Genomes and Genes
short interspersed nucleotide elements
Summary: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).
- Lindblad Toh K, Wade C, Mikkelsen T, Karlsson E, Jaffe D, Kamal M, et al. Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature. 2005;438:803-19 pubmed..The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health. ..
- Anbar M, Bracha R, Nuchamowitz Y, Li Y, Florentin A, Mirelman D. Involvement of a short interspersed element in epigenetic transcriptional silencing of the amoebapore gene in Entamoeba histolytica. Eukaryot Cell. 2005;4:1775-84 pubmed..These results suggest the involvement of SINE1 in triggering the gene silencing and the role of histone modification in its epigenetic maintenance. ..
- Ohshima K, Okada N. SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet Genome Res. 2005;110:475-90 pubmed..We also use several biological examples to discuss the impact and significance of SINEs and LINEs in the evolution of vertebrate genomes. ..
- Barnes M, Lobo N, Coulibaly M, Sagnon N, Costantini C, Besansky N. SINE insertion polymorphism on the X chromosome differentiates Anopheles gambiae molecular forms. Insect Mol Biol. 2005;14:353-63 pubmed
- Tu Z, Li S, Mao C. The changing tails of a novel short interspersed element in Aedes aegypti: genomic evidence for slippage retrotransposition and the relationship between 3' tandem repeats and the poly(dA) tail. Genetics. 2004;168:2037-47 pubmed
- Salem A, Ray D, Batzer M. Identity by descent and DNA sequence variation of human SINE and LINE elements. Cytogenet Genome Res. 2005;108:63-72 pubmed..No completely or partially deleted Alu or L1 alleles were identified during the analysis. These data suggest that mobile element insertions are identical by descent characters for the study of human population genetics. ..
- Sasaki T, Takahashi K, Nikaido M, Miura S, Yasukawa Y, Okada N. First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea. Mol Biol Evol. 2004;21:705-15 pubmed..This information may be applied to the phylogenetic resolution of relevant turtle lineages. ..
- Ke X, Thomas N, Robinson D, Collins A. The distinguishing sequence characteristics of mouse imprinted genes. Mamm Genome. 2002;13:639-45 pubmed..The differences between the sequence characteristics of imprinted and control genes have also enabled us to develop a discriminant function that can be used in a genome-wide screen to identify candidate imprinted genes. ..
- Ogiwara I, Miya M, Ohshima K, Okada N. V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit. Genome Res. 2002;12:316-24 pubmed..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. ..
- Weiner A. SINEs and LINEs: the art of biting the hand that feeds you. Curr Opin Cell Biol. 2002;14:343-50 pubmed..Taken together, these studies promise to explain the birth and death of SINEs and LINEs, and the contribution of these repetitive sequence families to the evolution of genomes. ..
- Schmid C. Does SINE evolution preclude Alu function?. Nucleic Acids Res. 1998;26:4541-50 pubmed..Since Alus have appeared only recently within the primate lineage, this proposal provokes the challenging question of how Alu RNA could have possibly assumed a significant role in cell physiology. ..
- Smit A. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev. 1999;9:657-63 pubmed..The many new examples of human genes derived from single transposon insertions highlight the large contribution of selfish DNA to genomic evolution. ..
- Lenoir A, Lavie L, Prieto J, Goubely C, Côté J, Pelissier T, et al. The evolutionary origin and genomic organization of SINEs in Arabidopsis thaliana. Mol Biol Evol. 2001;18:2315-22 pubmed..In these territories, SINE elements are closely associated with genes. A retroposition partnership between Arabidopsis SINEs and LINEs is proposed. ..
- Kajikawa M, Okada N. LINEs mobilize SINEs in the eel through a shared 3' sequence. Cell. 2002;111:433-44 pubmed..We also demonstrated that short repeats at the 3' end of UnaL2 are required for retrotransposition suggesting that UnaL2 retrotransposes in a manner reminiscent of the reverse transcriptase activity of telomerases. ..
- Bejerano G, Lowe C, Ahituv N, King B, Siepel A, Salama S, et al. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature. 2006;441:87-90 pubmed
- Greally J. Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome. Proc Natl Acad Sci U S A. 2002;99:327-32 pubmed..Methylation-induced silencing could lead to deleterious consequences at imprinted loci, where inactivation of one allele is already established, and expression is often essential for embryonic growth and survival. ..
- Lee J, Ji Z, Tian B. Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3'-end of genes. Nucleic Acids Res. 2008;36:5581-90 pubmed publisher..Our results establish a conservation pattern for alternative poly(A) sites in several vertebrate species, and indicate that the 3'-end of genes can be dynamically modified by TEs through evolution. ..
- Ke X, Thomas N, Robinson D, Collins A. A novel approach for identifying candidate imprinted genes through sequence analysis of imprinted and control genes. Hum Genet. 2002;111:511-20 pubmed..We have applied this function to a number of genes whose imprinting status is disputed or uncertain. ..
