Nucleic Acids Research, Vol 27, Issue 22 4457-4467, Copyright © 1999 by Oxford University Press
V Bourdeau, G Ferbeyre, M Pageau, B Paquin and R Cedergren
Functional analysis of genome sequences has largely ignored RNA genes and
their structures. We introduce here the notion of 'ribonomics' to describe
the search for the distribution of and eventually the determination of the
physiological roles of these RNA structures found in the sequence
databases. The utility of this approach is illustrated here by the
identification in the GenBank database of RNA motifs having known binding
or chemical activity. The frequency of these motifs indicates that most
have originated from evolutionary drift and are selectively neutral. On the
other hand, their distribution among species and their location within
genes suggest that the destiny of these motifs may be more elaborate. For
example, the hammerhead motif has a skewed organismal presence, is
phylogenetically stable and recent work on a schistosome version confirms
its in vivo biological activity. The under-representation of the
valine-binding motif and the Rev- binding element in GenBank hints at a
detrimental effect on cell growth or viability. Data on the presence and
the location of these motifs may provide critical guidance in the design of
experiments directed towards the understanding and the manipulation of RNA
complexes and activities in vivo.
ARTICLES
The distribution of RNA motifs in natural sequences
Departement de Biochimie, Universite de Montreal, C.P. 6128, Succursale Centre-Ville, Montreal, QC H3C 3J7, Canada.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. Briones, M. Stich, and S. C. Manrubia The dawn of the RNA World: Toward functional complexity through ligation of random RNA oligomers RNA, May 1, 2009; 15(5): 743 - 749. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. N. Vemuri and A. A. Aristidou Metabolic Engineering in the -omics Era: Elucidating and Modulating Regulatory Networks Microbiol. Mol. Biol. Rev., June 1, 2005; 69(2): 197 - 216. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. H. Gan, S. Pasquali, and T. Schlick Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design Nucleic Acids Res., June 1, 2003; 31(11): 2926 - 2943. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Z. Barciszewska, E. Wyszko, R. Bald, V. A. Erdmann, and J. Barciszewski 5S rRNA Is a Leadzyme. A Molecular Basis for Lead Toxicity J. Biochem., March 1, 2003; 133(3): 309 - 315. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. Nagaswamy, M. Larios-Sanz, J. Hury, S. Collins, Z. Zhang, Q. Zhao, and G. E. Fox NCIR: a database of non-canonical interactions in known RNA structures Nucleic Acids Res., January 1, 2002; 30(1): 395 - 397. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. J. Carter, I. Dubchak, and S. R. Holbrook A computational approach to identify genes for functional RNAs in genomic sequences Nucleic Acids Res., October 1, 2001; 29(19): 3928 - 3938. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Graf, D. Strothmann, S. Kurtz, and G. Steger HyPaLib: a database of RNAs and RNA structural elements defined by hybrid patterns Nucleic Acids Res., January 1, 2001; 29(1): 196 - 198. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. A. Rojas, A. Vazquez-Tello, G. Ferbeyre, F. Venanzetti, L. Bachmann, B. Paquin, V. Sbordoni, and R. Cedergren Hammerhead-mediated processing of satellite pDo500 family transcripts from Dolichopoda cave crickets Nucleic Acids Res., October 15, 2000; 28(20): 4037 - 4043. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Ferbeyre, V. Bourdeau, M. Pageau, P. Miramontes, and R. Cedergren Distribution of Hammerhead and Hammerhead-like RNA Motifs Through the GenBank Genome Res., July 1, 2000; 10(7): 1011 - 1019. [Abstract] [Full Text]
|
|