Computational prediction of microRNAs encoded in viral and other genomes

Journal of Biomedicine and Biotechnology

Volumn 2006, Issue , 2006, Pages

  Thomassen, Gard O S ^a   Røsok, Øystein ^a   Rognes, Torbjørn ^a,b  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MICRORNA;

CAENORHABDITIS; CAENORHABDITIS BRIGGSAE; CAENORHABDITIS ELEGANS; COMPUTER PREDICTION; DROSOPHILA; DROSOPHILA MELANOGASTER; GENE EXPRESSION REGULATION; LABORATORY DIAGNOSIS; MATHEMATICAL COMPUTING; MOLECULAR CLONING; NONHUMAN; NORTHERN BLOTTING; REVIEW; RNA ANALYSIS; SYSTEMATIC REVIEW; VIRUS GENOME;

EID: 33746795816     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/JBB/2006/95270     Document Type: Review

References (68)

1. S F Altschul W Gish W Miller E W Myers D J Lipman Basic local alignment search tool. Journal of Molecular Biology 215 1990 3 403 410
2. V Ambros vambros@dartmouth.edu R C Lee A Lavanway P T Williams D Jewell MicroRNAs and other tiny endogenous RNAs in C. elegans. Current Biology 13 10 2003 807 818
3. L Argaman R Hershberg J Vogel Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Current Biology 11 12 2001 941 950
4. D P Bartel dbartel@wi.mit.edu MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 2 2004 281 297
5. Y Bennasser S-Y Le M Benkirane K-T Jeang kj7e@nih.gov Evidence that HIV-1 encodes an siRNA and a suppressor of RNA silencing. Immunity 22 5 2005 607 619
6. Y Bennasser YBennasser@niaid.nih.gov S-Y Le shuyun@ncifcrf.gov M L Yeung yeungm@niaid.nih.gov K-T Jeang KJEANG@niaid.nih.gov HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology 1 1 2004 43
7. E Berezikov V Guryev J van de Belt E Wienholds R H-A Plasterk plasterk@niob.knaw.nl E Cuppen Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120 1 2005 21 24
8. E Berezikov berezikov@niob.knaw.nl R HA Plasterk Camels and zebrafish, viruses and cancer: a microRNA update. Human Molecular Genetics 14 suppl 2 2005 R183 R190
9. E Bernstein S Y Kim M A Carmell Dicer is essential for mouse development. Nature Genetics 35 3 2003 215 217
10. B Billoud R De Paepe D Baulcombe M Boccara boccara@ccr.jussieu.fr Identification of new small non-coding RNAs from tobacco and Arabidopsis. Biochimie 87 9-10 2005 905 910
11. D Boffelli J McAuliffe D Ovcharenko Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299 5611 2003 1391 1394
12. M T Bohnsack K Czaplinski D Görlich dg@zmbh.uni-heidelberg.de Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10 2 2004 185 191
13. X Cai S Lu Z Zhang C M Gonzalez B Damania B R Cullen culle002@mc.duke.edu Kaposi's sarcoma-associated herpesvirus expresses an array of viral microRNAs in latently infected cells. Proceedings of the National Academy of Sciences of the United States of America 102 15 2005 5570 5575
14. G A Calin C Sevignani C D Dumitru Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proceedings of the National Academy of Sciences of the United States of America 101 9 2004 2999 3004
15. P Y Chen G Meister meister@biochem.mpg.de MicroRNA-guided posttranscriptional gene regulation. Biological Chemistry 386 12 2005 1205 1218
16. T Dezulian dezulian@informatik.uni-tuebingen.de M Remmert J F Palatnik D Weigel D H Huson Identification of plant microRNA homologs. Bioinformatics 22 3 2006 359 360
17. A J Enright B John U Gaul T Tuschl C Sander D S Marks MicroRNA targets in Drosophila. Genome Biology 5 1 2003 R1
18. Y Grad J Aach G D Hayes Computational and experimental identification of C. elegans microRNAs. Molecular Cell 11 5 2003 1253 1263
19. F Grey greyf@ohsu.edu A Antoniewicz E Allen Identification and characterization of human cytomegalovirus-encoded microRNAs. Journal of Virology 79 18 2005 12095 12099
20. S Griffiths-Jones sgj@sanger.ac.uk The microRNA registry. Nucleic Acids Research 32 Database issue 2004 D109 D111
21. S Griffiths-Jones R J Grocock S van Dongen A Bateman A J Enright miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Research 34 Database issue 2006 D140 D144
22. A Grishok A E Pasquinelli D Conte Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106 1 2001 23 34
23. D Grün Y-L Wang D Langenberger K C Gunsalus N Rajewsky MicroRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Computational Biology 1 2005 1 e13
24. I L Hofacker W Fontana P F Stadler L S Bonhöffer M Tacker P Schuster Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie 125 1994 2 167 188
25. G Hutvágner J McLachlan A E Pasquinelli É Bálint T Tuschl P D Zamore A cellular function for the RNA-interference enzyme dicer in the maturation of the let-7 small temporal RNA. Science 293 5531 2001 834 838
26. G Hutvágner P D Zamore A microRNA in a multiple-turnover RNAi enzyme complex. Science 297 5589 2002 2056 2060
27. B John A J Enright A Aravin T Tuschl C Sander D S Marks mirnatargets@cbio.mskcc.org Human microRNA targets. PLoS Biology 2 11 2004 e363
28. M W Jones-Rhoades D P Bartel dbartel@wi.mit.edu Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Molecular Cell 14 6 2004 787 799
29. M Kiriakidou P T Nelson A Kouranov A combined computational-experimental approach predicts human microRNA targets. Genes and Development 18 10 2004 1165 1178
30. A Krek D Grün M N Poy Combinatorial microRNA target predictions. Nature Genetics 37 5 2005 495 500
