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1 едеге е е ецедедеце, 2009, 43, 5, ег LTR-appleappleapple - apple applefl apple, apple- appleapple е appleapple apple - LINE (long interspersed elements) е 3 7 apple apple LINE apple apple apple- fl, apple apple appleapple- е -fl ( appleappleapple Gag) е fl appleapple-, fl apple apple appleapple е, applefl - apple fl apple fl apple- LINE, apple fl 15 [24] LINE apple apple apple- ; fl - apple appleapple [5] ед appleapple L1 [6] ед apple -, fl- fl fl fl, fl- L1 appleapple apple 5'- еф - fl applefl, apple apple appleapple fl appleеде едефец е ефе едееедебед ец ец ецеееде ебедец ецедефеце«ец ецедеце 2009 appleapple*, ец flapple е apple е,, ее apple ееapplefl apple apple fl appleappleapple appleflfl - apple apple appleapple (short interspersed elements, SINE) е apple apple appleapple apple, appleapple appleapple apple - ед, apple appleapple fl - applefl : apple SINE, fl, fl SHORT INTERSPERSED REPETITIVE SEQUENCES (SINEs) AND THEIR USE AS A PHYLOGENET- IC TOOL, by D A Kramerov*, N S Vassetzky (Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; * kramerov@eimbru) The data on one of the most common repetitive elements of eukaryotic genomes, short interspersed elements (SINEs), are reviewed Their structure, origin, and functioning in the genome are discussed The variation and abundance of these neutral genomic markers makes them a convenient and reliable tool for phylogenetic analysis The main methods of such analysis are presented, and the potential and limitations of this approach are discussed using specific examples Key words: short interspersed elements, SINEs, evolution, phylogeny * еде едефец е ефе едееедебед е fl appleflfl - - fl apple apple- ееfl appleflfl apple, apple flfl : -apple appleappleapple -apple apple apple apple- ееfl -apple apple applefl (cut and paste), apple apple apple, apple apple е appleapple apple applefl, apple apple apple flfl, - applefl apple apple appleapple ( applefl, copy and paste), -apple, flfl appleapple- apple, apple ( ) apple (long terminal repeat, LTR) [1] еф- appleappleapple 8 apple apple apple fl, apple apple apple appleapple (appleapple) * е : kramerov@eimbru 795

2 796 7SL PHK (A) n B1 LINE еф SINE е е 1 appleapple apple appleapple: B1 () е SINE () apple apple; apple flfl fl applefl applefl - applefl fl L1 ее -,, applefl apple apple, fl ефfl fl fl appleapple, appleappleapple apple apple applefl - apple (SINE, short interspersed elements) apple appleapple е«apple SINE flfl - fl fl fl apple - fl 1030%, - applefl fl SINE SINE, fl apple, apple - apple [7] SINE - applefl, apple, apple, apple ( appleapple apple) SINE apple fl applefl - fl apple apple LINE (apple 1) [8, 9] еф apple, SINE applefl ееapple apple appleapple- 1 B2, apple [10 13], Alu apple [14] applefl - SINE, fl -, apple apple- B1 Alu 7SL е, е ее-, - applefl- appleapple apple [15] ееapple 1 apple fl SL е, -, - (apple 1) 1 fl -, А А Alu apple 1 - apple - apple еф apple, Alu flflfl apple SINE е«apple apple- 7SL е, е B2 apple е,, е ееapple 2 е, apple - applefl, 3'- apple- fl - fl SINE applefl (apple 1), fl е -appleapple-, е -apple apple applefl е apple appleapple appleappleapple [7], apple apple apple- apple, applefl 5S appleе apple apple fl apple Danio rerio [16] apple apple appleapple applefl -, applefl 5S appleе, SINE apple [17] - [18] apple apple apple - apple appleapple

