Analysis of human small nucleolar RNAs (snoRNA) and the development of snoRNA modulator of gene expression vectors

Molecular Biology of the Cell

Volumn 21, Issue 9, 2010, Pages 1569-1584

  Ono, Motoharu ^a   Yamada, Kayo ^a   Avolio, Fabio ^a   Scott, Michelle S ^a   Van Koningsbruggen, Silvana ^a   Barton, Geoffrey J ^a   Lamond, Angus I ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; COMPLEMENTARY DNA; FIBRILLARIN; HYBRID PROTEIN; SMALL NUCLEOLAR RNA;

ARTICLE; GENE EXPRESSION; GENE SEQUENCE; GENE TARGETING; GENE VECTOR; HELA CELL; HUMAN; HUMAN CELL; MAMMAL CELL; PRIORITY JOURNAL; RNA ANALYSIS;

CELL NUCLEOLUS; CHROMOSOMAL PROTEINS, NON-HISTONE; CLONING, MOLECULAR; GENE EXPRESSION; GENE KNOCKDOWN TECHNIQUES; GENE LIBRARY; GENETIC VECTORS; GREEN FLUORESCENT PROTEINS; HELA CELLS; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICROSCOPY, FLUORESCENCE; MUTATION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA INTERFERENCE; RNA, SMALL NUCLEOLAR; SURVIVAL OF MOTOR NEURON 1 PROTEIN; TRANSFECTION;

MAMMALIA;

EID: 77951744202     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.E10-01-0078     Document Type: Article

References (36)

1. Andersen, J. S., Lam, Y. W., Leung, A. K., Ong, S. E., Lyon, C. E., Lamond, A. I., and Mann, M. (2005). Nucleolar proteome dynamics. Nature 433, 77-83.
2. Andersen, J. S., Lyon, C. E., Fox, A. H., Leung, A. K., Lam, Y. W., Steen, H., Mann, M., and Lamond, A. I. (2002). Directed proteomic analysis of the human nucleolus. Curr. Biol. 12, 1-11.
3. Boisvert, F. M., van Koningsbruggen, S., Navascues, J., and Lamond, A. I. (2007). The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 8, 574-585.
4. Bushati, N., and Cohen, S. M. (2007). microRNA functions. Annu. Rev. Cell Dev. Biol. 23, 175-205.
5. 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.
6. Cavaille, J., Nicoloso, M., and Bachellerie, J. P. (1996). Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 383, 732-735. (Pubitemid 26360652)
7. Chapman, E. J., and Carrington, J. C. (2007). Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet. 8, 884-896.
8. Chen, D., and Huang, S. (2001). Nucleolar components involved in ribosome biogenesis cycle between the nucleolus and nucleoplasm in interphase cells. J. Cell Biol. 153, 169-176. (Pubitemid 34280203)
9. Elbashir, S. M., Harborth, J., Lendeckel, W., Yalcin, A., Weber, K., and Tuschl, T. (2001). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411, 494-498. (Pubitemid 32494397)
10. Gonsalvez, G. B., Tian, L., Ospina, J. K., Boisvert, F. M., Lamond, A. I., and Matera, A. G. (2007). Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins. J. Cell Biol. 178, 733-740. (Pubitemid 47347358)
11. Goraczniak, R., Behlke, M. A., and Gunderson, S. I. (2009). Gene silencing by synthetic U1 adaptors. Nat. Biotechnol. 27, 257-263.
12. Greber, D., El-Baba, M. D., and Fussenegger, M. (2008). Intronically encoded siRNAs improve dynamic range of mammalian gene regulation systems and toggle switch. Nucleic Acids Res. 36, e101.
13. Greber, D., and Fussenegger, M. (2007). Multi-gene engineering: simultaneous expression and knockdown of six genes off a single platform. Biotechnol. Bioeng. 96, 821-834.
14. Hsieh-Li, H. M., Chang, J. G., Jong, Y. J., Wu, M. H., Wang, N. M., Tsai, C. H., and Li, H. (2000). A mouse model for spinal muscular atrophy. Nat. Genet. 24, 66-70.
15. Kent, W. J. (2002). BLAT-the BLAST-like alignment tool. Genome Res. 12, 656-664.
16. Kent, W. J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D. (2003). Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc. Natl. Acad. Sci. USA 100, 11484-11489.
17. Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., and Haussler, D. (2002). The human genome browser at UCSC. Genome Res. 12, 996-1006.
18. Kishore, S., and Stamm, S. (2006). The snoRNA HBII-52 regulates alternative splicing of the serotonin receptor 2C. Science 311, 230-232. (Pubitemid 43108188)
19. Kiss, T. (2001). Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J. 20, 3617-3622.
20. 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.
21. Lam, Y. W., Lamond, A. I., Mann, M., and Andersen, J. S. (2007). Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins. Curr. Biol. 17, 749-760.
22. Lemm, I., Girard, C., Kuhn, A. N., Watkins, N. J., Schneider, M., Bordonne, R., and Luhrmann, R. (2006). Ongoing U snRNP biogenesis is required for the integrity of Cajal bodies. Mol. Biol. Cell 17, 3221-3231.
23. 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.
24. Leung, A. K., Gerlich, D., Miller, G., Lyon, C., Lam, Y. W., Lleres, D., Daigle, N., Zomerdijk, J., Ellenberg, J., and Lamond, A. I. (2004). Quantitative kinetic analysis of nucleolar breakdown and reassembly during mitosis in live human cells. J. Cell Biol. 166, 787-800. (Pubitemid 39249831)
25. Maden, B. E. (1990). The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog. Nucleic Acid Res. Mol. Biol. 39, 241-303.
26. Matera, A. G., Terns, R. M., and Terns, M. P. (2007). Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat. Rev. Mol. Cell Biol. 8, 209-220.
27. Pall, G. S., Codony-Servat, C., Byrne, J., Ritchie, L., and Hamilton, A. (2007). Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot. Nucleic Acids Res. 35, e60.s. (Pubitemid 47073696)
28. Phair, R. D., and Misteli, T. (2000). High mobility of proteins in the mammalian cell nucleus. Nature 404, 604-609.
29. Ruby, J. G., Jan, C. H., and Bartel, D. P. (2007). Intronic microRNA precursors that bypass Drosha processing. Nature 448, 83-86.
30. Siepel, A., et al. (2005). Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050. (Pubitemid 41126859)
31. Smith, C. M., and Steitz, J. A. (1998). Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5′-terminal oligopyrimidine gene family reveals common features of snoRNA host genes. Mol. Cell. Biol. 18, 6897-6909.
32. Trinkle-Mulcahy, L., Andersen, J., Lam, Y. W., Moorhead, G., Mann, M., and Lamond, A. I. (2006). Repo-Man recruits PP1 gamma to chromatin and is essential for cell viability. J. Cell Biol. 172, 679-692. (Pubitemid 43306225)
33. Trinkle-Mulcahy, L., et al. (2008). Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J. Cell Biol. 183, 223-239.
34. Tycowski, K. T., You, Z. H., Graham, P. J., and Steitz, J. A. (1998). Modification of U6 spliceosomal RNA is guided by other small RNAs. Mol. Cell 2, 629-638.
35. Weinstein, L. B., and Steitz, J. A. (1999). Guided tours: from precursor snoRNA to functional snoRNP. Curr. Opin. Cell Biol. 11, 378-384.
36. Zhou, X. D., Liu, L. Z., Qian, G. S., Huang, G. J., and Chen, J. (2002). [Cloning and sequence analysis of a new, full-length cDNA fragment of drug resistance-related gene in human lung adenocarcinoma]. Ai Zheng 21, 341-345.