31. M Lagos-Quintana R Rauhut W Lendeckel T Tuschl Identification of novel genes coding for small expressed RNAs. Science 294 5543 2001 853 858
32. E C Lai P Tomancak R W Williams G M Rubin Computational identification of Drosophila microRNA genes. Genome Biology 4 7 2003 R42
33. N C Lau L P Lim E G Weinstein D P Bartel An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294 5543 2001 858 862
34. Y Lee C Ahn J Han The nuclear RNase III Drosha initiates microRNA processing. Nature 425 6956 2003 415 419
35. R C Lee V Ambros An extensive class of small RNAs in Caenorhabditis elegans. Science 294 5543 2001 862 864
36. R C Lee R L Feinbaum V Ambros The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75 5 1993 843 854
37. Y Lee K Jeon J-T Lee S Kim V N Kim MicroRNA maturation: stepwise processing and subcellular localization. EMBO Journal 21 17 2002 4663 4670
38. Y Lee M Kim J Han MicroRNA genes are transcribed by RNA polymerase II. EMBO Journal 23 20 2004 4051 4060
39. B P Lewis C B Burge cburge@mit.edu D P Bartel dbartel@wi.mit.edu Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120 1 2005 15 20
40. B P Lewis I-H Shih M W Jones-Rhoades D P Bartel dbartel@wi.mit.edu C B Burge cburge@mit.edu Prediction of mammalian microRNA targets. Cell 115 7 2003 787 798
41. L P Lim M E Glasner S Yekta C B Burge D P Bartel Vertebrate microRNA genes. Science 299 5612 2003 1540
42. L P Lim N C Lau E G Weinstein The microRNAs of Caenorhabditis elegans. Genes and Development 17 8 2003 991 1008
43. C Llave Z Xie K D Kasschau J C Carrington Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297 5589 2002 2053 2056
44. T M Lowe S R Eddy eddy@genetics.wustl.edu tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25 5 1997 955 964
45. S Lu B R Cullen culle002@mc.duke.edu Adenovirus VA1 noncoding RNA can inhibit small interfering RNA and microRNA biogenesis. Journal of Virology 78 23 2004 12868 12876
46. J Lu G Getz E A Miska MicroRNA expression profiles classify human cancers. Nature 435 7043 2005 834 838
47. E Lund S Güttinger A Calado J E Dahlberg dahlberg@wisc.edu U Kutay ulrike.kutay@bc.biol.ethz.ch Nuclear export of microRNA precursors. Science 303 5654 2004 95 98
48. Z Mourelatos J Dostie S Paushkin miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes and Development 16 6 2002 720 728
49. K Okamura A Ishizuka H Siomi siomi@genome.tokushima-u.ac.jp M C Siomi Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways. Genes and Development 18 14 2004 1655 1666
50. S Pfeffer A Sewer M Lagos-Quintana Identification of microRNAs of the herpesvirus family. Nature Methods 2 4 2005 269 276
51. S Pfeffer M Zavolan F A Grässer Identification of virus-encoded microRNAs. Science 304 5671 2004 734 736
52. B J Reinhart F J Slack M Basson The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403 6772 2000 901 906
53. E Rivas R J Klein T A Jones S R Eddy Computational identification of noncoding RNAs in E. coli by comparative genomics. Current Biology 11 17 2001 1369 1373
54. H Robins hrobins@ias.edu Y Li R W Padgett Incorporating structure to predict microRNA targets. Proceedings of the National Academy of Sciences of the United States of America 102 11 2005 4006 4009
55. A Rodriguez S Griffiths-Jones J L Ashurst A Bradley abradley@sanger.ac.uk Identification of mammalian microRNA host genes and transcription units. Genome Research 14 10 A 2004 1902 1910
56. T Rognes ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches. Nucleic Acids Research 29 7 2001 1647 1652
57. F J Slack M Basson Z Liu V Ambros H R Horvitz G Ruvkun The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor. Molecular Cell 5 4 2000 659 669
58. N R Smalheiser smalheiser@psych.uic.edu EST analyses predict the existence of a population of chimeric microRNA precursor-mRNA transcripts expressed in normal human and mouse tissues. Genome Biology 4 7 2003 403
59. T F Smith M S Waterman Identification of common molecular subsequences. Journal of Molecular Biology 147 1 1981 195 197
60. C S Sullivan A T Grundhoff S Tevethia J M Pipas D Ganem ganem@cgl.ucsf.edu SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 435 7042 2005 682 686
61. X J Wang J L Reyes N H Chua T Gaasterland Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biology 5 9 2004 R65
62. X Wang J Zhang F Li MicroRNA identification based on sequence and structure alignment. Bioinformatics 21 18 2005 3610 3614
63. K M Wassarman F Repoila C Rosenow G Storz S Gottesman Identification of novel small RNAs using comparative genomics and microarrays. Genes and Development 15 13 2001 1637 1651
64. B Wightman I Ha G Ruvkun Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75 5 1993 855 862
65. R Yi Y Qin I G Macara B R Cullen culle002@mc.duke.edu Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes and Development 17 24 2003 3011 3016
66. S Yoon sryoon@stanford.edu G De Micheli Prediction of regulatory modules comprising microRNAs and target genes. Bioinformatics 21 suppl 2 2005 ii93 ii100
67. Y Zeng R Yi B R Cullen culle002@mc.duke.edu MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proceedings of the National Academy of Sciences of the United States of America 100 17 2003 9779 9784
68. M Zuker Prediction of RNA secondary structure by energy minimization. Methods in Molecular Biology 25 1994 267 294