3 еде едефец е ефе едееедебед ец ец ецеееде ебедец 797 apple е, apple apple apple applefl е -apple III, е -apple II, - applefl appleappleapple, apple, LINE apple appleapple appleappleapplefl е -apple III, apple- applefl е [19, 20] еф, SINE appleappleapplefl apple, apple- apple е -apple II, appleapple е -apple- III, applefl appleapple е, 5S appleе, 7SL е, apple applefl apple appleappleapple [7, 21] еф apple, apple appleapple е SINE fl fl fl - - appleapple SINE apple- apple, apple -, applefl appleapple appleappleapplefl, appleapple apple appleapple appleapple е -- apple III SINE, apple е 7SL е, appleapple 11,, apple apple SINE, 5S appleе, appleapple apple, IE appleapple flfl apple apple apple appleapple fl apple- apple е -apple III ец, apple- applefl, flfl е -apple, appleapplefl apple еф [19, 21] ецapple, SINE appleapple е, appleapplefl applefl apple fl еф-- apple 3'- apple fl SINE applefl -- ее appleapple - apple appleapple- apple [22] ег, apple 2- apple-, appleapple appleapple-, еф еф SINE flfl еф +, SINE apple- apple еф еф ефappleapplefl B2 SINE fl еф-, 3'- - applefl е applefl () [23] fl applefl еф е appleapple applefl - apple е -apple III ее(), apple- fl appleapple SINE, - apple applefl е apple apple apple - fl А А SINE apple apple ( apple SINE ) apple : apple fl apple 35 (apple 2) SINE -, apple apple 30100, 3'-- apple LINE (apple 2) [24], appleapple Bov-B, CR-1, L2, RSg-1 apple apple ег-, е SINE fl appleapple LINE, apple apple appleapple е apple SINE - apple -, apple LINE- L1 fl, - () - е SINE, appleapple [25, 26] ее apple applefl apple SINE apple - [27, 28] е SINE appleapple LINE appleappleapplefl flapple, - fl, appleapple-, - SINE е apple, - fl е applefl, 3'- apple appleapple apple appleapple ее apple apple- appleapplefl apple apple apple apple apple -apple apple - applefl fl fl SINE, applefl applefl apple 816 (target site duplication, TSD) applefl fl TSD applefl apple apple appleapplefl - fl apple ее apple appleapple apple TSD, appleapple SINE applefl apple SINE, apple ееfl apple, appleflfl - appleapple apple apple, apple appleapple flfl apple Ther-1 SINE apple, Ther-1, applefl Alu apple applefl [29], fl А apple А fl - apple appleapple:, apple Alu applefl; apple apple apple, SINE, flfl apple, - applefl [30] ецеееде ебедец еде едефец е ефе едееедебедед ецедефеце«ец ецедеце 90- apple apple apple- appleapple apple apple - apple

4 798 OPC1 LINE OPC2 SINE fl fl SINE ефappleapplefl е -apple II ефappleapplefl е -apple III PK LINE ефappleflfl едapplefl appleapplefl applefl едapplefl appleapple LINE е 2 apple apple appleapple еде applefl apple fl (); apple flfl apple apple apple apple, - fl apple apple apple А NatureА, applefl apple [31] apple - flapple, apple- apple,, apple applefl apple- apple apple apple ед,, - flapple, - fl applefl, apple apple apple, flapple - appleapple apple fl apple apple [3234] ец fl apple -, applefl,, е apple apple ед fl -, fl apple е apple apple, - apple 90- apple SINE apple [3537] fl, -, apple SINE, е -apple - apple apple (еее ), - SINE, apple- applefl apple apple apple,, apple - apple 3 1, 2 3 apple - SINE, 4 apple applefl, SINE 1 2, 3 4 е fl apple apple, - apple apple 3 ец apple, apple apple apple - apple appleapple appleapple- apple, fl - apple apple, apple [38] applefl еее apple - apple appleapple е -apple III apple fl SINE, apple apple, applefl еее -apple, apple apple apple apple apple apple - fl apple SINE, fl - SINE, apple - fl appleapple apple-

