SINEBase: a database and tool for SINE analysis

Vassetzky, Nikita S.; Крамеров, Д. А.

doi:10.1093/nar/gks1263

Cited by 140 publications

(178 citation statements)

References 97 publications

(14 reference statements)

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“…This automatic characterization was performed with the RepeatModeler pipeline (18) and led to the identification of 53,452 TE families assigned to 98 superfamilies (Dataset S2). These exclude 3,417 families whose consensus sequences were found to include genes that may not belong to TEs (SI Materials and Methods), as well as all short interspersed element (SINE) consensus sequences, which might correspond to RNA pseudogenes (19). For each species, the consensus sequences of TE families were used to locate TE copies in genomic contigs.…”

Section: Resultsmentioning

confidence: 99%

Massive horizontal transfer of transposable elements in insects

Peccoud

Loiseau

Cordaux

et al. 2017

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

201

236

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Horizontal transfer (HT) of genetic material is central to the architecture and evolution of prokaryote genomes. Within eukaryotes, the majority of HTs reported so far are transfers of transposable elements (TEs). These reports essentially come from studies focusing on specific lineages or types of TEs. Because of the lack of large-scale survey, the amount and impact of HT of TEs (HTT) in eukaryote evolution, as well as the trends and factors shaping these transfers, are poorly known. Here, we report a comprehensive analysis of HTT in 195 insect genomes, representing 123 genera and 13 of the 28 insect orders. We found that these insects were involved in at least 2,248 HTT events that essentially occurred during the last 10 My. We show that DNA transposons transfer horizontally more often than retrotransposons, and unveil phylogenetic relatedness and geographical proximity as major factors facilitating HTT in insects. Even though our study is restricted to a small fraction of insect biodiversity and to a recent evolutionary timeframe, the TEs we found to be horizontally transferred generated up to 24% (2.08% on average) of all nucleotides of insect genomes. Together, our results establish HTT as a major force shaping insect genome evolution.horizontal transfer | transposable elements | insects | genome evolution | biogeography H orizontal transfer (HT) is the transmission of genetic material between organisms through a mechanism other than reproduction. In prokaryotes, HT is pervasive, its mechanisms are well understood, and it is now viewed as one of the main forces shaping genome architecture and evolution (1, 2). In contrast, the study of HT in eukaryotes is less documented, but has been increasingly investigated. The majority of genes horizontally acquired by eukaryotes come from bacteria, but the extent to which these transfers have contributed to eukaryote evolution is still unclear (3, 4). Gene transfers from eukaryote to eukaryote appear to be largely limited to filamentous organisms, such as oomycetes and fungi (5, 6).In animals and plants, very few cases of such horizontal gene transfers (HGTs) have been reported so far (7,8). In fact, most of the genetic material that is horizontally transferred in animals and plants consists of transposable elements (TEs) (9-11), which are pieces of DNA able to move from a chromosomal locus to another (12). The greater ability of TEs to move between organisms certainly relates to their intrinsic ability to transpose within genomes, which genes cannot do. HT of TEs (HTT) may allow these elements to enter naive genomes, which they invade by making copies of themselves, and then escape before they become fully silenced by anti-TE defenses (13). A growing number of studies have identified such HTT (11,[14][15][16]. However, a common drawback of these studies has been the inclusion of a limited set of TEs (11) or organisms (16), which hampers our understanding of the breadth of HTT, its contribution to genome evolution, and of the factors and barriers shaping these transfe...

