Psiscan: A computational approach to identify H/ACA-like and AGA-like non-coding RNA in trypanosomatid genomes

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Myslyuk, Inna ^a   Doniger, Tirza ^a   Horesh, Yair ^b   Hury, Avraham ^a   Hoffer, Ran ^a   Ziporen, Yaara ^a   Michaeli, Shulamit ^a   Unger, Ron ^a  

^a BAR ILAN UNIVERSITY   (Israel)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL ANALYSIS; COMPUTATIONAL APPROACH; COMPUTATIONAL TOOLS; EXPERIMENTAL ANALYSIS; EXPERIMENTAL APPROACHES; EXPERIMENTAL VALIDATIONS; LOWEST ENERGY STRUCTURE; NON-CODING RNA (NCRNA);

BIOINFORMATICS; COMPUTATIONAL METHODS; GENES; RNA; SUPPORT VECTOR MACHINES;

MOLECULES;

SMALL NUCLEAR RNA;

ANIMAL; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; GENETICS; GENOMICS; METHODOLOGY; MUTAGENESIS; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; TRYPANOSOMA;

ANIMALS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; GENOMICS; MODELS, GENETIC; MUTAGENESIS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; RNA, SMALL NUCLEAR; SOFTWARE; TRYPANOSOMA;

EID: 58149352501     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-471     Document Type: Article

References (73)

