Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids.

Takasaki, N; Murata, Shigenori; Saitoh, Masako; Kobayashi, Takanori; Park, Linda; Okada, Norihiro

doi:10.1073/pnas.91.21.10153

Cited by 47 publications

(19 citation statements)

References 41 publications

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“…Generally, the distribution of these variants in the host genomes corresponds to the host evolution with a few exceptions; e.g., DR2 duplication is found in half of feliform CANs but not in caniform ones, but the insertion insI is found in the feliform CANs and a single caniform sequence Mus-07. A similar interspersion of variants was observed for other SINEs too; for instance, salmonid Hpa I family (Hamada et al 1997;Takasaki et al 1994). We believe that various ancestor variants were formed before their active amplification (and radiation of carnivores) so that later independent choice of a particular variant could correspond or not to the host evolution, and single copies of most variants can be found.…”

Section: Evolution Of Can Sines and Carnivoressupporting

confidence: 73%

CAN—a pan-carnivore SINE family

Vassetzky

Крамеров

2002

Mammalian Genome

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Abstract. Short retroposons or short interspersed elements (SINEs) constituting 5-10% genome have been isolated from various organisms. CAN SINEs initially found in American mink were named after dogs (Canis), and the range of their distribution in the genomes of carnivores and mammals in general remained topical. Here we demonstrate CAN sequences in representatives of all carnivore families, but not beyond carnivores, on the basis of sequence bank search and genomic PCR. Analysis of their distribution supports division of carnivores into caniform (dogs, mustelids, raccoons, bears, and pinnipeds) and feliform (cats, civets, and hyenas) lineages. CAN structure is considered in the context of their function and evolution.A significant portion of the eukaryotic genome is composed of mobile elements propagated by retroposition, a process involving transcription and reverse transcription (Rogers 1985). Long retroposons (LINEs) code for the activities required for retroposition (reverse transcriptase and endonuclease), while short retroposons (SINEs) lack these.SINEs are genomic repeats 80-400 bp long, apparently originating from RNA (more commonly tRNA); a typical SINE consists of three regions; a tRNA-related region, a tRNA-unrelated region, and an A-rich region. The tRNA-related region contains an internal promoter of RNA polymerase III and provides for its transcription (Daniels and Deininger 1985;Jagadeeswaran et al. 1981). Owing to the mechanism of amplification, the 3Ј-part of SINEs is A-rich, and the genomic elements are flanked by short direct repeats.SINEs can be classified as members of several superfamilies sharing structural similarity, apparently inherited from a common ancestor [e.g., members of Alu/B1 superfamily originate from an ancient element FAM (Quentin 1992)]. The vast majority of SINE copies in the genome are incapable of active amplification, and the process is due to a few master sequences as indicated by the presence of distinct subfamilies and the activity of one or a few at any given time.

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Section: Evolution Of Can Sines and Carnivoressupporting

confidence: 73%

CAN—a pan-carnivore SINE family

Vassetzky

Крамеров

2002

Mammalian Genome

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“…Repetitive families are particularly diverse and abundant in different mammalian lineages and they might have been an important factor in explosive mammalian radiation after the extinction of the dinosaurs. In this context, repetitive sequences preserved in the genomic fossil record may serve as valuable markers for understanding mammalian and other metazoan speciation (Batzer et al, 1994;Usdin et al, 1995;Takasaki et al, 1994;Lee et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

Identification of new medium reiteration frequency repeats in the genomes of Primates, Rodentia and Lagomorpha

et al. 1996

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We report eleven new families of MEdium Reiteration frequency (MER) interspersed repeats in the genomes of Primates, Rodentia, and Lagomorpha. Two families of the human repeats, MER 46 and MER 47, represent non-autonomous DNA transposons. These sequences are flanked by TA target site duplications and have terminal inverted repeats (TIRs) similar to TIRs of DNA transposons. The sequences of five other families of repeats, MER41, MER48, MER50, MER51, and RMER3, resemble long terminal repeats of retroviruses. A potential involvement of some of the reported MER repeats in the regulation of transcription and genetic rearrangements is suggested. Age estimations place the origin of most MER repeats at the time of decline in MIR (Mammalian-wide Interspersed Repeats) retroposition and before the origin of the Alu family.

