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Plant Physiol, November 2001, Vol. 127, pp. 765-776
Identification and Analysis of Arabidopsis Expressed Sequence
Tags Characteristic of Non-Coding RNAs1
Gustavo C.
MacIntosh,
Curtis
Wilkerson, and
Pamela J.
Green*
Michigan State University and Department of Energy Plant Research
Laboratory (G.C.M., C.W., P.J.G.) and Department of Biochemistry
(P.J.G.), Michigan State University, East Lansing, Michigan
48824
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.
1
This work was supported by the National Science
Foundation (grant no. DBN9872638 to P.J.G.) and by the U.S. Department
of Energy (grant no. DE-FG02-91ER20021 to P.J.G.).
*
Corresponding author; e-mail green{at}msu.edu; fax
517-355-9298.
© 2001 American Society of Plant Physiologists
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