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. 2001 Nov;127(3):765-76.

Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs

G C MacIntosh  1 , C Wilkerson, P J Green
Affiliations

Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs

G C MacIntosh et al. Plant Physiol. 2001 Nov.

Abstract

Sequencing of the Arabidopsis genome has led to the identification of thousands of new putative genes based on the predicted proteins they encode. Genes encoding tRNAs, ribosomal RNAs, and small nucleolar RNAs have also been annotated; however, a potentially important class of genes has largely escaped previous annotation efforts. These genes correspond to RNAs that lack significant open reading frames and encode RNA as their final product. Accumulating evidence indicates that such "non-coding RNAs" (ncRNAs) can play critical roles in a wide range of cellular processes, including chromosomal silencing, transcriptional regulation, developmental control, and responses to stress. Approximately 15 putative Arabidopsis ncRNAs have been reported in the literature or have been annotated. Although several have homologs in other plant species, all appear to be plant specific, with the exception of signal recognition particle RNA. Conversely, none of the ncRNAs reported from yeast or animal systems have homologs in Arabidopsis or other plants. To identify additional genes that are likely to encode ncRNAs, we used computational tools to filter protein-coding genes from genes corresponding to 20,000 expressed sequence tag clones. Using this strategy, we identified 19 clones with characteristics of ncRNAs, nine putative peptide-coding RNAs with open reading frames smaller than 100 amino acids, and 11 that could not be differentiated between the two categories. Again, none of these clones had homologs outside the plant kingdom, suggesting that most Arabidopsis ncRNAs are likely plant specific. These data indicate that ncRNAs represent a significant and underdeveloped aspect of Arabidopsis genomics that deserves further study.

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Figures

Figure 1
Figure 1
Schematic representation of the computational methods and individual inspection used to identify ESTs with characteristics of potential ncRNAs or with ORFs smaller than 100 aa.
Figure 2
Figure 2
Criteria used to classify individual ESTs as putative ncRNAs or pepRNAs. A, Criterion used for ESTs with homologs in other species. Left, Comparison of a putative peptide-coding Arabidopsis (At) EST (289G12T7) with homologs from B. rapa (Br) and tomato (Le) at the nt (top) and aa (bottom) levels. Right, Same comparison for an EST corresponding to an ncRNA (AtGut15) with homologs from G. max (Gm) and tomato. Black and gray boxes indicate identity and similarity, respectively. Asterisk, Indicates third-position base changes that do not produce changes in aa of the corresponding ORF. M, Start codon of the longest conserved ORF. B, Criterion used for ESTs without homologs in other species. In this case, six-frame translation was used to predict ORFs. ESTs with no significant ORF, such as EST 91E4T7 depicted in this figure, were classified as ncRNAs. Arrows indicate length and strand of putative ORFs.
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