V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit.

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 5'-end tRNA-related region and followed by a potentially recombinogenic (TG)(n) tract, with a 3' tail derived from the 3' 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 approximately 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 3' tails of V-SINEs differ from one another, it is possible that the original 3' tail might have been replaced, via recombination, by the 3' 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.

[1]  M. P. Cummings.  PHYLIP (Phylogeny Inference Package) , 2004 .

[2]  J. Deragon,et al.  An analysis of retroposition in plants based on a family of SINEs from Brassica napus , 1994, Journal of Molecular Evolution.

[3]  David I. K. Martin,et al.  Retrotransposons as epigenetic mediators of phenotypic variation in mammals , 2001, Nature Genetics.

[4]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[5]  M. Batzer,et al.  Potential gene conversion and source genes for recently integrated Alu elements. , 2000, Genome research.

[6]  R. Dunham,et al.  The skeletal muscle alpha-actin gene of channel catfish (Ictalurus punctatus) and its association with piscine specific SINE elements. , 2000, Gene.

[7]  N Okada,et al.  SINE insertions: powerful tools for molecular systematics. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[8]  Andrew Fire,et al.  The rde-1 Gene, RNA Interference, and Transposon Silencing in C. elegans , 1999, Cell.

[9]  J. Brosius,et al.  RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. , 1999, Gene.

[10]  N Okada,et al.  Retropositional parasitism of SINEs on LINEs: identification of SINEs and LINEs in elasmobranchs. , 1999, Molecular biology and evolution.

[11]  N. Okada,et al.  Genealogy of families of SINEs in cetaceans and artiodactyls: the presence of a huge superfamily of tRNA(Glu)-derived families of SINEs. , 1999, Molecular biology and evolution.

[12]  T. Eickbush,et al.  The age and evolution of non-LTR retrotransposable elements. , 1999, Molecular biology and evolution.

[13]  D. Labuda,et al.  CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[14]  T. Heidmann,et al.  Taming of transposable elements by homology-dependent gene silencing , 1999, Nature Genetics.

[15]  N. Okada,et al.  SINE cousins: the 3'-end tails of the two oldest and distantly related families of SINEs are descended from the 3' ends of LINEs with the same genealogical origin. , 1998, Molecular biology and evolution.

[16]  C. Schmid,et al.  Does SINE evolution preclude Alu function? , 1998, Nucleic acids research.

[17]  N. M. Brooke,et al.  A molecular timescale for vertebrate evolution , 1998, Nature.

[18]  M. Nishida,et al.  A novel family of short interspersed repetitive elements (SINEs) from cichlids: the patterns of insertion of SINEs at orthologous loci support the proposed monophyly of four major groups of cichlid fishes in Lake Tanganyika. , 1998, Molecular biology and evolution.

[19]  C. Schmid,et al.  Potential Alu Function: Regulation of the Activity of Double-Stranded RNA-Activated Kinase PKR , 1998, Molecular and Cellular Biology.

[20]  N. Okada,et al.  SINEs and LINEs share common 3' sequences: a review. , 1997, Gene.

[21]  N. Okada,et al.  Determination of the entire sequence of turtle CR1: the first open reading frame of the turtle CR1 element encodes a protein with a novel zinc finger motif. , 1997, Molecular biology and evolution.

[22]  D. Kordis,et al.  Bov-B long interspersed repeated DNA (LINE) sequences are present in Vipera ammodytes phospholipase A2 genes and in genomes of Viperidae snakes. , 1997, European journal of biochemistry.

[23]  Robert L. Carroll,et al.  Patterns and Processes of Vertebrate Evolution , 1997 .

[24]  Z. Izsvák,et al.  Repetitive elements and their genetic applications in zebrafish. , 1997, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[25]  A. Smit,et al.  The origin of interspersed repeats in the human genome. , 1996, Current opinion in genetics & development.

[26]  N. Okada,et al.  The 3' ends of tRNA-derived short interspersed repetitive elements are derived from the 3' ends of long interspersed repetitive elements , 1996, Molecular and cellular biology.

[27]  M. Ekker,et al.  Mermaid, a family of short interspersed repetitive elements, is useful for zebrafish genome mapping. , 1996, Biochemical and biophysical research communications.

[28]  A. Smit,et al.  Tiggers and DNA transposon fossils in the human genome. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Z. Izsvák,et al.  DANA elements: a family of composite, tRNA-derived short interspersed DNA elements associated with mutational activities in zebrafish (Danio rerio). , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[30]  T. Eickbush,et al.  RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element , 1995, Molecular and cellular biology.

[31]  N. Okada,et al.  Generality of the tRNA origin of short interspersed repetitive elements (SINEs). Characterization of three different tRNA-derived retroposons in the octopus. , 1994, Journal of molecular biology.

[32]  N. Okada,et al.  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. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[33]  R. Britten,et al.  Evolutionary selection against change in many Alu repeat sequences interspersed through primate genomes. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[34]  N. Okada,et al.  Molecular characterization of a short interspersed repetitive element from tobacco that exhibits sequence homology to specific tRNAs. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[35]  N. Okada,et al.  Several short interspersed repetitive elements (SINEs) in distant species may have originated from a common ancestral retrovirus: characterization of a squid SINE and a possible mechanism for generation of tRNA-derived retroposons. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Andrew P. Martin,et al.  Body size, metabolic rate, generation time, and the molecular clock. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[37]  T. Eickbush,et al.  Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition , 1993, Cell.

[38]  C. Schmid,et al.  Transcriptional regulation and transpositional selection of active SINE sequences. , 1992, Current opinion in genetics & development.

[39]  N. Okada,et al.  SINEs: Short interspersed repeated elements of the eukaryotic genome. , 1991, Trends in ecology & evolution.

[40]  K. Matsumoto,et al.  Shaping and reshaping of salmonid genomes by amplification of tRNA-derived retroposons during evolution. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[41]  T. Eickbush,et al.  Origin and evolution of retroelements based upon their reverse transcriptase sequences. , 1990, The EMBO journal.

[42]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[43]  W P Wahls,et al.  The Z-DNA motif d(TG)30 promotes reception of information during gene conversion events while stimulating homologous recombination in human cells in culture , 1990, Molecular and cellular biology.

[44]  T. Rabbitts,et al.  Alternating purine‐pyrimidine tracts may promote chromosomal translocations seen in a variety of human lymphoid tumours. , 1989, The EMBO journal.

[45]  M. A. McClure,et al.  Origins and Evolutionary Relationships of Retroviruses , 1989, The Quarterly Review of Biology.

[46]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[47]  R. Britten,et al.  Rates of DNA sequence evolution differ between taxonomic groups. , 1986, Science.

[48]  A. Weiner,et al.  Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. , 1986, Annual review of biochemistry.