SINEs as driving forces in genome evolution

Genome Dynamics

Volumn 7, Issue , 2012, Pages 92-107

  Schmitz, J ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; DOUBLE STRANDED RNA; MESSENGER RNA; MESSENGER RNA PRECURSOR; NUCLEAR FACTOR; PIWI PROTEIN; PROTEIN NUCLEAR PRELAMIN A RECOGNITION FACTOR; RIBOSOME RNA; RNA POLYMERASE II; SIGNAL RECOGNITION PARTICLE; SMALL NUCLEOLAR RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA; ZINC FINGER PROTEIN; ZINC FINGER PROTEIN 639; RNA;

ARTHROPOD; ARTICLE; DNA METHYLATION; DOWN REGULATION; ECHINODERM; ENDOGENOUS RETROVIRUS; EUCHROMATIN; EVOLUTION; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE INSERTION; GENE REARRANGEMENT; GENE REGULATORY NETWORK; GENETIC CONSERVATION; GENETIC TRANSCRIPTION; HOMOLOGOUS RECOMBINATION; HOST CELL; HOUSEKEEPING GENE; HUMAN; HUMAN GENOME; INTRON; LAST COMMON ANCESTOR; LEMURIDAE; LIVING FOSSIL; LIZARD; LONG INTERSPERSED REPEAT; MARSUPIAL; MONOTREMATE; MULTIGENE FAMILY; NEMATODE; NONHUMAN; PLANT GENOME; PLATYHELMINTH; PLATYPUS; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; PSEUDOGENE; RETROPOSON; RNA EDITING; RNA INTERFERENCE; SEGMENTAL DUPLICATION; SHORT INTERSPERSED REPEAT; TAENIOPYGIA GUTTATA; TRANSPOSON; ZEBRA FISH; ANIMAL; GENETIC HETEROGENEITY; GENETIC SELECTION; GENETICS; GENOME; GENOME SIZE; MAMMAL; PHYLOGENY; REVERSE TRANSCRIPTION; REVIEW;

EUKARYOTA; MAMMALIA;

ANIMALS; BIOLOGICAL EVOLUTION; GENE EXPRESSION REGULATION; GENETIC HETEROGENEITY; GENOME; GENOME SIZE; HUMANS; LONG INTERSPERSED NUCLEOTIDE ELEMENTS; MAMMALS; PHYLOGENY; REVERSE TRANSCRIPTION; RNA; SELECTION, GENETIC; SHORT INTERSPERSED NUCLEOTIDE ELEMENTS;

EID: 84866457101     PISSN: 16609263     EISSN: 16623797     Source Type: Book Series    
DOI: 10.1159/000337117     Document Type: Article

References (61)

