Systematic identification and characterization of porcine snoRNAs: Structural, functional and developmental insights

Animal Genetics

Volumn 44, Issue 1, 2013, Pages 24-33

  Liu, Nan ^a   Xiao, Bang ^a   Ren, Hong Yan ^a   Tang, Zhong Lin ^a   Li, Kui ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

characterization; expression pattern; identification; pig; snoRNA

Indexed keywords

COMPLEMENTARY DNA; RNA; SMALL NUCLEOLAR RNA;

ANIMAL; ANIMAL DISEASE; ARTICLE; CHROMOSOME; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETIC ASSOCIATION; GENETICS; METABOLISM; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; REAL TIME POLYMERASE CHAIN REACTION; SWINE;

ANIMALS; BASE SEQUENCE; CHROMOSOMES, MAMMALIAN; CLONING, MOLECULAR; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOME-WIDE ASSOCIATION STUDY; REAL-TIME POLYMERASE CHAIN REACTION; RNA; RNA, SMALL NUCLEOLAR; SUS SCROFA;

ANIMALIA; BUXUS SEMPERVIRENS; SUIDAE; SUS; SUS SCROFA;

EID: 84872080598     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2012.02363.x     Document Type: Article

References (36)

1. Bachellerie J.P., Cavaille J., &, Huttenhofer A., (2002) The expanding snoRNA world. Biochimie 84, 775-90.
2. Balakin A.G., Smith L., &, 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, 823-34.
3. Barneche F., Gaspin C., Guyot R., &, Echeverria M., (2001) Identification of 66 box C/D snoRNAs in Arabidopsis thaliana: extensive gene duplications generated multiple isoforms predicting new ribosomal RNA 2′-O-methylation sites. Journal of Molecular Biology 311, 57-73.
4. Baxter-Roshek J.L., Petrov A.N., &, Dinman J.D., (2007) Optimization of ribosome structure and function by rRNA base modification. PLoS ONE 2, e174.
5. Brown J.W., Clark G.P., Leader D.J., Simpson C.G., &, Lowe T., (2001) Multiple snoRNA gene clusters from Arabidopsis. RNA 7, 1817-32.
6. Brown J.W., Echeverria M., Qu L.H., Lowe T.M., Bachellerie J.P., Huttenhofer A., Kastenmayer J.P., Green P.J., Shaw P., &, Marshall D.F., (2003) Plant snoRNA database. Nucleic Acids Research 31, 432-5.
7. Chen C.L., Liang D., Zhou H., Zhuo M., Chen Y.Q., &, Qu L.H., (2003) The high diversity of snoRNAs in plants: identification and comparative study of 120 snoRNA genes from Oryza sativa. Nucleic Acids Research 31, 2601-13.
8. Decatur W.A., &, Fournier M.J., (2002) rRNA modifications and ribosome function. Trends in Biochemical Sciences 27, 344-51.
9. Ganot P., Bortolin M.L., &, Kiss T., (1997a) Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89, 799-809.
10. Ganot P., Caizergues-Ferrer M., &, Kiss T., (1997b) The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondary structure and ubiquitous sequence elements essential for RNA accumulation. Genes & Development 11, 941-56.
11. Gardner P.P., Bateman A., &, Poole A.M., (2010) SnoPatrol: how many snoRNA genes are there? Journal of Biology 9, 4.
12. Gaspin C., Cavaille J., Erauso G., &, Bachellerie J.P., (2000) Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: lessons from the Pyrococcus genomes. Journal of Molecular Biology 297, 895-906.
13. Gerbi S.A., Borovjagin A.V., Ezrokhi M., &, Lange T.S., (2001) Ribosome biogenesis: role of small nucleolar RNA in maturation of eukaryotic rRNA. Cold Spring Harbor Symposia on Quantitative Biology 66, 575-90.
14. Guffanti E., Ferrari R., Preti M., Forloni M., Harismendy O., Lefebvre O., &, Dieci G., (2006) A minimal promoter for TFIIIC-dependent in vitro transcription of snoRNA and tRNA genes by RNA polymerase III. Journal of Biological Chemistry 281, 23945-57.
15. Jin H., Loria J.P., &, Moore P.B., (2007) Solution structure of an rRNA substrate bound to the pseudouridylation pocket of a box H/ACA snoRNA. Molecular Cell 26, 205-15.