5 еде едефец е ефе едееедебед ец ец ецеееде ебедец apple apple- applefl fl [40] ее apple apple apple apple- apple apple apple flapple [41] apple -, applefl Afrotheria [33] apple, apple, fl apple, apple apple apple, apple apple - fl apple fl - apple - apple appleapple AfroSINE [42] е apple apple fl Afrotheria, apple -apple, fl applefl Supraprimates ( Euarchontoglires) [33] - - applefl еб еб ееapplefl fl applefl ееappleapple ' ееappleapple ' SINE е 3 ец apple appleapple fl еб appleapple /' /' fl apple appleapple apple apple flfl apple appleapple еее applefl ее apple - apple, apple- - е 4 appleapple apple fl applefl apple А А apple, fl apple Romer [39], - appleapple apple appleapple apple е apple, B1-dID, - applefl apple- B1-dID apple apple - : (Sciuridae), (Aplodontidae) (Gliridae) apple Romer apple apple apple () apple ( apple 4 ) ец appleapplefl B1-dID

6 800 B1 ID B4 45SH 45S1 B2 B1-dID IDL-Geo DIP Cricetidae Muridae Spalacidae Rhizomyidae Dipodidae Zapodidae Geomyidae Heteromyidae Gliridae Aplodontidae Sciuridae Castoridae Hystricidae Anomaluridae Hydrochoeridae Caviidae Dasyproctidae DIP B2, 45S1 B4, 45SH IDL-Geo B1-dID е 4 е apple apple ее apple apple appleapple apple - apple [37, 40, 46, 7274] apple apple flfl apple appleapple еб fl Gliridae Romer [39]

7 еде едефец е ефе едееедебед ец ец ецеееде ебедец 801 apple apple fl appleapple [43, 44] ед, apple apple applefl, apple, apple, apple apple apple 7SL е, apple apple [45],, - apple apple, applefl applefl apple, - 7SL е apple apple SINE 1 apple Alu apple appleapple SINE, - еф, apple apple 1 apple apple - 1 apple apple fl apple apple, fl fl appleapplefl apple- apple apple apple - apple apple [46] appleappleapple appleapple -, - apple appleapple applefl SINE apple - apple [47] е - еее - apple fl, - apple SINE (apple 5) apple apple apple, apple SINE fl applefl apple - apple apple, SINE, apple SINE, apple apple,, apple -, apple apple - apple- flapple- е apple apple fl fl - fl apple [48] - [49] apple (/) SINE Alu apple fl fl apple, applefl apple apple ( apple [30] ) fl apple, appleapple,, applefl - apple (Cetacea) applefl apple apple applefl apple (Artiodactyla) еф apple, fl, fl [50, 51] ее apple apple apple apple apple - flapple [32] ецapple-sine-еее, apple fl apple appleapple- е, apple-sineеее, fl еее, apple - apple apple SINE ееappleapple apple apple, apple, apple fl SINE (apple 6) apple apple- fl apple еее applefl apple, apple - fl apple applefl е apple fl apple [52] apple apple- fl appleapple [53], fl- [5456], flapple [57] apple [58] apple, apple appleapple fl apple appleapple fl apple, fl, applefl А appleа еф apple, apple apple, apple apple apple ( ), apple appleapple - appleapple apple ед ( apple apple) apple appleapple apple, apple- apple е apple apple, ее, apple appleapple- -, apple fl (rare genomic changes), apple apple fl, apple LINE apple apple, applefl -, [59] -, apple appleapple apple -, apple apple, SINE apple ( apple fl - ) apple - apple apple - fl apple applefl, apple apple appleapple fl 1 -, SINE applefl, applefl 4

8 еее SINE е 5 ец apple appleapple fl apple apple apple fl apple apple apple apple appleapple apple, fl SINE appleflfl apple applefl, apple apple appleapple apple apple applefl applefl - apple SINE - apple 3 apple appleapple apple- fl apple, apple, apple SINE apple ( apple - apple) еф, fl apple apple appleapple- appleapple appleflfl apple, applefl- apple SINE, applefl apple appleapple- appleapple apple [60] [61], - fl fl fl apple appleapple еф apple - fl apple apple appleapple ефfl fl apple -, apple, apple- applefl ( fl- apple,

