Systematic identification and characterization of chicken (Gallus gallus) ncRNAs

Nucleic Acids Research

Volumn 37, Issue 19, 2009, Pages 6562-6574

  Zhang, Yong ^a   Wang, Jie ^b   Huang, Shoujun ^a   Zhu, Xiaopeng ^b   Liu, Jun ^c   Yang, Ning ^d   Song, Dandan ^e   Wu, Rimao ^a   Deng, Wei ^b   Skogerbø, Geir ^b   Wang, Xiu Jie ^c   Chen, Runsheng ^b   Zhu, Dahai ^a  

^a INSTITUTE OF BASIC MEDICAL SCIENCES   (China)

^b INSTITUTE OF BIOPHYSICS   (China)

^c INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^d CHINA AGRICULTURAL UNIVERSITY   (China)

^e TSINGHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

6 PHOSPHOFRUCTOKINASE; UNTRANSLATED RNA;

ARTICLE; CHICKEN; CONTROLLED STUDY; GENE EXPRESSION; GENE LIBRARY; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CONSERVATION; INTRON; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA ANALYSIS; SPECIES DIFFERENCE;

ANIMALS; BASE SEQUENCE; CHICKENS; INTRONS; MOLECULAR SEQUENCE DATA; RNA SPLICING; RNA, SMALL NUCLEOLAR; RNA, UNTRANSLATED;

GALLUS GALLUS; MAMMALIA; VERTEBRATA;

EID: 71049154451     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp704     Document Type: Article

References (58)