1. Singer MF: SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell 1982;28:433-434.
2. Ludwig A, Rozhdestvensky TS, Kuryshev VY, Schmitz J, Brosius J: An unusual primate locus that attracted two independent Alu insertions and facilitates their transcription. J Mol Biol 2005;350:200-214.
3. Kramerov DA, Vassetzky NS: SINEs. Wiley Inter-discip Rev RNA 2011;2:772-786.
4. Smit AF, Riggs AD: MIRs are classic, tRNA-derived SINEs that amplified before the mammalian radiation. Nucleic Acids Res 1995;23:98-102.
5. 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.
6. Houck CM, Rinehart F P, Schmid CW: A ubiquitous family of repeated DNA sequences in the human genome. J Mol Biol 1979;132:289-306.
7. Kramerov DA, Vassetzky NS: Short retroposons in eukaryotic genomes. Int Rev Cytol 2005;247:165-221.
8. Hancks DC, Goodier JL, Mandal PK, Cheung LE, Kazazian HH Jr: Retrotransposition of marked SVA elements by human L1s in cultured cells. Hum Mol Genet 2011;20:3386-3400.
9. Wang H, Xing J, Grover D, Hedges DJ, Han K, et al: SVA elements: a hominid-specific retroposon family. J Mol Biol 2005;354:994-1007.
10. Quentin Y: The Alu family developed through successive waves of fixation closely connected with primate lineage history. J Mol Evol 1988;27:194-202.
11. Kapitonov VV, Pavlicek A, Jurka J: Anthology of human repetitive DNA; in Weinheim RAM (ed): Encyclopedia of Molecular Cell Biology and Molecular Medicine. Wiley-VCH, 2004, pp 251-305.
12. Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL: Diverse cis factors controlling Alu retrotranspo-sition: what causes Alu elements to die? Genome Res 2009;19:545-555.
13. Kazazian HH Jr: Mobile elements: drivers of genome evolution. Science 2004;303:1626-1632.
14. Nilsson MA, Churakov G, Sommer M, Tran N V, Zemann A, et al: Tracking marsupial evolution using archaic genomic retroposon insertions. PLoS Biol 2010;8:e1000436.
15. Smit AF: Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 1999;9:657-663.
16. Jurka J: Sequence patterns indicate an enzymatic involvement in integration of mammalian retropo-sons. Proc Natl Acad Sci USA 1997;94:1872-1877.
17. Nigumann P, Redik K, Matlik K, Speek M: Many human genes are transcribed from the antisense promoter of L1 retrotransposon. Genomics 2002; 79:628-634.
18. Graham T, Boissinot S: The genomic distribution of L1 elements: the role of insertion bias and natural selection. J Biomed Biotech 2006;2006:75327.
19. Belle EM, Webster MT, Eyre-Walker A: Why are young and old repetitive elements distributed differently in the human genome? J Mol Evol 2005; 60:290-296.
20. SanMiguel P, Tikhonov A, Jin YK, Motchoulskaia N, Zakharov D, et al: Nested retrotransposons in the intergenic regions of the maize genome. Science 1996;274:765-768.
21. Schmitz J, Churakov G, Zischler H, Brosius J: A novel class of mammalian-specific tailless ret-ropseudogenes. Genome Res 2004;14:1911-1915.
22. Schmitz J, Zemann A, Churakov G, Kuhl H, Grutzner F, et al: Retroposed SNOfall-a mammalian-wide comparison of platypus snoRNAs. Genome Res 2008;18:1005-1010.
23. Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, et al: Genome analysis of the platypus reveals unique signatures of evolution. Nature 2008;453:175-183.
24. Mandal PK, Kazazian HH Jr: SnapShot: vertebrate transposons. Cell 2008;135:192-192.e1.
25. Piskurek O, Austin CC, Okada N: Sauria SINEs: novel short interspersed retroposable elements that are widespread in reptile genomes. J Mol Evol 2006;62:630-644.
26. Alfoldi J, Di Palma F, Grabherr M, Williams C, Kong L, et al: The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 2011;477:587-591.
27. Izsvak Z, Ivics Z, Garcia-Estefania D, Fahrenkrug SC, Hackett PB: DANA elements: a family of composite, tRNA-derived short interspersed DNA elements associated with mutational activities in zebrafish (Danio rerio). Proc Natl Acad Sci USA 1996;93:1077-1081.
28. Callinan PA, Batzer MA: Retrotransposable elements and human disease. Genome Dyn 2006;1:104-115.
29. Xing J, Zhang Y, Han K, Salem AH, Sen SK, et al: Mobile elements create structural variation: analysis of a complete human genome. Genome Res 2009; 19:1516-1526.
30. 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.
31. Liu G, Zhao S, Bailey JA, Sahinalp SC, Alkan C, et al: Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res 2003;13:358-368.
