SINEs

Wiley Interdisciplinary Reviews: RNA

Volumn 2, Issue 6, 2011, Pages 772-786

  Kramerov, Dmitri A ^a   Vassetzky, Nikita S ^a  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; MESSENGER RNA; UNTRANSLATED RNA;

3' UNTRANSLATED REGION; GENE AMPLIFICATION; GENE EXPRESSION; GENE INTERACTION; GENE SEQUENCE; GENETIC CODE; HUMAN; NONHUMAN; NUCLEIC ACID STRUCTURE; PARASITE; POLYADENYLATION; PRIORITY JOURNAL; REVERSE TRANSCRIPTION; REVIEW; RNA PROCESSING; RNA SPLICING; SHORT INTERSPERSED ELEMENT; SYMBIONT; TRANSCRIPTION REGULATION; ANIMAL; BIOLOGICAL MODEL; GENETIC TRANSCRIPTION; GENETICS; HOST PARASITE INTERACTION; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; PHYSIOLOGY; SHORT INTERSPERSED REPEAT; SYMBIOSIS;

EUKARYOTA;

ANIMALS; EVOLUTION, MOLECULAR; HOST-PARASITE INTERACTIONS; HUMANS; MODELS, GENETIC; PHYLOGENY; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA SPLICING; RNA, MESSENGER; RNA, UNTRANSLATED; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS; SYMBIOSIS; TRANSCRIPTION, GENETIC;

EID: 84856514080     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.91     Document Type: Review

References (112)

