Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs

Wiley Interdisciplinary Reviews: RNA

Volumn 5, Issue 5, 2014, Pages 591-600

  Matylla Kulinska, Katarzyna ^a   Tafer, Hakim ^a   Weiss, Adam ^a   Schroeder, Renée ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

SATELLITE RNA; SIGNAL RECOGNITION PARTICLE; SMALL NUCLEAR RNA; SMALL NUCLEOLAR RNA; TRANSFER RNA; UNTRANSLATED RNA; 7SL RNA; RETROPOSON; SMALL CYTOPLASMIC RNA; U1 SMALL NUCLEAR RNA;

ALU SEQUENCE; ARTICLE; CHROMOSOME STRUCTURE; ENZYME ACTIVITY; GENE AMPLIFICATION; GENE CONVERSION; GENE FUNCTION; HUMAN; HYPOTHESIS; LONG TERMINAL REPEAT; PRIORITY JOURNAL; RESERVOIR; RETROPOSON; RNA SEQUENCE; SHORT INTERSPERSED REPEAT; SHORT TANDEM REPEAT; GENETICS; HUMAN GENOME;

GENOME, HUMAN; HUMANS; RETROELEMENTS; RNA, SATELLITE; RNA, SMALL CYTOPLASMIC; RNA, SMALL NUCLEAR; RNA, TRANSFER; RNA, UNTRANSLATED; SIGNAL RECOGNITION PARTICLE;

EID: 84906265458     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.1243     Document Type: Article

References (88)