1. Dennis PP Omer A Lowe T A guided tour: Small RNA function in Archaea Mol Microbiol 2001, 40(3):509-519. 11359559
2. Omer AD Lowe TM Russell AG Ebhardt H Eddy SR Dennis PP Homologs of small nucleolar RNAs in Archaea Science 2000, 288(5465):517-522. 10775111
3. Filipowicz W Pogacic V Biogenesis of small nucleolar ribonucleoproteins Curr Opin Cell Biol 2002, 14(3):319-327. 12067654
4. Kiss T Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions Cell 2002, 109(2):145-148. 12007400
5. Tollervey D Kiss T Function and synthesis of small nucleolar RNAs Curr Opin Cell Biol 1997, 9(3):337-342. 9159079
6. Decatur WA Fournier MJ RNA-guided nucleotide modification of ribosomal and other RNAs J Biol Chem 2003, 278(2):695-698. 12431975
7. Ganot P Bortolin ML Kiss T Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs Cell 1997, 89(5):799-809. 9182768
8. Kiss-Laszlo Z Henry Y Bachellerie JP Caizergues-Ferrer M Kiss T Site-specific ribose methylation of preribosomal RNA: A novel function for small nucleolar RNAs Cell 1996, 85(7):1077-1088. 8674114
9. Ni J Tien AL Fournier MJ Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA Cell 1997, 89(4):565-573. 9160748
10. Darzacq X Jady BE Verheggen C Kiss AM Bertrand E Kiss T Cajal body-specific small nuclear RNAs: A novel class of 2'-O-methylation and pseudouridylation guide RNAs Embo J 2002, 21(11):2746-2756. 126017 12032087
11. Uliel S Liang XH Unger R Michaeli S Small nucleolar RNAs that guide modification in trypanosomatids: Repertoire, targets, genome organisation, and unique functions Int J Parasitol 2004, 34(4):445-454. 15013734
12. Kishore S Stamm S The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C Science 2006, 311(5758):230-232. 16357227
13. Yu YT Terns RM Terns MP Fine-tuning of RNA Functions by Modification and Editing Topics in Current Genetics 2005, 12:223-262.
14. Collins K The biogenesis and regulation of telomerase holoenzymes Nat Rev Mol Cell Biol 2006, 7(7):484-494. 16829980
15. Bortolin ML Ganot P Kiss T Elements essential for accumulation and function of small nucleolar RNAs directing site-specific pseudouridylation of ribosomal RNAs Embo J 1999, 18(2):457-469. 1171139 9889201
16. Bousquet-Antonelli C Henry Y G'Elugne JP Caizergues-Ferrer M Kiss T A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs Embo J 1997, 16(15):4770-4776. 1170103 9303321
17. Dragon F Pogacic V Filipowicz W In vitro assembly of human H/ACA small nucleolar RNPs reveals unique features of U17 and telomerase RNAs Mol Cell Biol 2000, 20(9):3037-3048. 85579 10757788
18. Henras A Henry Y Bousquet-Antonelli C Noaillac-Depeyre J Gelugne JP Caizergues-Ferrer M Nhp2p and Nop10p are essential for the function of H/ ACA snoRNPs Embo J 1998, 17(23):7078-7090. 1171055 9843512
19. Lafontaine DL Tollervey D Birth of the snoRNPs: The evolution of the modification-guide snoRNAs Trends Biochem Sci 1998, 23(10):383-388. 9810226
20. Rozhdestvensky TS Tang TH Tchirkova IV Brosius J Bachellerie JP Huttenhofer A Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea Nucleic Acids Res 2003, 31(3):869-877. 149196 12560482
21. Watanabe Y Gray MW Evolutionary appearance of genes encoding proteins associated with box H/ACA snoRNAs: Cbf5p in Euglena gracilis, an early diverging eukaryote, and candidate Gar1p and Nop10p homologs in archaebacteria Nucleic Acids Res 2000, 28(12):2342-2352. 102724 10871366
22. Watkins NJ Gottschalk A Neubauer G Kastner B Fabrizio P Mann M Luhrmann R Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ ACA-motif snoRNPs and constitute a common bipartite structure Rna 1998, 4(12):1549-1568. 1369725 9848653
23. Li L Ye K Crystal structure of an H/ACA box ribonucleoprotein particle Nature 2006, 443(7109):302-307. 16943774
24. Sogin ML Elwood HJ Gunderson JH Evolutionary diversity of eukaryotic small-subunit rRNA genes Proc Natl Acad Sci USA 1986, 83(5):1383-1387. 323080 2419907
25. Liang XH Haritan A Uliel S Michaeli S trans and cis splicing in trypanosomatids: Mechanism, factors, and regulation Eukaryot Cell 2003, 2(5):830-840. 219355 14555465
26. Simpson L Sbicego S Aphasizhev R Uridine insertion/deletion RNA editing in trypanosome mitochondria: A complex business Rna 2003, 9(3):265-276. 1370392 12591999