- Nishihara H, Kuno S, Nikaido M, Okada N. MyrSINEs: a novel SINE family in the anteater genomes. Gene. 2007;400:98-103 pubmed..We also speculate that the simple structure of t-SINEs may be a potential evolutionary source for the generation of the typical SINE structure...
- Gilbert N, Labuda D. Evolutionary inventions and continuity of CORE-SINEs in mammals. J Mol Biol. 2000;298:365-77 pubmed..The proposed mechanism suggests that such an adaptation to the changing amplification machinery facilitated the survival and prosperity of CORE-elements over long evolutionary periods in different lineages...
- Belancio V, Hedges D, Deininger P. Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. Genome Res. 2008;18:343-58 pubmed publisher..We consider their potential impact on host biology as well as their ultimate implications for the nature of the TE-host relationship. ..
- Nikaido M, Matsuno F, Hamilton H, Brownell R, Cao Y, Ding W, et al. Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins. Proc Natl Acad Sci U S A. 2001;98:7384-9 pubmed..The combination of SINE and flanking sequence analysis suggests a topology and set of divergence times for odontocete relationships, offering alternative explanations for several long-standing problems in cetacean evolution...
- Munemasa M, Nikaido M, Nishihara H, Donnellan S, Austin C, Okada N. Newly discovered young CORE-SINEs in marsupial genomes. Gene. 2008;407:176-85 pubmed..By compiling the information of CORE-SINEs characterized to date, we propose a comprehensive picture of how SINE evolution occurred in the genomes of marsupials...
- Gu W, Ray D, Walker J, Barnes E, Gentles A, Samollow P, et al. SINEs, evolution and genome structure in the opossum. Gene. 2007;396:46-58 pubmed..Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state. ..
- Luchetti A. Identification of a short interspersed repeat in the Reticulitermes lucifugus (Isoptera Rhinotermitidae) genome. DNA Seq. 2005;16:304-7 pubmed..The presence of the SINE also in the Kalotermitidae family, suggests the usefulness of Talua as a taxonomic marker at the family level. The importance of this element on termite genome evolution is discussed. ..
- Medstrand P, van de Lagemaat L, Mager D. Retroelement distributions in the human genome: variations associated with age and proximity to genes. Genome Res. 2002;12:1483-95 pubmed..Such a process may provide an explanation for the shifting distributions of retroelements with time. ..
- Allen T, Von Kaenel S, Goodrich J, Kugel J. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol. 2004;11:816-21 pubmed..Moreover, we identify a function for B2 RNA, which is transcribed from short interspersed elements that are abundant in the mouse genome and historically considered to be 'junk DNA.' ..
- Pélissier T, Bousquet Antonelli C, Lavie L, Deragon J. Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana. Nucleic Acids Res. 2004;32:3957-66 pubmed..The observation that primary SINE transcripts can be post-transcriptionally processed in vivo into a poly(A)-ending species introduces the possibility that this paRNA is used as a retroposition intermediate. ..
- Baba S, Kajikawa M, Okada N, Kawai G. Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2. RNA. 2004;10:1380-7 pubmed
- Piskurek O, Nikaido M, Boeadi -, Baba M, Okada N. Unique mammalian tRNA-derived repetitive elements in dermopterans: the t-SINE family and its retrotransposition through multiple sources. Mol Biol Evol. 2003;20:1659-68 pubmed..t-SINE amplification occurred through multiple sources and is supposedly mobilized via the L1-encoded reverse transcriptase-dependent retrotranspositional mechanism in trans. ..
- Walker J, Hughes D, Anders B, Shewale J, Sinha S, Batzer M. Quantitative intra-short interspersed element PCR for species-specific DNA identification. Anal Biochem. 2003;316:259-69 pubmed..The SINE-based PCR methods we report here are species-specific, are highly sensitive, and will improve the detection limits for DNA sequences derived from these species. ..
- Kapitonov V, Jurka J. A novel class of SINE elements derived from 5S rRNA. Mol Biol Evol. 2003;20:694-702 pubmed..Given the common structural features, it is highly likely that the enzymatic machinery encoded by CR1-like elements powers proliferation of SINE3. ..
- Carrière L, Graziani S, Alibert O, Ghavi Helm Y, Boussouar F, Humbertclaude H, et al. Genomic binding of Pol III transcription machinery and relationship with TFIIS transcription factor distribution in mouse embryonic stem cells. Nucleic Acids Res. 2012;40:270-83 pubmed publisher..We found that, as in Saccharomyces cerevisiae, TFIIS is associated with class III genes and also with SINEs suggesting that TFIIS is a Pol III transcription factor in mammals. ..
- Kroutter E, Belancio V, Wagstaff B, Roy Engel A. The RNA polymerase dictates ORF1 requirement and timing of LINE and SINE retrotransposition. PLoS Genet. 2009;5:e1000458 pubmed publisher..We present a model that highlights the critical differences of LINE and SINE transcripts that likely define their retrotransposition timing. ..