1. The ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816.
2. Jason de Koning AP, Gu W, Castoe TA, Batzer MA, Pollock DD. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet 2011, 7:e1002384.
3. Cordaux R, Hedges DJ, Herke SW, Batzer M. Estimating the retrotransposition rate of human Alu elements. Gene 2006, 373:134-137.
4. McDonald JF. Transposable elements: possible catalysts of organismic evolution. Trends Ecol Evol 1995, 10:123-126.
5. Kazazian HH. Mobile elements: drivers of genome evolution. Science 2004, 303:1626-1632.
6. Makalowski W. Genomic scrap yard: how genomes utilize all that junk. Gene 2000, 259:61-67.
7. Kramerov DA, Vassetzky NS. SINEs. Wiley Interdiscip Rev RNA 2011, 2:772-786.
8. Volff JN. Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. Bioessays 2006, 28:913-922.
9. Brosius J. RNAs from all categories generate retrosequences that may be exapted as novel genes or regulatory elements. Gene 1999, 238:115-134.
10. Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J, Devon K. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
11. Waring M, Britten RJ. Nucleotide sequence repetition: a rapidly reassociating fraction of mouse DNA. Science 1966, 154:791-794.
12. Weber JL. Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms. Genomics 1990, 7:524-530.
13. Pheasant M, Mattick JS. Raising the estimate of functional human sequences. Genome Res 2007, 17:1245-1253.
14. Doolittle WF. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA 2013, 110:5294-5300.
15. Mattick JS, Dinger ME. The extent of functionality in the human genome. Hugo J 2013, 7:2.
16. Kazazian HH. Mobile elements: drivers of genome evolution. Science 2004, 303:1626-1632.
17. Ullu E, Tschudi C. Alu sequences are processed 7SL RNA genes. Nature 1984, 312:171-172.
18. Quentin Y. Fusion of monomer a free left Alu monomer and a free right Alu at the origin of the Alu family in the primate. Nucleic Acids Res 1992, 20:487-493.
19. Quentin Y. A master sequence related to a free left Alu monomer (FLAM) at the origin of the B1 family in rodent genomes. Nucleic Acids Res 1994, 22:2222-2227.
20. Jurka J. Evolutionary impact of human Alu repetitive elements. Curr Opin Genet Dev 2004, 14:603-608.
21. Veniaminova NA, Vassetzky NS, Kramerov DA. B1 SINEs in different rodent families. Genomics 2007, 89:678-686.
22. 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.
23. 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.
24. Sorek R, Ast G, Graur D. Alu-containing exons are alternatively spliced. Genome Res 2002, 12:1060-1067.
25. Singer SS, Männel DN, Hehlgans T, Brosius J, Schmitz J. From "junk" to gene: curriculum vitae of a primate receptor isoform gene. J Mol Biol 2004, 341:883-886.
26. Kramerov DA, Vassetzky NS. Origin and evolution of SINEs in eukaryotic genomes. Heredity (Edinb) 2011, 107:487-495.
27. Tsirigos A, Rigoutsos I. Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes. PLoS Comput Biol 2009, 5:e1000610.
28. Wei W, Gilbert N, Ooi SL, Lawler JF, Ostertag EM, Kazazian HH, Boeke JD, Moran JV. Human L1 retrotransposition: cis preference versus trans complementation. Mol Cell Biol 2001, 21:1429-1439.
29. Vassetzky NS, Kramerov DA. SINEBase: a database and tool for SINE analysis. Nucleic Acids Res 2013, 41:D83-D89.
30. Okada N. SINEs. Curr Opin Genet Dev 1991, 1:498-504.
31. Lin D, Pestova TV, Hellen CUT, 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.
32. Taylor BA, Navin A, Skryabin BV, Brosius J. Localization of the mouse gene (Bc1) encoding neural BC1 RNA near the fibroblast growth factor 3 locus (Fgf3) on distal chromosome 7. Genomics 1997, 44:153-154.
33. Martignetti JA, Brosius J. BC1 RNA: transcriptional analysis of a neural cell-specific RNA polymerase III transcript. Mol Cell Biol 1995, 15:1642-1650.
34. Kramerov DA, Grigoryan A, Ryskov A, Georgiev G. 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.
35. Fornace AJ, Mitchell JB. Induction of B2 RNA polymerase III transcription by heat shock: enrichment for heat shock induced sequences in rodent cells by hybridization subtraction. Nucleic Acids Res 1986, 14:5793-5811.
36. Daniels GR, Deininger PL. Repeat sequence families derived from mammalian tRNA genes. Nature 1985, 317:819-822.
37. Kramerov DA, Tillib S, Ryskov A, Georgiev G. Nucleotide sequence of small polyadenylated B2 RNA. Nucleic Acids Res 1985, 13:6423-6437.
38. Espinoza C, Allen T, Hieb A, Kugel JF, Goodrich JA. B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nat Struct Mol Biol 2004, 11:822-829.
39. Yakovchuk P, Goodrich JA, Kugel JF. B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Natl Acad Sci USA 2009, 106:5569-5574.
40. Espinoza CA, Goodrich JA, Kugel JF. Characterization of the structure, function, and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA 2007, 13:583-596.
41. Willard HF. Chromosome-specific organization of human alpha satellite DNA. Am J Hum Genet 1985, 37:524-532.
42. Rudd MK, Schueler MG, Willard HF. Sequence organization and functional annotation of human centromeres. Cold Spring Harb Symp Quant Biol 2003, 68:141-150.
43. Schindelhauer D, Schwarz T. Evidence for a fast, intrachromosomal conversion mechanism from mapping of nucleotide variants within a homogeneous α satellite DNA array. Genome Res 2002, 12:1815-1826.
44. Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF. Genomic and genetic definition of a functional human centromere. Science 2001, 294:109-115.
45. Kazakov AE, Shepelev VA, Tumeneva IG, Alexandrov A, Yurov YB, Alexandrov IA. Interspersed repeats are found predominantly in the "old" α satellite families. Genomics 2003, 82:619-627.
46. Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AFA, Finn RD. Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic Acids Res 2013, 41:D70-D82.
47. Shepelev VA, Alexandrov AA, Yurov YB, Alexandrov IA. The evolutionary origin of man can be traced in the layers of defunct ancestral alpha satellites flanking the active centromeres of human chromosomes. PLoS Genet 2009, 5:e1000641.