1. Krayev AS, Kramerov DA, Skryabin KG, Ryskov AP, Bayev AA, Georgiev GP. The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of mouse fold-back RNA. Nucleic Acids Res 1980, 8:1201-1215.
2. Krayev AS, Markusheva TV, Kramerov DA, Ryskov AP, Skryabin KG, Bayev AA, Georgiev GP. Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing. Nucleic Acids Res 1982, 10:7461-7475.
3. Deininger PL, Jolly DJ, Rubin CM, Friedmann T, Schmid CW. Base sequence studies of 300 nucleotide renatured repeated human DNA clones. J Mol Biol 1981, 151:17-33.
4. Babushok DV, Kazazian HH Jr. Progress in understanding the biology of the human mutagen LINE-1. Hum Mutat 2007, 28:527-539.
5. Luan DD, Korman MH, Jakubczak JL, Eickbush TH. Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Cell 1993, 72:595-605.
6. Bailey JA, Liu G, Eichler EE. An Alu transposition model for the origin and expansion of human segmental duplications. Am J Hum Genet 2003, 73:823-834.
7. Eickbush T, Malik H. Origins and evolution of retrotransposons. In: Craig NL, Craigie R, Gellert M, Lambowitz AL, eds. Mobile DNA II. Washington, DC: ASM Press; 2002, 1111-1144.
8. Lovsin N, Gubensek F, Kordis D. Evolutionary dynamics in a novel L2 clade of non-LTR retrotransposons in Deuterostomia. Mol Biol Evol 2001, 18:2213-2224.
9. Eickbush TH, Jamburuthugoda VK. The diversity of retrotransposons and the properties of their reverse transcriptases. Virus Res 2008, 134:221-234.
10. Ostertag EM, Kazazian HH Jr. Biology of mammalian L1 retrotransposons. Annu Rev Genet 2001, 35:501-538.
11. Deragon JM, Zhang X. Short interspersed elements (SINEs) in plants: origin, classification, and use as phylogenetic markers. Syst Biol 2006, 55:949-956.
12. Kramerov DA, Vassetzky NS. Short retroposons in eukaryotic genomes. Int Rev Cytol 2005, 247:165-221.
13. Nishihara H, Terai Y, Okada N. Characterization of novel Alu- and tRNA-related SINEs from the tree shrew and evolutionary implications of their origins. Mol Biol Evol 2002, 19:1964-1972.
14. Vassetzky NS, Ten OA, Kramerov DA. B1 and related SINEs in mammalian genomes. Gene 2003, 319:149-160.
15. Zietkiewicz E, Richer C, Sinnett D, Labuda D. Monophyletic origin of Alu elements in primates. J Mol Evol 1998, 47:172-182.
16. Kapitonov VV, Jurka J. A novel class of SINE elements derived from 5S rRNA. Mol Biol Evol 2003, 20:694-702.
17. Nishihara H, Smit AF, Okada N. Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res 2006, 16:864-874.
18. Gogolevsky KP, Vassetzky NS, Kramerov DA. 5S rRNA-derived and tRNA-derived SINEs in fruit bats. Genomics 2009, 93:494-500.
19. Gogolevsky KP, Vassetzky NS, Kramerov DA. Bov-B-mobilized SINEs in vertebrate genomes. Gene 2008, 407:75-85.
20. Gilbert N, Labuda D. CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs. Proc Natl Acad Sci U S A 1999, 96:2869-2874.
21. 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, 12:316-324.
22. Akasaki T, Nikaido M, Nishihara H, Tsuchiya K, Segawa S, Okada N. Characterization of a novel SINE superfamily from invertebrates: "Ceph-SINEs" from the genomes of squids and cuttlefish. Gene 2010, 454:8-19.
23. Ohshima K, Hamada M, Terai Y, Okada N. The 3′ ends of tRNA-derived short interspersed repetitive elements are derived from the 3′ ends of long interspersed repetitive elements. Mol Cell Biol 1996, 16:3756-3764.
24. Okada N, Hamada M. The 3′ ends of tRNA-derived SINEs originated from the 3′ ends of LINEs: a new example from the bovine genome. J Mol Evol 1997, 44:52-56.
25. Kajikawa M, Okada N. LINEs mobilize SINEs in the eel through a shared 3′ sequence. Cell 2002, 111:433-444.
26. Kramerov D, Vassetzky N, Serdobova I. The evolutionary position of dormice (Gliridae) in Rodentia determined by a novel short retroposon. Mol Biol Evol 1999, 16:715-717.
27. Veniaminova NA, Vassetzky NS, Kramerov DA. B1 SINEs in different rodent families. Genomics 2007, 89:678-686.
28. Nishihara H, Satta Y, Nikaido M, Thewissen JG, Stanhope MJ, Okada N. A retroposon analysis of Afrotherian phylogeny. Mol Biol Evol 2005, 22:1823-1833.
29. Shedlock AM, Okada N. SINE insertions: powerful tools for molecular systematics. Bioessays 2000, 22:148-160.
30. Nishihara H, Okada N. Retroposons: genetic footprints on the evolutionary paths of life. Methods Mol Biol 2008, 422:201-225.