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Section: Resultsmentioning

confidence: 99%

Massive horizontal transfer of transposable elements in insects

Peccoud

Loiseau

Cordaux

et al. 2017

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

201

236

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“…For instance, Alu, a well-characterized SINE from primates, exists in >1,500,000 copies in the human genome, covers >11 % of the total genome and played an important role in human population genetics and evolution (Venter et al 2001;Batzer and Deininger 2002). In the Brassicaceae, 16 SINE families have been reported, including 1270 and 2364 members in the B. rapa and B. oleracea genomes, respectively (Vassetzky and Kramerov 2013). SINEs are distributed in various genomic locations of B. rapa and B. oleracea, with 599 (47.1 %) and 1154 (48.8 %) of the members, respectively, present in close association with genic regions with <2 kb of a gene ).…”

Section: Sinesmentioning

confidence: 99%

Miniature Transposable Elements (mTEs): Impacts and Uses in the Brassica Genome

Sampath

Lee

Cheng

et al. 2015

Compendium of Plant Genomes

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Transposable elements occupy large portions of eukaryotic genomes and play an important role in genome evolution. Terminal repeat retrotransposons in miniature (TRIMs), short interspersed elements (SINEs) and miniature inverted-repeat transposable elements (MITEs) are representative forms of so-called miniature transposable elements (mTEs), which are present in very high-copy numbers, stable, widely distributed and in close association with genic regions in plant genomes. These features make mTEs useful for applications such as developing marker systems, functional characterization of associated genes, and elucidating the contribution of TEs to gene evolution. Here, we summarize the characteristics, copy numbers and distribution patterns of five TRIM families, 14 short interspersed elements (SINE) families and 20 MITE families in the Brassica rapa genome. We also show the comparative distribution pattern of paralogous mTE family members in Brassica oleracea and 11 B. rapa accessions. In addition, we describe putative roles for mTEs in the evolution of the triplicated Brassica genome and discuss the utility of mTEs for analysis of genome evolution and for developing practical marker systems.

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“…In mammalian species, a total of ~70 SINE families have been identified (Vassetzky and Kramerov, 2013) (Table 1). Their sequence information can be retrieved at RepBase (http://www.girinst.org/) and SINEBase (http:// sines.eimb.ru/).…”

Section: Transcription and Retrotransposition Of Sinesmentioning

confidence: 99%

“…Examples of mammalian SINEs are human Alu (named for the presence of an AluI cleavage site) (Rubin et al, 1980;Deininger et al, 1981) and mouse B1 and B2 (named for their homology to double-stranded regions in nuclear pre-mRNAs, called as dsRNA-B) (Kramerov et al, 1979). Currently, 175 SINE families have been identified in a wide variety of eukaryotes (Vassetzky and Kramerov, 2013). In mammals, more than a million copies of SINEs are present in a genome, making up > 10% of the total genomic sequence (Lander et al, 2001;Waterston et al, 2002;Lindblad-Toh et al, 2005;Mikkelsen et al, 2005Mikkelsen et al, , 2007Elsik et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs

Ichiyanagi

2013

Genes Genet. Syst.

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Short interspersed elements (SINEs) are a class of retrotransposons, which amplify their copy numbers in their host genomes by retrotransposition. More than a million copies of SINEs are present in a mammalian genome, constituting over 10% of the total genomic sequence. In contrast to the other two classes of retrotransposons, long interspersed elements (LINEs) and long terminal repeat (LTR) elements, SINEs are transcribed by RNA polymerase III. However, like LINEs and LTR elements, the SINE transcription is likely regulated by epigenetic mechanisms such as DNA methylation, at least for human Alu and mouse B1. Whereas SINEs and other transposable elements have long been thought as selfish or junk DNA, recent studies have revealed that they play functional roles at their genomic locations, for example, as distal enhancers, chromatin boundaries and binding sites of many transcription factors. These activities imply that SINE retrotransposition has shaped the regulatory network and chromatin landscape of their hosts. Whereas it is thought that the epigenetic mechanisms were originated as a host defense system against proliferation of parasitic elements, this review discusses a possibility that the same mechanisms are also used to regulate the SINE-derived functions.

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SINEBase: a database and tool for SINE analysis

Cited by 140 publications

References 97 publications

Massive horizontal transfer of transposable elements in insects

Massive horizontal transfer of transposable elements in insects

Miniature Transposable Elements (mTEs): Impacts and Uses in the Brassica Genome

Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs

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