48. Schmitz J, Zemann A, Churakov G, Kuhl H, Grützner F, Reinhardt R, Brosius J. Retroposed SNOfall-a mammalian-wide comparison of platypus snoRNAs. Genome Res 2008, 18:1005-1010.
49. Alawi F, Lin P. Dyskerin localizes to the mitotic apparatus and is required for orderly mitosis in human cells. PLoS One 2013, 8:e80805.
50. Pidoux AL, Allshire RC. Centromeres: getting a grip of chromosomes. Curr Opin Cell Biol 2000, 12:308-319.
51. Csink A, Henikoff S. Something from nothing: the evolution and utility of satellite repeats. Trends Genet 1998, 14:200-204.
52. Karpen GH, Allshire RC. The case for epigenetic effects on centromere identity and function. Trends Genet 1997, 13:489-496.
53. Wong LH, Brettingham-Moore KH, Chan L, Quach JM, Anderson MA, Northrop EL, Hannan R, Saffery R, Shaw ML, Williams E, et al. Centromere RNA is a key component for the assembly of nucleoproteins at the nucleolus and centromere. Genome Res 2007, 17:1146-1160.
54. Hastings KEM. SL trans-splicing: easy come or easy go? Trends Genet 2005, 21:240-247.
55. Cheng G, Cohen L, Ndegwa D, Davis RE. The flatworm spliced leader 3′-terminal AUG as a translation initiator methionine. J Biol Chem 2006, 281:733-743.
56. Bruzik JP, Steitz JA. Spliced leader RNA sequences can substitute for the essential 5′ end of U1 RNA during splicing in a mammalian in vitro system. Cell 1990, 62:889-899.
57. Derelle R, Momose T, Manuel M, Da Silva C, Wincker P, Houliston E. Convergent origins and rapid evolution of spliced leader trans-splicing in Metazoa: insights from the Ctenophora and Hydrozoa. RNA 2010, 16:696-707.
58. Douris V, Telford MJ, Averof M. Evidence for multiple independent origins of trans-splicing in Metazoa. Mol Biol Evol 2010, 27:684-693.
59. Marz M, Kirsten T, Stadler PF. Evolution of spliceosomal snRNA genes in metazoan animals. J Mol Evol 2008, 67:594-607.
60. Bernstein LB, Manser T, Weiner AM. Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transposition. Mol Cell Biol 1985, 5:2159-2171.
61. Pelliccia F, Barzotti R, Bucciarelli E, Rocchi A. 5S ribosomal and U1 small nuclear RNA genes: a new linkage type in the genome of a crustacean that has three different tandemly repeated units containing 5S ribosomal DNA sequences. Genome 2001, 44:331-335.
62. Manchado M, Zuasti E, Cross I, Merlo A, Infante C, Rebordinos L. Molecular characterization and chromosomal mapping of the 5S rRNA gene in Solea senegalensis: a new linkage to the U1, U2, and U5 small nuclear RNA genes. Genome 2006, 49:79-86.
63. Sierra-Montes JM, Pereira-Simon S, Smail SS, Herrera RJ. The silk moth Bombyx mori U1 and U2 snRNA variants are differentially expressed. Gene 2005, 352:127-136.
64. Kyriakopoulou C, Larsson P, Liu L, Schuster J, Soderbom F, Kirsebom LA, Virtanen A. U1-like snRNAs lacking complementarity to canonical 5′ splice sites. RNA 2006, 12:1603-1611.
65. Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res 2003, 31:439-441.
66. Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform 2009, 23:205-211.
67. Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21:951-960.
68. Smalheiser NR, Torvik VI. Mammalian microRNAs derived from genomic repeats. Trends Genet 2005, 21:318-322.
69. Hadjiargyrou M, Delihas N. The intertwining of transposable elements and non-coding RNAs. Int J Mol Sci 2013, 14:13307-13328.
70. Bejerano G, Lowe CB, Ahituv N, King B, Siepel A, Salama SR, Rubin EM, Kent WJ, Haussler D. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 2006, 441:87-90.
71. Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS, Haussler D. Ultraconserved elements in the human genome. Science 2004, 304:1321-1325.
72. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler AD. The human genome browser at UCSC. Genome Res 2002, 12:996-1006.
73. Ting DT, Lipson D, Paul S, Brannigan BW, Akhavanfard S, Coffman EJ, Contino G, Deshpande V, Iafrate AJ, Letovsky S, et al. Aberrant overexpression of satellite repeats in pancreatic and other epithelial cancers. Science 2011, 331:593-596.
74. Zimmermann B, Bilusic I, Lorenz C, Schroeder R. Genomic SELEX: a discovery tool for genomic aptamers. Methods 2010, 52:125-132.
75. Gogolevskaya IK, Kramerov DA. Evolutionary history of 4.5SI RNA and indication that it is functional. J Mol Evol 2002, 54:354-364.
76. Gogolevskaya IK, Koval AP, Kramerov DA. Evolutionary history of 4.5SH RNA. Mol Biol Evol 2005, 22:1546-1554.
77. Parrott AM, Mathews MB. snaR genes: recent descendants of Alu involved in the evolution of chorionic gonadotropins. Cold Spring Harb Symp Quant Biol 2009, 74:363-373.
78. Cech TR. Beginning to understand the end of the chromosome. Cell 2004, 116:273-279.
79. Blackburn EH, Greider CW, Szostak JW. Telomeres and telomerase: the path from maize, tetrahymena and yeast to human cancer and aging. Nat Med 2006, 12:1133-1138.
80. Canella D, Praz V, Reina JH, Cousin P, Hernandez N. Defining the RNA polymerase III transcriptome: genome-wide localization of the RNA polymerase III transcription machinery in human cells. Genome Res 2010, 20:710-721.
81. Kleinschmidt RA, LeBlanc KE, Donze D. Autoregulation of an RNA polymerase II promoter by the RNA polymerase III transcription factor III C (TF(III)C) complex. Proc Natl Acad Sci USA 2011, 108:8385-8389.
82. Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol 2010, 17:635-640.
83. Hull MW, Erickson J, Johnston M, Engelke DR. tRNA genes as transcriptional repressor elements. Mol Cell Biol 1994, 14:1266-1277.
84. Raab JR, Chiu J, Zhu J, Katzman S, Kurukuti S, Wade PA, Haussler D, Kamakaka RT. Human tRNA genes function as chromatin insulators. EMBO J 2012, 31:330-350.
85. Drouin G, de Sá MM. The concerted evolution of 5S ribosomal genes linked to the repeat units of other multigene families. Mol Biol Evol 1995, 12:481-493.
86. Durfy SJ, Willard HF. Concerted evolution of primate alpha satellite DNA. J Mol Biol 1990, 216:555-566.
87. Innan H. Population genetic models of duplicated genes. Genetica 2009, 137:19-37.
88. Nei M, Rooney AP. Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 2005, 39:121-152.