9 еде едефец е ефе едееедебед ец ец ецеееде ебедец fl д fl д fl д fl д еее д д е 6 ец apple appleapple fl ецapple-sine-еее apple apple- apple SINE apple apple apple д д apple appleapple apple),, -, apple TSD ее apple- 051% apple-, fl apple Alu, fl, apple- SINE [62] ед apple - fl, apple, appleflfl apple apple apple appleapple applefl - е,, 3'- - LINE, appleapple SINE ед apple- apple - ед fl - - applefl apple apple е -apple apple apple - SINE, apple apple apple fl, applefl е, - [63] еф, apple appleapple- ID apple, Vic-1 apple Das-1 apple-, applefl е, apple apple еф apple, apple apple appleapple - ( apple fl) apple apple apple appleappleapple- appleflapple fl appleapple apple apple fl -apple LTR-appleappleapple [64] apple apple appleapple, fl,, apple - LINE ( LINE Bov-B [18, 65]), appleapple apple- apple apple appleapple ( - А apple apple SINEА appleapple [65]), - apple apple - LINE, apple apple applefl apple appleapple apple apple SINE - apple appleapple apple- appleapple [66] apple appleapple SmaI appleappleapple apple, apple, apple, apple, applefl apple - е - apple [66] apple- apple, fl, apple fl: apple appleapple- apple - apple apple, apple apple, А А apple flflfl apple, - fl apple - apple, apple apple- apple fl,, 4*

10 804 fl А«А» ецapplefl SINE fl А«+А» fl А«+А» е 7 apple apple apple apple, apple apple apple appleapple - apple apple ее apple SINE apple fl appleapple [67], apple- apple apple appleapple applefl apple apple, - Schistosoma japonicum [68, 69] ед apple apple appleapple apple apple, ( appleapple) А apple appleа [70] - apple apple apple- apple appleflfl apple applefl, SINE -, apple apple - appleapple- apple LINE еф apple, apple SINE apple apple apple appleapple ( apple apple), apple SINE fl apple, apple - apple appleapple ед fl, apple apple- SINE - fl apple е fl, appleapple : apple apple apple - apple apple ( fl SINE apple ) appleflfl apple applefl applefl apple apple- (apple 7) fl, - apple apple apple [71] ее apple- apple-, applefl apple- fl apple applefl apple apple- apple fl -, apple, appleappleapple - SINE, apple fl appleapple apple -, fl - fl fl applefl apple applefl applefl, - applefl apple еб apple apple applefl fl apple, apple flfl, apple- apple apple - fl applefl apple applefl apple apple fl - fl SINE - fl apple applefl appleapple applefl apple apple apple appleapple fl fl apple -, apple, fl fl,, apple fl apple, apple