- Piskurek O, Nishihara H, Okada N. The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis. Gene. 2009;441:111-8 pubmed publisher..The new SINEs and LINEs and other ubiquitous genomic elements characterized in the Anolis genome will prove very useful for studies in comparative genomics, phylogenetics, and functional genetics. ..
- Xu J, Liu T, Li D, Zhang Z, Xia Q, Zhou Z. BmSE, a SINE family with 3' ends of (ATTT) repeats in domesticated silkworm (Bombyx mori). J Genet Genomics. 2010;37:125-35 pubmed publisher..Our analysis might assist in developing BmSE as a potential marker and in understanding the evolutionary roles of SINEs in the domesticated silkworm. ..
- Takahashi K, Terai Y, Nishida M, Okada N. Phylogenetic relationships and ancient incomplete lineage sorting among cichlid fishes in Lake Tanganyika as revealed by analysis of the insertion of retroposons. Mol Biol Evol. 2001;18:2057-66 pubmed
- Deragon J, Zhang X. Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers. Syst Biol. 2006;55:949-56 pubmed..The importance of these new data for the use of Brassicaceae SINEs as molecular markers in future applications is discussed. ..
- Ray D. SINEs of progress: Mobile element applications to molecular ecology. Mol Ecol. 2007;16:19-33 pubmed..In this review, I discuss the application of mobile element markers, especially short interspersed elements (SINEs), to phylogenetic and population data, with an emphasis on potential applications to molecular ecology. ..
- Fawcett J, Kawahara T, Watanabe H, Yasui Y. A SINE family widely distributed in the plant kingdom and its evolutionary history. Plant Mol Biol. 2006;61:505-14 pubmed..truncatula and L. japonicus. This is the first report of a plant SINE family present in multiple lineages, and the evolution of Au SINE in the plant kingdom, especially in Gramineae and Fabaceae is discussed. ..
- Nishihara H, Smit A, Okada N. Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res. 2006;16:864-74 pubmed..The conservation is strongest over the central domain. Thus, AmnSINE1 appears to be the best example of a transposable element of which a significant fraction of the copies have acquired genomic functionality. ..
- Kramerov D, Vassetzky N. Short retroposons in eukaryotic genomes. Int Rev Cytol. 2005;247:165-221 pubmed
- Meunier J, Khelifi A, Navratil V, Duret L. Homology-dependent methylation in primate repetitive DNA. Proc Natl Acad Sci U S A. 2005;102:5471-6 pubmed..This observation strongly suggests the existence of a homology-dependent methylation (HDM) mechanism in mammalian genomes. We propose that HDM is a direct consequence of interfering RNA-induced transcriptional gene silencing. ..
- Bringaud F, Garcia Perez J, Heras S, Ghedin E, El Sayed N, Andersson B, et al. Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi. Mol Biochem Parasitol. 2002;124:73-8 pubmed..In addition, the genome of Leishmania major contains the same conserved motif present in the trypanosome retroelements, whicle no transposable elements have been detected so far in Leishmania sp. ..
- Pecon Slattery J, Pearks Wilkerson A, Murphy W, O Brien S. Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family felidae as a species tree. Mol Biol Evol. 2004;21:2299-309 pubmed..Overall, our data suggest X-degenerate genes within the NRY are singularly powerful markers and offer a valuable patrilineal perspective in species evolution...
- Schmitz J, Zischler H. A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates. Mol Phylogenet Evol. 2003;28:341-9 pubmed..Nevertheless it is a valuable device to reconstruct the evolutionary steps from a functional tRNA to an interspersed SINE element. ..
- Nikaido M, Nishihara H, Hukumoto Y, Okada N. Ancient SINEs from African endemic mammals. Mol Biol Evol. 2003;20:522-7 pubmed..We characterized the structures of the AfroSINEs from all afrotherian representatives by PCR, and we discuss how they were generated as well as the phylogenetic relationships of their host species...
- Stratil A, Blažková P, Kopecny M, Bartenschlager H, Van Poucke M, Peelman L, et al. Characterization of a SINE indel polymorphism in the porcine AGL gene and assignment of the gene to chromosome 4q. Anim Genet. 2003;34:146-8 pubmed
- Schmitz J, Ohme M, Zischler H. SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates. Genetics. 2001;157:777-84 pubmed..The three Alu insertions characterized underpin the monophyly of haplorhine primates (Anthropoidea and Tarsioidea) from a novel perspective...
- Goodier J, Kazazian H. Retrotransposons revisited: the restraint and rehabilitation of parasites. Cell. 2008;135:23-35 pubmed publisher..Recent insights and new technologies promise answers to fundamental questions about the biology of transposable elements. ..
- Nikaido M, Hamilton H, Makino H, Sasaki T, Takahashi K, Goto M, et al. Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Baleen whale phylogeny and a past extensive radiation event revealed by SINE insertion analysis. Mol Biol Evol. 2006;23:866-73 pubmed..L., T. W. Reeder, and A. Berta. 2004. Phylogeny of mysticete whales based on mitochondrial and nuclear data. Mol. Phylogenet. Evol. 32:892-901), provide a nearly complete picture of the evolutionary history of baleen whales. ..