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First published online May 11, 2007; 10.1104/pp.107.100396 Plant Physiology 144:1247-1255 (2007) © 2007 American Society of Plant Biologists Distinct Expression Patterns of Natural Antisense Transcripts in Arabidopsis1,[C],[W]Max Planck Institute for Developmental Biology, Department of Molecular Biology, D–72076 Tuebingen, Germany (S.R.H., J.U.L., D.W., M.S.); and Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331 (J.S.C., K.D.K., J.C.C.)
It has been shown that overlapping cis-natural antisense transcripts (cis-NATs) can form a regulatory circuit in which small RNAs derived from one transcript regulate stability of the other transcript, which manifests itself as anticorrelated expression. However, little is known about how widespread antagonistic expression of cis-NATs is. We have determined how frequently cis-NAT pairs, which make up 7.4% of annotated transcription units in the Arabidopsis (Arabidopsis thaliana) genome, show anticorrelated expression patterns. Indeed, global expression profiles of pairs of cis-NATs on average have significantly lower pairwise Pearson correlation coefficients than other pairs of neighboring genes whose transcripts do not overlap. However, anticorrelated expression that is greater than expected by chance is found in only a small number of cis-NAT pairs. The degree of anticorrelation does not depend on the length of the overlap or on the distance of the 5' ends of the transcripts. Consistent with earlier findings, cis-NATs do not exhibit an increased likelihood to give rise to small RNAs, as determined from available small RNA sequences and massively parallel signature sequencing tags. However, the overlapping regions of cis-NATs appeared to be enriched for small RNA loci compared to nonoverlapping regions. Furthermore, expression of cis-NATs was not disproportionately affected in various RNA-silencing mutants. Our results demonstrate that there is a trend toward anticorrelated expression of cis-NAT pairs in Arabidopsis, but currently available data do not produce a strong signature of small RNA-mediated silencing for this process.
1 This work was supported by the Max Planck Society, by the National Science Foundation (grant no. MCB–0618433 to J.C.C.), and by the U.S. Department of Agriculture (grant no. 2005–35319–15280 to J.C.C.). The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Markus Schmid (markus.schmid{at}tuebingen.mpg.de). [C] Some figures in this article are displayed in color online but in black and white in the print edition. [W] Online version contains Web-only data. www.plantphysiol.org/cgi/doi/10.1104/pp.107.100396 * Corresponding author; e-mail markus.schmid{at}tuebingen.mpg.de; fax 49–7071–601–1412. Received March 29, 2007; accepted May 2, 2007; published May 11, 2007. This article has been cited by other articles:
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