31. Perna NT, Batzer MA, Deininger PL, Stoneking M. Alu insertion polymorphism: a new type of marker for human population studies. Hum Biol 1992, 64:641-648.
32. Churakov G, Sadasivuni MK, Rosenbloom KR, Huchon D, Brosius J, Schmitz J. Rodent evolution: back to the root. Mol Biol Evol 2010, 27:1315-1326.
33. Murata S, Takasaki N, Saitoh M, Okada N. Determination of the phylogenetic relationships among Pacific salmonids by using short interspersed elements (SINEs) as temporal landmarks of evolution. Proc Natl Acad Sci U S A 1993, 90:6995-6999.
34. Nikaido M, Rooney AP, Okada N. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interpersed elements: Hippopotamuses are the closest extant relatives of whales. Proc Natl Acad Sci U S A 1999, 96:10261-10266.
35. Kramerov DA, Grigoryan AA, Ryskov AP, Georgiev GP. 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 1979, 6:697-713.
36. Lev-Maor G, Sorek R, Levanon EY, Paz N, Eisenberg E, Ast G. RNA-editing-mediated exon evolution. Genome Biol 2007, 8:R29.
37. Chesnokov I, Schmid CW. Flanking sequences of an Alu source stimulate transcription in vitro by interacting with sequence-specific transcription factors. J Mol Evol 1996, 42:30-36.
38. Arnaud P, Yukawa Y, Lavie L, Pelissier T, Sugiura M, Deragon JM. Analysis of the SINE S1 Pol III promoter from Brassica; impact of methylation and influence of external sequences. Plant J 2001, 26:295-305.
39. Schramm L, Hernandez N. Recruitment of RNA polymerase III to its target promoters. Genes Dev 2002, 16:2593-2620.
40. Endoh H, Okada N. Total DNA transcription in vitro: a procedure to detect highly repetitive and transcribable sequences with tRNA-like structures. Proc Natl Acad Sci U S A 1986, 83:251-255.
41. Matsumoto K, Takii T, Okada N. Characterization of a new termination signal for RNA polymerase III responsible for generation of a discrete-sized RNA transcribed from salmon total genomic DNA in a HeLa cell extract. J Biol Chem 1989, 264:1124-1131.
42. Mochizuki K, Umeda M, Ohtsubo H, Ohtsubo E. Characterization of a plant SINE, p-SINE1, in rice genomes. Jpn J Genet 1992, 67:155-166.
43. Liu WM, Chu WM, Choudary PV, Schmid CW. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res 1995, 23:1758-1765.
44. Bachvarova R. Small B2 RNAs in mouse oocytes, embryos, and somatic tissues. Dev Biol 1988, 130:513-523.
45. Kim J, Kass DH, Deininger PL. Transcription and processing of the rodent ID repeat family in germline and somatic cells. Nucleic Acids Res 1995, 23:2245-2251.
46. Grigoryan MS, Kramerov DA, Tulchinsky EM, Revasova ES, Lukanidin EM. Activation of putative transposition intermediate formation in tumor cells. EMBO J 1985, 4:2209-2215.
47. White RJ, Stott D, Rigby PW. Regulation of RNA polymerase III transcription in response to Simian virus 40 transformation. EMBO J 1990, 9:3713-3721.
48. Borodulina OR, Kramerov DA. Short interspersed elements (SINEs) from insectivores. Two classes of mammalian SINEs distinguished by A-rich tail structure. Mamm Genome 2001, 12:779-786.
49. Kramerov DA, Tillib SV, Shumyatsky GP, Georgiev GP. The most abundant nascent poly(A) + RNAs are transcribed by RNA polymerase III in murine tumor cells. Nucleic Acids Res 1990, 18:4499-4506.
50. Borodulina OR, Kramerov DA. Transcripts synthesized by RNApolymerase III can be polyadenylated in an AAUAAA-dependent manner. RNA 2008, 14:1865-1873.
51. Roy-Engel AM, El-Sawy M, Farooq L, Odom GL, Perepelitsa-Belancio V, Bruch H, Oyeniran OO, Deininger PL. Human retroelements may introduce intragenic polyadenylation signals. Cytogenet Genome Res 2005, 110:365-371.
52. Muddashetty R, Khanam T, Kondrashov A, Bundman M, Iacoangeli A, Kremerskothen J, Duning K, Barnekow A, Huttenhofer A, Tiedge H, et al. Poly(A)-binding protein is associated with neuronal BC1 and BC200 ribonucleoprotein particles. J Mol Biol 2002, 321:433-445.
53. West N, Roy-Engel AM, Imataka H, Sonenberg N, Deininger P. Shared protein components of SINE RNPs. J Mol Biol 2002, 321:423-432.
54. Dewannieux M, Heidmann T. L1-mediated retrotransposition of murine B1 and B2 SINEs recapitulated in cultured cells. J Mol Biol 2005, 349:241-247.
55. Shumyatsky GP, Tillib SV, Kramerov DA. B2 RNA and 7SK RNA, RNA polymerase III transcripts, have a cap-like structure at their 5′ end. Nucleic Acids Res 1990, 18:6347-6351.