11 еде едефец е ефе едееедебед ец ец ецеееде ебедец 805 ееецед ецефе ефеге 1 Havecker ER, Gao X, Voytas DF 2004 The diversity of LTR retrotransposons Genome Biol 5, Malik HS, Eickbush TH 2000 NeSL-1, an ancient lineage of site-specific non-ltr retrotransposons from Caenorhabditis elegans Genetics 154, Lovsin N, Gubensek F, Kordis D 2001 Evolutionary dynamics in a novel L2 clade of non-ltr retrotransposons in Deuterostomia Mol Biol Evol 18, Burke WD, Malik HS, Rich SM, et al 2002 Ancient lineages of non-ltr retrotransposons in the primitive eukaryote, Giardia lamblia Mol Biol Evol 19, Eickbush TH, Jamburuthugoda VK 2008 The diversity of retrotransposons and the properties of their reverse transcriptases Virus Res 134, Ostertag EM, Kazazian HH, Jr 2001 Biology of mammalian L1 retrotransposons Annu Rev Genet 35, Kramerov DA, Vassetzky NS 2005 Short retroposons in eukaryotic genomes Int Rev Cytol 247, Kajikawa M, Okada N 2002 LINEs mobilize SINEs in the eel through a shared 3' sequence Cell 111, Dewannieux M, Esnault C, Heidmann T 2003 LINEmediated retrotransposition of marked Alu sequences Nat Genet 35, Kramerov DA, Grigoryan AA, Ryskov AP, et al 1979 Long double-stranded sequences (dsrna-b) of nuclear pre-mrna consist of a few highly abundant classes of sequences: evidence from DNA cloning experiments Nucleic Acids Res 6, Haynes SR, Toomey TP, Leinwand L, et al 1981 The Chinese hamster Alu-equivalent sequence: a conserved highly repetitious, interspersed deoxyribonucleic acid sequence in mammals has a structure suggestive of a transposable element Mol Cell Biol 1, Krayev AS, Kramerov DA, Skryabin KG, et al 1980 The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA Nucleic Acids Res 8, Krayev AS, Markusheva TV, Kramerov DA, et al 1982 Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing Nucleic Acids Res 10, Deininger PL, Jolly DJ, Rubin CM, et al 1981 Base sequence studies of 300 nucleotide renatured repeated human DNA clones J Mol Biol 151, Ullu E, Tschudi C 1984 Alu sequences are processed 7SL RNA genes Nature 312, Kapitonov VV, Jurka J 2003 A Novel Class of SINE elements derived from 5S rrna Mol Biol Evol 20, Nishihara H, Smit AF, Okada N 2006 Functional noncoding sequences derived from SINEs in the mammalian genome Genome Res 16, Gogolevsky KP, Vassetzky NS, Kramerov DA 2008 Bov-B-mobilized SINEs in vertebrate genomes Gene 407, Haynes SR, Jelinek WR 1981 Low molecular weight RNAs transcribed in vitro by RNA polymerase III from Alu-type dispersed repeats in Chinese hamster DNA are also found in vivo Proc Natl Acad Sci USA 78, Kramerov DA, Lekakh IV, Samarina OP, et al 1982 The sequences homologous to major interspersed repeats B1 and B2 of mouse genome are present in mrna and small cytoplasmic poly(a) + RNA Nucleic Acids Res 10, Schramm L, Hernandez N 2002 Recruitment of RNA polymerase III to its target promoters Genes Dev 16, Borodulina OR, Kramerov DA 2001 Short interspersed elements (SINEs) from insectivores Two classes of mammalian SINEs distinguished by A-rich tail structure Mamm Genome 12, Borodulina OR, Kramerov DA 2008 Transcripts synthesized by RNA polymerase III can be polyadenylated in an AAUAAA-dependent manner RNA 14, Ohshima K, Hamada M, Terai Y, et al 1996 The 3' ends of trna-derived short interspersed repetitive elements are derived from the 3' ends of long interspersed repetitive elements Mol Cell Biol 16, Dewannieux M, Heidmann T 2005 L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells J Mol Biol 349, Dewannieux M, Heidmann T 2005 Role of poly(a) tail length in Alu retrotransposition Genomics 86, Luan DD, Korman MH, Jakubczak JL, et al 1993 Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non- LTR retrotransposition Cell 72, Jurka J 1997 Sequence patterns indicate an enzymatic involvement in integration of mammalian retroposons Proc Natl Acad Sci USA 94, International Human Genome Sequencing Consortium 2001 Initial sequencing and analysis of the human genome Nature 409, Batzer MA, Deininger PL 2002 Alu repeats and human genomic diversity Nat Rev Genet 3, DА»Erchia AM, Gissi C, Pesole G, et al 1996 The guinea-pig is not a rodent Nature 381, Murphy WJ, Eizirik E, OА»Brien SJ, et al 2001 Resolution of the early placental mammal radiation using Bayesian phylogenetics Science 294, Murphy WJ, Eizirik E, Johnson WE, et al 2001 Molecular phylogenetics and the origins of placental mammals Nature 409, Dunn CW, Hejnol A, Matus DQ, et al 2008 Broad phylogenomic sampling improves resolution of the animal tree of life Nature 452, apple ец, appleapple 1993 ец- appleapple 2 fl fl - 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Mol Biol Evol 20, Gogolevskaya IK, Kramerov DA 2002 Evolutionary history of 45SI RNA and indication that it is functional J Mol Evol 54, Gogolevskaya IK, Koval AP, Kramerov DA 2005 Evolutionary history of 45SH RNA Mol Biol Evol 22, Gogolevsky KP, Kramerov DA 2006 Short interspersed elements (SINEs) of the Geomyoidea superfamily rodents Gene 373, 6774