1. Gibbs,R.A., Weinstock,G.M., Metzker,M.L., Muzny,D.M., Sodergren,E.J., Scherer,S., Scott,G., Steffen,D., Worley,K.C., Burch,P.E. et al. (2004) Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 428, 493-521.
2. Lander,E.S., Linton,L.M., Birren,B., Nusbaum,C., Zody,M.C., Baldwin,J., Devon,K., Dewar,K., Doyle,M., FitzHugh,W. et al. (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.
3. Waterston,R.H., Lindblad-Toh,K., Birney,E., Rogers,J., Abril,J.F., Agarwal,P., Agarwala,R., Ainscough,R., Alexandersson,M., An,P. et al. (2002) Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562.
4. Hillier,L.W., Miller,W., Birney,E., Warren,W., Hardison,R.C., Ponting,C.P., Bork,P., Burt,D.W., Groenen,M.A., Delany,M.E. et al. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature, 432, 695-716.
5. Cheng,J., Kapranov,P., Drenkow,J., Dike,S., Brubaker,S., Patel,S., Long,J., Stern,D., Tammana,H., Helt,G. et al. (2005) Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science, 308, 1149-1154.
6. Kapranov,P., Cawley,S.E., Drenkow,J., Bekiranov,S., Strausberg,R.L., Fodor,S.P. and Gingeras,T.R. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science, 296, 916-919.
7. Bertone,P., Stolc,V., Royce,T.E., Rozowsky,J.S., Urban,A.E., Zhu,X., Rinn,J.L., Tongprasit,W., Samanta,M., Weissman,S. et al. (2004) Global identification of human transcribed sequences with genome tiling arrays. Science, 306, 2242-2246.
8. Birney,E., Stamatoyannopoulos,J.A., Dutta,A., Guigo,R., Gingeras,T.R., Margulies,E.H., Weng,Z., Snyder,M., Dermitzakis,E.T., Thurman,R.E. et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447 799-816.
9. Huttenhofer,A., Kiefmann,M., Meier-Ewert,S., O'Brien,J., Lehrach,H., Bachellerie,J.P. and Brosius,J. (2001) RNomics: An experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. EMBO J., 20, 2943-2953.
10. Numata,K., Kanai,A., Saito,R., Kondo,S., Adachi,J., Wilming,L.G., Hume,D.A., Hayashizaki,Y. and Tomita,M. (2003) Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res., 13, 1301-1306.
11. Mercer,T.R., Dinger,M.E., Sunkin,S.M., Mehler,M.F. and Mattick,J.S. (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc. Natl Acad. Sci. USA, 105, 716-721.
12. Aravin,A., Gaidatzis,D., Pfeffer,S., Lagos-Quintana,M., Landgraf,P., Iovino,N., Morris,P., Brownstein,M.J., Kuramochi-Miyagawa,S., Nakano,T. et al. (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature, 442, 203-207.
13. Girard,A., Sachidanandam,R., Hannon,G.J. and Carmell,M.A. (2006) A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature, 442, 199-202.
14. Ruby,J.G., Jan,C., Player,C., Axtell,M.J., Lee,W., Nusbaum,C., Ge,H. and Bartel,D.P. (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell, 127, 1193-1207.
15. Storz,G., Altuvia,S. and Wassarman,K.M. (2005) An abundance of RNA regulators. Annu. Rev. Biochem., 74, 199-217.
16. Plasterk,R.H. (2006) Micro RNAs in animal development. Cell, 124, 877-881.
17. Kiss,T. (2001) Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J., 20, 3617-3622.
18. Prasanth,K.V. and Spector,D.L. (2007) Eukaryotic regulatory RNAs: An answer to the 'genome complexity' conundrum. Genes Dev., 21, 11-42.
19. Kishore,S. and Stamm,S. (2006) The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science, 311, 230-232.
20. Couzin,J. (2008) MicroRNAs make big impression in disease after disease. Science, 319, 1782-1784.
21. Burt,D.W., Bruley,C., Dunn,I.C., Jones,C.T., Ramage,A., Law,A.S., Morrice,D.R., Paton,I.R., Smith,J., Windsor,D. et al. (1999) The dynamics of chromosome evolution in birds and mammals. Nature, 402, 411-413.
22. Hubbard,T.J., Aken,B.L., Ayling,S., Ballester,B., Beal,K., Bragin,E., Brent,S., Chen,Y., Clapham,P., Clarke,L. et al. (2009) Ensembl 2009. Nucleic Acids Res., 37, D690-D697.
23. Shao,P., Yang,J.H., Zhou,H., Guan,D.G. and Qu,L.H. (2009) Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs. BMC Genomics, 10, 86.
24. Shao,P., Zhou,H., Xiao,Z.D., He,J.H., Huang,M.B., Chen,Y.Q. and Qu,L.H. (2008) Identification of novel chicken microRNAs and analysis of their genomic organization. Gene, 418, 34-40.
25. Burnside,J., Ouyang,M., Anderson,A., Bernberg,E., Lu,C., Meyers,B.C., Green,P.J., Markis,M., Isaacs,G., Huang,E. et al. (2008) Deep sequencing of chicken microRNAs. BMC Genomics, 9, 185.
26. Glazov,E.A., Cottee,P.A., Barris,W.C., Moore,R.J., Dalrymple,B.P. and Tizard,M.L. (2008) A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res., 18, 957-964.
27. Yuan,G., Klambt,C., Bachellerie,J.P., Brosius,J. and Huttenhofer,A. (2003) RNomics in Drosophila melanogaster: Identification of 66 candidates for novel non-messenger RNAs. Nucleic Acids Res., 31 2495-2507.
28. Eddy,S.R. (2002) Computational genomics of noncoding RNA genes. Cell 109, 137-140.
29. Vogel,J., Bartels,V., Tang,T.H., Churakov,G., Slagter-Jager,J.G., Huttenhofer,A. and Wagner,E.G. (2003) RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res., 31, 6435-6443.