56. Shumyatsky G, Shimba S, Reddy R. Capping signals correspond to the 5′ end in four eukaryotic small RNAs containing gamma-monomethylphosphate cap structure. Gene Expr 1994, 4:29-41.
57. Shimba S, Reddy R. Purification of human U6 small nuclear RNA capping enzyme. Evidence for a common capping enzyme for gamma-monomethyl-capped small RNAs. J Biol Chem 1994, 269:12419-12423.
58. Shumyatsky G, Wright D, Reddy R. Methylphosphate cap structure increases the stability of 7SK, B2 and U6 small RNAs in Xenopus oocytes. Nucleic Acids Res 1993, 21:4756-4761.
59. Matsumoto K, Murakami K, Okada N. Pseudouridylic modification of a 6S RNA transcribed in vitro from highly repetitive and transcribable (Hirt) sequences of salmon total DNA. Biochem Biophys Res Commun 1984, 124:514-522.
60. Sakamoto K, Okada N. 5-Methylcytidylic modification of in vitro transcript from the rat identifier sequence; evidence that the transcript forms a tRNA-like structure. Nucleic Acids Res 1985, 13:7195-7206.
61. Rozhdestvensky TS, Crain PF, Brosius J. Isolation and posttranscriptional modification analysis of native BC1 RNA from mouse brain. RNA Biol 2007, 4:11-15.
62. Sun FJ, Fleurdepine S, Bousquet-Antonelli C, Caetano-Anolles G, Deragon JM. Common evolutionary trends for SINE RNA structures. Trends Genet 2007, 23:26-33.
63. Neeman Y, Levanon EY, Jantsch MF, Eisenberg E. RNA editing level in the mouse is determined by the genomic repeat repertoire. RNA 2006, 12: 1802-1809.
64. Dewannieux M, Esnault C, Heidmann T. LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 2003, 35:41-48.
65. Doolittle WF, Sapienza C. Selfish genes, the phenotype paradigm and genome evolution. Nature 1980, 284:601-603.
66. Orgel LE, Crick FH. Selfish DNA: the ultimate parasite. Nature 1980, 284:604-607.
67. Belancio VP, Hedges DJ, Deininger P. Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. Genome Res 2008, 18:343-358.
68. Cordaux R, Hedges DJ, Herke SW, Batzer MA. Estimating the retrotransposition rate of human Alu elements. Gene 2006, 373:134-137.
69. Batzer MA, Deininger PL. Alu repeats and human genomic diversity. Nat Rev Genet 2002, 3:370-379.
70. Konkel MK, Batzer MA. A mobile threat to genome stability: the impact of non-LTR retrotransposons upon the human genome. Semin Cancer Biol 2010, 20:211-221.
71. Kaneko H, Dridi S, Tarallo V, Gelfand BD, Fowler BJ, Cho WG, Kleinman ME, Ponicsan SL, Hauswirth WW, Chiodo VA, et al. DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature 2011, 471:325-330.
72. Kato Y, Kaneda M, Hata K, Kumaki K, Hisano M, Kohara Y, Okano M, Li E, Nozaki M, Sasaki H. Role of the Dnmt3 family in de novo methylation of imprinted and repetitive sequences during male germ cell development in the mouse. Hum Mol Genet 2007, 16:2272-2280.
73. Hulme AE, Bogerd HP, Cullen BR, Moran JV. Selective inhibition of Alu retrotransposition by APOBEC3G. Gene 2007, 390:199-205.
74. Khatua AK, Taylor HE, Hildreth JE, Popik W. Inhibition of LINE-1 and Alu retrotransposition by exosomes encapsidating APOBEC3G and APOBEC3F. Virology 2010, 400:68-75.
75. Ohshima K, Hattori M, Yada T, Gojobori T, Sakaki Y, Okada N. Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates. Genome Biol 2003, 4:R74.
76. Quentin Y. Successive waves of fixation of B1 variants in rodent lineage history. J Mol Evol 1989, 28:299-305.
77. Makalowski W. Genomic scrap yard: how genomes utilize all that junk. Gene 2000, 259:61-67.
78. Babich V, Aksenov N, Alexeenko V, Oei SL, Buchlow G, Tomilin N. Association of some potential hormone response elements in human genes with the Alu family repeats. Gene 1999, 239:341-349.
79. Laperriere D, Wang TT, White JH, Mader S. Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution. BMC Genomics 2007, 8:23.
80. Sasaki T, Nishihara H, Hirakawa M, Fujimura K, Tanaka M, Kokubo N, Kimura-Yoshida C, Matsuo I, Sumiyama K, Saitou N, et al. Possible involvement of SINEs in mammalian-specific brain formation. Proc Natl Acad Sci U S A 2008, 105:4220-4225.
81. Hirakawa M, Nishihara H, Kanehisa M, Okada N. Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes. Gene 2009, 441:100-110.
82. Lunyak VV, Prefontaine GG, Nunez E, Cramer T, Ju BG, Ohgi KA, Hutt K, Roy R, Garcia-Diaz A, Zhu X, et al. Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science 2007, 317:248-251.
83. Sorek R, Ast G, Graur D. Alu-containing exons are alternatively spliced. Genome Res 2002, 12: 1060-1067.