27. White TC Rudenko G Borst P Three small RNAs within the 10 kb trypanosome rRNA transcription unit are analogous to domain VII of other eukaryotic 28S rRNAs Nucleic Acids Res 1986, 14:9471-9489. 311971 3797245
28. Liang XH Liu L Michaeli S Identification of the first trypanosome H/ACA RNA that guides pseudouridine formation on rRNA J Biol Chem 2001, 276(43):40313-40318. 11483606
29. Tang TH Bachellerie JP Rozhdestvensky T Bortolin ML Huber H Drungowski M Elge T Brosius J Huttenhofer A Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus Proc Natl Acad Sci USA 2002, 99(11):7536-7541. 124276 12032318
30. Russell AG Schnare MN Gray MW Pseudouridine-guide RNAs and other Cbf5p-associated RNAs in Euglena gracilis Rna 2004, 10(7):1034-1046. 1370595 15208440
31. Brown JW Echeverria M Qu LH Plant snoRNAs: Functional evolution and new modes of gene expression Trends Plant Sci 2003, 8(1):42-49. 12523999
32. Liang XH Hury A Hoze E Uliel S Myslyuk I Apatoff A Unger R Michaeli S Genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Leishmania major indicates conservation among trypanosomatids in the repertoire and in their rRNA targets Eukaryot Cell 2007, 6(3):361-377. 1828925 17189491
33. Liang XH Uliel S Hury A Barth S Doniger T Unger R Michaeli S A genome-wide analysis of C/D and H/ACA-like small nucleolar RNAs in Trypanosoma brucei reveals a trypanosome-specific pattern of rRNA modification Rna 2005, 11(5):619-645. 1370750 15840815
34. Liang XH Liu Q Michaeli S Small nucleolar RNA interference induced by antisense or double-stranded RNA in trypanosomatids Proc Natl Acad Sci USA 2003, 100(13):7521-7526. 164619 12808138
35. Xu Y Liu L Lopez-Estrano C Michaeli S Expression studies on clustered trypanosomatid box C/D small nucleolar RNAs J Biol Chem 2001, 276(17):14289-14298. 11278327
36. Dunbar DA Chen AA Wormsley S Baserga SJ The genes for small nucleolar RNAs in Trypanosoma brucei are organized in clusters and are transcribed as a polycistronic RNA Nucleic Acids Res 2000, 28(15):2855-2861. 102681 10908346
37. Roberts TG Sturm NR Yee BK Yu MC Hartshorne T Agabian N Campbell DA Three small nucleolar RNAs identified from the spliced leader-associated RNA locus in kinetoplastid protozoans Mol Cell Biol 1998, 18(8):4409-4417. 109026 9671450
38. Barth S Shalem B Hury A Tkacz ID Liang XH Uliel S Myslyuk I Doniger T Salmon-Divon M Unger R et al.Elucidating the role of C/D snoRNA in rRNA processing and modification in Trypanosoma brucei Eukaryot Cell 2008, 7(1):86-101. 2224155 17981991
39. Gray MW The ribosomal RNA of the trypanosomatid protozoan Crithidia fasciculata: Physical characteristics and methylated sequences Can J Biochem 1979, 57(6):914-926. 476525
40. Russell AG Schnare MN Gray MW A large collection of compact box C/D snoRNAs and their isoforms in Euglena gracilis: Structural, functional and evolutionary insights J Mol Biol 2006, 357(5):1548-1565. 16497322
41. Torchet C Badis G Devaux F Costanzo G Werner M Jacquier A The complete set of H/ACA snoRNAs that guide rRNA pseudouridylations in Saccharomyces cerevisiae Rna 2005, 11(6):928-938. 1370777 15923376
42. Fedorov A Stombaugh J Harr MW Yu S Nasalean L Shepelev V Computer identification of snoRNA genes using a Mammalian Orthologous Intron Database Nucleic Acids Res 2005, 33(14):4578-4583. 1184218 16093549
43. Gaspin C Cavaille J Erauso G Bachellerie JP Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: Lessons from the Pyrococcus genomes J Mol Biol 2000, 297(4):895-906. 10736225
44. Lowe TM Eddy SR A computational screen for methylation guide snoRNAs in yeast Science 1999, 283(5405):1168-1171. 10024243
45. Schattner P Barberan-Soler S Lowe TM A computational screen for mammalian pseudouridylation guide H/ACA RNAs Rna 2006, 12(1):15-25. 1370881 16373490
46. Brown JW Clark GP Leader DJ Simpson CG Lowe T Multiple snoRNA gene clusters from Arabidopsis Rna 2001, 7(12):1817-1832. 1370220 11780637
47. Barneche F Gaspin C Guyot R Echeverria M Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: Extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2'-O-methylation sites J Mol Biol 2001, 311(1):57-73. 11469857
48. Qu LH Meng Q Zhou H Chen YQ Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana Nucleic Acids Res 2001, 29(7):1623-1630. 31268 11266566
