. This phenomenon, which we named "TRAIN" (for "transcription of repeats activates interferon"), was observed in spontaneous tumors in two models of cancer-prone mice, presumably reflecting naturally occurring DNA hypomethylation and p53 inactivation in cancer. These observations suggest that p53 and IFN cooperate to prevent accumulation of cells with activated repeats and provide a plausible explanation for the deregulation of IFN function frequently seen in tumors. Overall, this work reveals roles for p53 and IFN that are key for genetic stability and therefore relevant to both tumorigenesis and the evolution of species.interferon alpha-beta receptor | RNA sequencing | epigenetic repression | microarray hybridization

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Origin and evolution of SINEs in eukaryotic genomes

Cited by 149 publications

References 77 publications

Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution

Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution

SINEUPs: A new class of natural and synthetic antisense long non-coding RNAs that activate translation

p53 cooperates with DNA methylation and a suicidal interferon response to maintain epigenetic silencing of repeats and noncoding RNAs

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