84. Pattanakitsakul S, Zheng JH, Natsuume-Sakai S, Takahashi M, Nonaka M. Aberrant splicing caused by the insertion of the B2 sequence into an intron of the complement C4 gene is the basis for low C4 production in H-2k mice. J Biol Chem 1992, 267:7814-7820.
85. Shimamura M, Nikaido M, Ohshima K, Okada N. A SINE that acquired a role in signal transduction during evolution. Mol Biol Evol 1998, 15:923-925.
86. Vorechovsky I. Transposable elements in disease-associated cryptic exons. Hum Genet 2010, 127:135-154.
87. Moller-Krull M, Zemann A, Roos C, Brosius J, Schmitz J. Beyond DNA: RNA editing and steps toward Alu exonization in primates. J Mol Biol 2008, 382:601-609.
88. Ryskov AP, Ivanov PL, Kramerov DA, Georgiev GP. Mouse ubiquitous B2 repeat in polysomal and cytoplasmic poly(A)+RNAs: uniderectional orientation and 3′-end localization. Nucleic Acids Res 1983, 11:6541-6558.
89. Lee JY, 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, 36:5581-5590.
90. Gogolevskaya IK, Kramerov DA. Evolutionary history of 4.5SI RNA and indication that it is functional. J Mol Evol 2002, 54:354-364.
91. Martignetti JA, Brosius J. Neural BC1 RNA as an evolutionary marker: guinea pig remains a rodent. Proc Natl Acad Sci U S A 1993, 90:9698-9702.
92. Kim J, Martignetti JA, Shen MR, Brosius J, Deininger P. Rodent BC1 RNA gene as a master gene for ID element amplification. Proc Natl Acad Sci U S A 1994, 91:3607-3611.
93. Lin D, Pestova TV, Hellen CU, Tiedge H. Translational control by a small RNA: dendritic BC1 RNA targets the eukaryotic initiation factor 4A helicase mechanism. Mol Cell Biol 2008, 28:3008-3019.
94. Gogolevskaya IK, Kramerov DA. 4.5SI RNA genes and the role of their 5′-flanking sequences in the gene transcription. Gene 2010, 451:32-37.
95. Gogolevskaya IK, Koval AP, Kramerov DA. Evolutionary history of 4.5SH RNA. Mol Biol Evol 2005, 22:1546-1554.
96. Schoeniger LO, Jelinek WR. 4.5S RNA is encoded by hundreds of tandemly linked genes, has a short half-life, and is hydrogen bonded in vivo to poly(A)-terminated RNAs in the cytoplasm of cultured mouse cells. Mol Cell Biol 1986, 6:1508-1519.
97. Parrott AM, Tsai M, Batchu P, Ryan K, Ozer HL, Tian B, Mathews MB. The evolution and expression of the snaR family of small non-coding RNAs. Nucleic Acids Res 2011, 39:1485-1500.
98. Borchert GM, Lanier W, Davidson BL. RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol 2006, 13:1097-1101.
99. Gu TJ, Yi X, Zhao XW, Zhao Y, Yin JQ. Alu-directed transcriptional regulation of some novel miRNAs. BMC Genomics 2009, 10:563.
100. Pouch-Pelissier MN, Pelissier T, Elmayan T, Vaucheret H, Boko D, Jantsch MF, Deragon JM. SINE RNA induces severe developmental defects in Arabidopsis thaliana and interacts with HYL1 (DRB1), a key member of the DCL1 complex. PLoS Genet 2008, 4:e1000096.
101. Chu WM, Ballard R, Carpick BW, Williams BR, Schmid CW. Potential Alu function: regulation of the activity of double-stranded RNA-activated kinase PKR. Mol Cell Biol 1998, 18:58-68.
102. Hasler J, Strub K. Alu RNP and Alu RNA regulate translation initiation in vitro. Nucleic Acids Res 2006, 34:2374-2385.
103. Rubin CM, Kimura RH, Schmid CW. Selective stimulation of translational expression by Alu RNA. Nucleic Acids Res 2002, 30:3253-3261.
104. Allen TA, Von Kaenel S, Goodrich JA, Kugel JF. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nat Struct Mol Biol 2004, 11:816-821.
105. Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 2008, 29:499-509.
106. Ponicsan SL, Kugel JF, Goodrich JA. Genomic gems: SINE RNAs regulate mRNA production. Curr Opin Genet Dev 2010, 20:149-155.
107. Espinoza CA, Allen TA, Hieb AR, Kugel JF, Goodrich JA. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat Struct Mol Biol 2004, 11:822-829.
108. Gong C, Maquat LE. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature 2011, 470:284-288.
109. Belancio VP, Roy-Engel AM, Deininger PL. All y'all need to know ';bout retroelements in cancer. Semin Cancer Biol 2010, 20:200-210.
110. Kramerov DA, Vassetzky NS. Short retroposons in eukaryotic genomes. Int Rev Cytol 2005, 247:165-221.
111. Kramerov DA, Vassetzky NS. Origin and evolution of SINEs in eukaryotic genomes. Heredity 2011, doi: 10.1038/hdy.2011.43.
112. Shedlock AM, Okada N. SINE insertions: powerful tools for molecular systematics. Bioessays 2000, 22:148-160.