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“…They have an internal RNA polymerase III (pol III) promoter but no open reading frames (Okada 1991;Schmid and Maraia 1992;Deininger and Batzer 1993;Okada and Ohshima 1995;Schmid 1998). Many families of SINEs have been identified in multicellular eukaryotes, such as invertebrates Ohshima and Okada 1994), plants (Yoshioka et al 1993;Deragon et al 1994), fishes (Kido et al 1991;Takasaki et al 1994;Takahashi et al 1998;Ogiwara et al 1999), and mammals (Shimamura et al 1999;Gilbert and Labuda 2000; see also Shedlock and Okada 2000 for review). Specific families of SINEs are found only in closely related species; thus, it has been postulated that each family of SINEs was created relatively recently on the evolutionary time scale.…”

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confidence: 99%

V-SINEs: A New Superfamily of Vertebrate SINEs That Are Widespread in Vertebrate Genomes and Retain a Strongly Conserved Segment within Each Repetitive Unit

Ogiwara

Miya²,

Ohshima³

et al. 2002

Genome Res.

100

103

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We have identified a new superfamily of vertebrate short interspersed repetitive elements (SINEs), designated V-SINEs, that are widespread in fishes and frogs. Each V-SINE includes a central conserved domain preceded by a 5Ј-end tRNA-related region and followed by a potentially recombinogenic (TG) n tract, with a 3Ј tail derived from the 3Ј untranslated region (UTR) of the corresponding partner long interspersed repetitive element (LINE) that encodes a functional reverse transcriptase. The central domain is strongly conserved and is even found in SINEs in the lamprey genome, suggesting that V-SINEs might be ∼550 Myr old or older in view of the timing of divergence of the lamprey lineage from the bony fish lineage. The central conserved domain might have been subject to some form of positive selection. Although the contemporary 3Ј tails of V-SINEs differ from one another, it is possible that the original 3Ј tail might have been replaced, via recombination, by the 3Ј tails of more active partner LINEs, thereby retaining retropositional activity and the ability to survive for long periods on the evolutionary time scale. It seems plausible that V-SINEs may have some function(s) that have been maintained by the coevolution of SINEs and LINEs during the evolution of vertebrates.[The sequences reported in this paper have been deposited in the DDBJ/GenBank database under accession nos. AB072981-AB073004. Supplemental figures are available online at http://www.genome.org.]Retroposons are genetic elements that have moved within and among genomes via an RNA intermediate (Weiner et al. 1986). They include SINEs, LINEs, LTR-retrotransposons, and retroviruses. L1 and Alu are representative of the LINEs and SINEs, respectively, in the human genome (Weiner et al. 1986;Eickbush 1994;Smit 1996). An analysis of the entire human genome revealed that retroposons constitute up to 40% of the genome and that protein-coding sequences account for only about 1.5% (International Human Genome Sequencing Consortium 2001). The above mentioned 40% of the human genome includes several clearly discernible groups of retroposons, such as L1, LINE2, Alu, and MIR, and these easily recognizable sequences represent the results of relatively recent amplifications over the past 200 Myr (International Human Genome Sequencing Consortium 2001). Accordingly, the proportion of the genome that originated from retroposons may increase up to as much as 60% to 70%, if we could identify and include ancient retroposons, which might have been amplified in the very distant past, are now barely recognizable as such, and are buried in the genome as debris. Such a putative extensive contribution of retroposons to the construction of the contemporary human genome has not been anticipated.Typical SINEs vary from 100 to 500 bp in length. They have an internal RNA polymerase III (pol III) promoter but no open reading frames (Okada 1991;Schmid and Maraia 1992;Deininger and Batzer 1993;Okada and Ohshima 1995;Schmid 1998). Many families of SINEs have been identified in multic...

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Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids.

Cited by 47 publications

References 41 publications

CAN—a pan-carnivore SINE family

CAN—a pan-carnivore SINE family

Identification of new medium reiteration frequency repeats in the genomes of Primates, Rodentia and Lagomorpha

V-SINEs: A New Superfamily of Vertebrate SINEs That Are Widespread in Vertebrate Genomes and Retain a Strongly Conserved Segment within Each Repetitive Unit

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