32. Kazazian HH Jr: Mobile elements and disease. Curr Opin Genet Dev 1998;8:343-350.
33. Bartolome C, Maside X, Charlesworth B: On the abundance and distribution of transposable elements in the genome of Drosophila melanogaster. Mol Biol Evol 2002;19:926-937.
34. Jordan IK, Rogozin IB, Glazko GV, Koonin EV: Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet 2003;19:68-72.
35. Lunyak V V, Prefontaine GG, Nunez E, Cramer T, Ju BG, et al: Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organo-genesis. Science 2007;317:248-251.
36. Conley AB, Miller WJ, Jordan IK: Human cis natural antisense transcripts initiated by transposable elements. Trends Genet 2008;24:53-56.
37. Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, et al: Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 2008;29:499-509.
38. Ferrigno O, Virolle T, Djabari Z, Ortonne J P, White RJ, Aberdam D: Transposable B2 SINE elements can provide mobile RNA polymerase II promoters. Nat Genet 2001;28:77-81.
39. Slotkin RK, Martienssen R: Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 2007;8:272-285.
40. Xie H, Wang M, Bonaldo Mde F, Rajaram V, Stellpflug W, et al: Epigenomic analysis of Alu repeats in human ependymomas. Proc Natl Acad Sci USA 2010;107:6952-6957.
41. Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, et al: Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res 2007;17:992-1004.
42. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, et al: A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 2006;441:87-90.
43. Nishihara H, Smit AF, Okada N: Functional non-coding sequences derived from SINEs in the mammalian genome. Genome Res 2006;16:864-874.
44. Okada N, Sasaki T, Shimogori T, Nishihara H: Emergence of mammals by emergency: exaptation. Genes Cells 2010;15:801-812.
45. DeChiara TM, Brosius J: Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content. Proc Natl Acad Sci USA 1987;84:2624-2628.
46. 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 USA 1994; 91:3607-3611.
47. Gilbert N, Labuda D: CORE-SINEs: eukaryotic short interspersed retroposing elements with common sequence motifs. Proc Natl Acad Sci USA 1999;96:2869-2874.
48. Santangelo AM, de Souza FS, Franchini LF, Bumaschny VF, Low MJ, Rubinstein M: Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene. PLoS Genet 2007; 3:1813-1826.
49. Sela N, Mersch B, Gal-Mark N, Lev-Maor G, Hotz-Wagenblatt A, Ast G: Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol 2007;8:R127.
50. Brosius J, Gould SJ: On 'genomenclature': a comprehensive (and respectful) taxonomy for pseudogenes and other 'junk DNA Proc Natl Acad Sci USA 1992;89:10706-10710.
51. Krull M, Petrusma M, Makalowski W, Brosius J, Schmitz J: Functional persistence of exonized mammalian-wide interspersed repeat elements (MIRs). Genome Res 2007;17:1139-1145.
52. Lev-Maor G, Sorek R, Shomron N, Ast G: The birth of an alternatively spliced exon:3' splice-site selection in Alu exons. Science 2003;300:1288-1291.
53. Gerber A, O'Connell MA, Keller W: Two forms of human double-stranded RNA-specific editase 1 (hRED1) generated by the insertion of an Alu cassette. RNA 1997;3:453-463.
54. Lev-Maor G, Sorek R, Levanon EY, Paz N, Eisenberg E, Ast G: RNA-editing-mediated exon evolution. Genome Biol 2007;8:R29.
55. Möller-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.
56. Sakurai M, Yano T, Kawabata H, Ueda H, Suzuki T: Inosine cyanoethylation identifies A-to-I RNA editing sites in the human transcriptome. Nat Chem Biol 2010;6:733-740.
57. Sorek R: The birth of new exons: mechanisms and evolutionary consequences. RNA 2007;13:1603-1608.
58. Rollins RA, Haghighi F, Edwards JR, Das R, Zhang MQ, et al: Large-scale structure of genomic methy-lation patterns. Genome Res 2006;16:157-163.
59. Beauregard A, Curcio MJ, Belfort M: The take and give between retrotransposable elements and their hosts. Ann Rev Genet 2008;42:587-617.
60. Soifer HS, Zaragoza A, Peyvan M, Behlke MA, Rossi JJ: A potential role for RNA interference in controlling the activity of the human LINE-1 retrotranspo-son. Nucleic Acids Res 2005;33:846-856.
61. Houwing S, Kamminga LM, Berezikov E, Cronembold D, Girard A, et al: A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell 2007;129:69-82.