Experimental RNomics: Identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana

Current Biology

Volumn 12, Issue 23, 2002, Pages 2002-2013

  Marker, Claudia ^a   Zemann, Anja ^a   Terhörst, Tanja ^a   Kiefmann, Martin ^a   Kastenmayer, James P ^b   Green, Pamela ^c   Bachellerie, Jean Pierre ^d   Brosius, Jürgen ^a   Hüttenhofer, Alexander ^a  

^a UNIVERSITY OF MÜNSTER   (Germany)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c UNIVERSITY OF DELAWARE   (United States)

^d Université Paul Sabatier   (France)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC RNA; MESSENGER RNA; TRANSFER RNA; PLANT RNA; SMALL INTERFERING RNA;

CLASSIFICATION; DNA LIBRARY; MOLECULE; RNA SEQUENCE; RNA TRANSLATION; TISSUE SPECIFICITY; ARABIDOPSIS; ARTICLE; CHLOROPLAST; GENE LIBRARY; GENETICS; GENOME; MITOCHONDRION; MOLECULAR GENETICS; OPEN READING FRAME;

ARABIDOPSIS THALIANA;

ARABIDOPSIS; CHLOROPLASTS; GENE LIBRARY; GENOME, PLANT; MITOCHONDRIA; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; RNA, PLANT; RNA, SMALL INTERFERING;

EID: 0036898607     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0960-9822(02)01304-0     Document Type: Article

References (27)

1. Filipowicz, W. (2000). Imprinted expression of small nueleolar RNAs in brain: Time for RNomics. Proc. Natl. Acad. Sci. USA 97, 14035-14037.
2. 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.
3. Hüttenhofer, 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.
4. Tang, T.-H., Bachellerie, J.-P., Rozhdestvensky, T., Bortolin, M.-L., Huber, H., Drungowski, M., Elge, T., Brosius, J., and Hüttenhofer, A. (2002). Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc. Nat. Acad. Sci. USA 99, 7537-7541.
5. Brown, C.J., Hendrich, B.D., Rupert, J.L., Lafreniere, R.G., Xing, Y., Lawrence, J., and Willard, H.F. (1992). The human XIST gene: Analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71, 527-542.
6. Ambros, V. (2001). microRNAs: Tiny regulators with great potential. Cell 107, 823-826.
7. The Arabidopsis Genome Initiative (2000). Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
8. Gaspin, C., Cavaille, J., Erauso, G., and Bachellerie, J.P. (2000). Archaeal homologs of eukaryotic methylation guide small nucleolar RNAs: Lessons from the Pyrococcus genomes. J. Mol. Biol. 297, 895-906.
9. Omer, A.D., Lowe, T.M., Russell, A.G., Ebhardt, H., Eddy, S.R., and Dennis, P.P. (2000). Homologs of small nucleolar RNAs in Archaea. Science 288, 517-522.
10. Klein, R.J., Misulovin, Z., and Eddy, S.R. (2002). Noncoding RNA genes identified in AT-rich hyperthermophiles. Proc. Natl. Acad. Sci. USA 99, 7542-7547.
11. Barneche, F., Gaspin, C., Guyot, R., and 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. J. Mol. Biol. 311, 57-73.
12. Brown, J.W., Clark, G.P., Leader, D.J., Simpson, C.G., and Lowe, T. (2001). Multiple snoRNA gene clusters from Arabidopsis. RNA 7, 1817-1832.
13. Liang-Hu, Q., Qing, M., Hui, Z., and Yue-Qin, C. (2001). Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana. Nucleic Acids Res. 29, 1623-1630.
14. Llave, C., Kasschau, K.D., Rector, M.A., and Carrington, J.C. (2002). Endogenous and silencing-associated small RNAs in plants. Plant Cell 14, 1605-1619.
15. Reinhart, B.J., Weinstein, E.G., Rhoades, M.W., Bartel, B., and Bartel, D.P. (2002). MicroRNAs in plants. Genes Dev. 16, 1616-1626.
16. Bachellerie, J.P., Cavaille, J., and Qu, L.H. (2000). Nucleotide modifications of eukaryotic rRNAs: The world of small nucleolar RNAs revisited. In Ribosome: Structure, Function, Antibiotics and Cellular Interactions, R. Garrett, S. Douthwaite, A. Liljas, A. Matheson, P.B. Moore, and H. Noller, eds. (Washington, D.C.: ASM Press), pp. 191-203.
17. Weinstein, L.B., and Steitz, J.A. (1999). Guided tours: From precursor snoRNA to functional snoRNP. Curr. Opin. Cell Biol. 11, 378-384.
18. Filipowicz, W., and Pogacic, V. (2002). Biogenesis of small nucleolar ribonucleoproteins. Curr. Opin. Cell Biol. 14, 319-327.
19. Massenet, S., Mougin, A., and Branlant, C. (1998). Posttranscriptional modifications in the U snRNAs. In Modification and Editing of RNA: The Alteration of RNA Structure and Function, H. Grosjean and R. Benne, eds. (Washington, D.C.: ASM Press), pp. 201-228.
20. Ganot, P., Bortolin, M.L., and Kiss, T. (1997). Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs. Cell 89, 799-809.
21. Smith, C.M., and Steitz, J.A. (1997). Sno storm in the nucleolus: New roles for myriad small RNPs. Cell 89, 669-672.
22. Jady, B.E., and Kiss, T. (2001). A small nucleolar guide RNA functions both in 2′-O-ribose methylation and pseudouridylation of the U5 spliceosomal RNA. EMBO J. 20, 541-551.
23. Ni, J., Tien, A.L., and Fournier, M.J. (1997). Small nueleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Cell 89, 565-573.
24. Ofengand, J., and Bakin, A. (1997). Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts. J. Mol. Biol. 266, 246-268.
25. Meinke, D.W., Cherry, J.M., Dean, C., Rounsley, S.D., and Koornneef, M. (1998). Arabidopsis thaliana: A model plant for genome analysis. Science 282, 679-82.
26. Hayes, R., Kudla, J., Schuster, G., Gabay, L., Maliga, P., and Gruissem, W. (1996). Chloroplast mRNA 3"-end processing by a high molecular weight protein complex is regulated by nuclear encoded RNA binding proteins. EMBO J. 15, 1132-1141.
27. Brosius, J., and Tiedge, H. (2001). Neuronal BC1 RNA: Intracellular transport and activity-dependent modulation. Results Probl. Cell Differ. 34, 129-138.