16. Kishore S., &, Stamm S., (2006) Regulation of alternative splicing by snoRNAs. Cold Spring Harbor Symposia on Quantitative Biology 71, 329-34.
17. Kiss T., (2001) Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO Journal 20, 3617-22.
18. Kiss T., Fayet E., Jady B.E., Richard P., &, Weber M., (2006) Biogenesis and intranuclear trafficking of human box C/D and H/ACA RNPs. Cold Spring Harbor Symposia on Quantitative Biology 71, 407-17.
19. Kiss-Laszlo Z., Henry Y., Bachellerie J.P., Caizergues-Ferrer M., &, Kiss T., (1996) Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85, 1077-88.
20. Lestrade L., &, Weber M.J., (2006) snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Research 34, D158-62.
21. Liang D., Zhou H., Zhang P., Chen Y.Q., Chen X., Chen C.L., &, Qu L.H., (2002) A novel gene organization: intronic snoRNA gene clusters from Oryza sativa. Nucleic Acids Research 30, 3262-72.
22. Liang X.H., Uliel S., Hury A., Barth S., Doniger T., Unger R., &, Michaeli S., (2005) 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 11, 619-45.
23. Liang X.H., Hury A., Hoze E., Uliel S., Myslyuk I., Apatoff A., Unger R., &, Michaeli S., (2007) 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. Eukaryotic Cell 6, 361-77.
24. Liapunova N.A., Egolina N.A., Mkhitarova E.V., &, Viktorov V.V., (1988) [Interindividual and intercellular differences in the total activity of ribosomal genes detectable by the Ag staining of nucleolus organizer regions in human acrocentric chromosomes]. Genetika 24, 1282-8.
25. Liu N., Xiao Z.D., Yu C.H., Shao P., Liang Y.T., Guan D.G., Yang J.H., Chen C.L., Qu L.H., &, Zhou H., (2009) SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights. BMC Genomics 10, 515.
26. Lowe T.M., &, Eddy S.R., (1999) A computational screen for methylation guide snoRNAs in yeast. Science 283, 1168-71.
27. Ni J., Tien A.L., &, Fournier M.J., (1997) Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell 89, 565-73.
28. Omer A.D., Lowe T.M., Russell A.G., Ebhardt H., Eddy S.R., &, Dennis P.P., (2000) Homologs of small nucleolar RNAs in Archaea. Science 288, 517-22.
29. Reichow S.L., Hamma T., Ferre-D'Amare A.R., &, Varani G., (2007) The structure and function of small nucleolar ribonucleoproteins. Nucleic Acids Research 35, 1452-64.
30. Schattner P., Decatur W.A., Davis C.A., Ares M. Jr, Fournier M.J., &, Lowe T.M., (2004) Genome-wide searching for pseudouridylation guide snoRNAs: analysis of the Saccharomyces cerevisiae genome. Nucleic Acids Research 32, 4281-96.
31. Shao P., Yang J.H., Zhou H., Guan D.G., &, Qu L.H., (2009) Genome-wide analysis of chicken snoRNAs provides unique implications for the evolution of vertebrate snoRNAs. BMC Genomics 10, 86.
32. Vitali P., Royo H., Seitz H., Bachellerie J.P., Huttenhofer A., &, Cavaille J., (2003) Identification of 13 novel human modification guide RNAs. Nucleic Acids Research 31, 6543-51.
33. Xiao B., Zhang X., Li Y., Tang Z., Yang S., Mu Y., Cui W., Ao H., &, Li K., (2009) Identification, bioinformatic analysis and expression profiling of candidate mRNA-like non-coding RNAs in Sus scrofa. Journal of Genetics and Genomics 36, 695-702.
34. Zhang Y., Liu J., Jia C., et al,. (2010) Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs. BMC Genomics 11, 61.
35. Zhou H., Zhao J., Yu C.H., Luo Q.J., Chen Y.Q., Xiao Y., &, Qu L.H., (2004) Identification of a novel box C/D snoRNA from mouse nucleolar cDNA library. Gene 327, 99-105.
36. Zimmermann R.A., &, Dahlberg A.E., (1996) Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis. CRC Press, Boca Raton, FL.