30. Deng,W., Zhu,X., Skogerbo,G., Zhao,Y., Fu,Z., Wang,Y., He,H., Cai,L., Sun,H., Liu,C. et al. (2006) Organization of the Caenorhabditis elegans small non-coding transcriptome: Genomic features, biogenesis, and expression. Genome Res., 16, 20-29.
31. Vitali,P., Royo,H., Seitz,H., Bachellerie,J.P., Huttenhofer,A. and Cavaille,J. (2003) Identification of 13 novel human modification guide RNAs. Nucleic Acids Res., 31, 6543-6551.
32. Maxwell,E.S. and Fournier,M.J. (1995) The small nucleolar RNAs. Annu. Rev. Biochem., 64, 897-934.
33. Zemann,A., op de Bekke,A., Kiefmann,M., Brosius,J. and Schmitz,J. (2006) Evolution of small nucleolar RNAs in nematodes. Nucleic Acids Res. 34, 2676-2685.
34. Balakin,A.G., Smith,L. and Fournier,M.J. (1996) The RNA world of the nucleolus: Two major families of small RNAs defined by different box elements with related functions. Cell, 86, 823-834.
35. Tycowski,K.T., Aab,A. and Steitz,J.A. (2004) Guide RNAs with 5′ caps and novel box C/D snoRNA-like domains for modification of snRNAs in metazoa. Curr. Biol., 14, 1985-1995.
36. Kiss,T., Fayet,E., Jady,B.E., Richard,P. and Weber,M. (2006) Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. Cold Spring Harb. Symp. Quant. Biol., 71, 407-417.
37. Filipowicz,W. and Pogacic,V. (2002) Biogenesis of small nucleolar ribonucleoproteins. Curr. Opin. Cell Biol., 14, 319-327.
38. Semenov,D.V., Vratskih,O.V., Kuligina,E.V. and Richter,V.A. (2008) Splicing by exon exclusion impaired by artificial box c/d RNA targeted to branch-point adenosine. Ann. NY Acad. Sci., 1137, 119-124.
39. Lukowiak,A.A., Narayanan,A., Li,Z.H., Terns,R.M. and Terns,M.P. (2001) The snoRNA domain of vertebrate telomerase RNA functions to localize the RNA within the nucleus. RNA, 7, 1833-1844.
40. Nicholls,R.D. and Knepper,J.L. (2001) Genome organization, function, and imprinting in Prader-Willi and Angelman syndromes. Annu. Rev. Genomics Hum. Genet., 2, 153-175.
41. Cavaille,J., Buiting,K., Kiefmann,M., Lalande,M., Brannan,C.I., Horsthemke,B., Bachellerie,J.P., Brosius,J. and Huttenhofer,A. (2000) Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc. Natl Acad. Sci. USA 97, 14311-14316.
42. Klein,R.J. and Eddy,S.R. (2003) RSEARCH: Finding homologs of single structured RNA sequences. BMC Bioinformatics, 4, 44.
43. Hertel,J., Hofacker,I.L. and Stadler,P.F. (2008) SnoReport: computational identification of snoRNAs with unknown targets. Bioinformatics, 24, 158-164.
44. Kent,W.J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
45. Zheng,Q. and Wang,X.J. (2008) GOEAST: A web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res., 36, W358-W363.
46. Yang,W., Zhang,Y., Ma,G., Zhao,X., Chen,Y. and Zhu,D. (2005) Identification of gene expression modifications in myostatin-stimulated myoblasts. Biochem. Biophys. Res. Commun., 326, 660-666.
47. Gardner,P.P., Daub,J., Tate,J.G., Nawrocki,E.P., Kolbe,D.L., Lindgreen,S., Wilkinson,A.C., Finn,R.D., Griffiths-Jones,S., Eddy,S.R. et al. (2009) Rfam: Updates to the RNA families database. Nucleic Acids Res., 37, D136-D140.
48. Zheng,Q., Zhang,Y., Chen,Y., Yang,N., Wang,X.J. and Zhu,D. (2009) Systematic identification of genes involved in divergent skeletal muscle growth rates of broiler and layer chickens. BMC Genomics, 10 87.
49. Pang,K.C., Stephen,S., Dinger,M.E., Engstrom,P.G., Lenhard,B. and Mattick,J.S. (2007) RNAdb 2.0-an expanded database of mammalian non-coding RNAs. Nucleic Acids Res., 35, D178-D182.
50. Lestrade,L. and Weber,M.J. (2006) snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res., 34, D158-D162.
51. Zhang,Z., Pang,A.W. and Gerstein,M. (2007) Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human. BMC Evol. Biol., 7 (Suppl. 1), S14.
52. Baskerville,S. and Bartel,D.P. (2005) Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA, 11, 241-247.
53. Zhao,Y., Ransom,J.F., Li,A., Vedantham,V., von Drehle,M., Muth,A.N., Tsuchihashi,T., McManus,M.T., Schwartz,R.J. and Srivastava,D. (2007) Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell, 129, 303-317.
54. Chen,J.F., Mandel,E.M., Thomson,J.M., Wu,Q., Callis,T.E., Hammond,S.M., Conlon,F.L. and Wang,D.Z. (2006) The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation. Nat. Genet., 38, 228-233.
55. Wegener,G. and Krause,U. (2002) Different modes of activating phosphofructokinase, a key regulatory enzyme of glycolysis, in working vertebrate muscle. Biochem. Soc. Trans., 30, 264-270.
56. Mehler,M.F. and Mattick,J.S. (2007) Noncoding RNAs and RNA editing in brain development, functional diversification, and neurological disease. Physiol. Rev., 87, 799-823.
57. Peters,J. (2008) Prader-Willi and snoRNAs. Nat. Genet., 40, 688-689.
58. Pober,B.R., Johnson,M. and Urban,Z. (2008) Mechanisms and treatment of cardiovascular disease in Williams-Beuren syndrome. J. Clin. Invest. 118, 1606-1615.