49. Edvardsson S Gardner PP Poole AM Hendy MD Penny D Moulton V A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction Bioinformatics 2003, 19(7):865-873. 12724297
50. Yang JH Zhang XC Huang ZP Zhou H Huang MB Zhang S Chen YQ Qu LH snoSeeker: An advanced computational package for screening of guide and orphan snoRNA genes in the human genome Nucleic Acids Res 2006, 34(18):5112-5123. 1636440 16990247
51. Schattner P Decatur WA Davis CA Ares M Jr Fournier MJ Lowe TM Genome-wide searching for pseudouridylation guide snoRNAs: Analysis of the Saccharomyces cerevisiae genome Nucleic Acids Res 2004, 32(1):4281-4296. 514388 15306656
52. Hertel J Hofacker IL Stadler PF SnoReport: Computational identification of snoRNAs with unknown targets Bioinformatics 2007. 17895272
53. Hertel J Hofacker IL Stadler PF SnoReport: Computational identification of snoRNAs with unknown targets Bioinformatics 2008, 24(2):158-164. 17895272
54. Muller S Charpentier B Branlant C Leclerc F A dedicated computational approach for the identification of archaeal H/ACA sRNAs Methods Enzymol 2007, 425:355-387. 17673091
55. Muller S Leclerc F Behm-Ansmant I Fourmann JB Charpentier B Branlant C Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs Nucleic Acids Res 2008, 36(8):2459-2475. 2377435 18304947
56. Barth S Hury A Liang X-h Michaeli S Elucidating the Role of H/ACA-like RNAs in trans-Splicing and rRNA Processing via RNA Interference Silencing of the Trypanosoma brucei CBF5 Pseudouridine Synthase THE JOURNAL OF BIOLOGICAL CHEMISTRY 2005, 280:34558-34568. 16107339
57. Berriman M Ghedin E Hertz-Fowler C Blandin G Renauld H Bartholomeu DC Lennard NJ Caler E Hamlin NE Haas B et al.The genome of the African trypanosome Trypanosoma brucei Science 2005, 309(5733):416-422. 16020726
58. Ivens AC Peacock CS Worthey EA Murphy L Aggarwal G Berriman M Sisk E Rajandream MA Adlem E Aert R et al. The genome of the kinetoplastid parasite, Leishmania major Science 2005, 309(5733):436-442. 1470643 16020728
59. El-Sayed NM Myler PJ Blandin G Berriman M Crabtree J Aggarwal G Caler E Renauld H Worthey EA Hertz-Fowler C et al. Comparative genomics of trypanosomatid parasitic protozoa Science 2005, 309(5733):404-409. 16020724
60. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215(3):403-410. 2231712
61. Zuker M Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res 2003, 31(13):3406-3415. 169194 12824337
62. Yang ZR Biological applications of support vector machines Brief Bioinform 2004, 5(4):328-338. 15606969
63. Vapnik VN The Nature of Statistical Learning Theory Springer-Velgrad 1995.
64. Joachims T Making large-Scale SVM Learning Practical Advances in Kernel Methods - Support Vector Learning 1999.
65. Glodring A Karchi M Michaeli S The spliced leader RNA gene of Leptomonas collosoma Exp Parasitol 1995, 80(2):333-338. 7895844
66. Liang XH Ochaion A Xu YX Liu Q Michaeli S Small nucleolar RNA clusters in trypanosomatid Leptomonas collosoma. Genome organization, expression studies, and the potential role of sequences present upstream from the first repeated cluster J Biol Chem 2004, 279(7):5100-5109. 14645367
67. Horesh Y Doniger T Michaeli S Unger R RNAspa: A shortest path approach for comparative prediction of the secondary structure of ncRNA molecules BMC Bioinformatics 2007, 8:366. 2147038 17908318
68. Griffiths-Jones S Moxon S Marshall M Khanna A Eddy SR Bateman A Rfam: annotating non-coding RNAs in complete genomes Nucleic Acids Res 2005, 33 (Database):D121-124. 540035 15608160
69. Maden BE Corbett ME Heeney PA Pugh K Ajuh PM Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA Biochimie 1995, 77(1-2):22-29. 7599273
70. Mattick JS Makunin IV Non-coding RNA Hum Mol Genet 2006, 15(Spec No 1):R17-29. 16651366
71. Carninci P Kasukawa T Katayama S Gough J Frith MC Maeda N Oyama R Ravasi T Lenhard B Wells C The transcriptional landscape of the mammalian genome Science 2005, 309(5740):1559-1563. 16141072
72. Cheng J Kapranov P Drenkow J Dike S Brubaker S Patel S Long J Stern D Tammana H Helt G et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution Science 2005, 308(5725):1149-1154. 15790807
73. Birney E Stamatoyannopoulos JA Dutta A Guigo R Gingeras TR Margulies EH Weng Z Snyder M Dermitzakis ET Thurman RE et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 2007, 447(7146):799-816. 2212820 17571346