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Published on May 11, 2007; 10.1104/pp.107.100396

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Received March 29, 2007
Accepted May 2, 2007

Distinct Expression Patterns of Natural Antisense Transcripts in Arabidopsis

Stefan R. Henz , Jason S. Cumbie , Kristin D. Kasschau , Jan U. Lohmann , James C. Carrington , Detlef Weigel , and Markus Schmid *

Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstrasse 37-39, D-72076 Tübingen, Germany; and Center for Genome Research and Biocomputing and Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA

* Corresponding author; email: markus.schmid{at}tuebingen.mpg.de.

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 anti-correlated 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 thaliana genome, show anti-correlated expression patterns. Indeed, global expression profiles of pairs of cis-NATs on average have significantly lower pairwise Pearson correlation coefficients (PCC) than other pairs of neighboring genes whose transcripts do not overlap. However, anti-correlated expression that is greater than expected by chance is only found in a small number of cis-NAT pairs. The degree of anti-correlation 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 MPSS tags. However, the overlapping regions of cis-NATs appeared to be enriched for small RNA loci compared to non-overlapping regions. Furthermore, expression of cis-NATs was not disproportionately affected in various RNA silencing mutants. Our results demonstrate that there is a trend towards anti-correlated 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.




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