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Published on October 6, 2006; 10.1104/pp.106.085639

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Received June 22, 2006
Accepted September 24, 2006

Large-scale Cis-element Detection by Analysis of Correlated Expression and Sequence Conservation between Arabidopsis and Brassica oleracea

Georg Haberer , Michael T Mader , Peter Kosarev , Manuel Spannagl , Li Yang , and Klaus FX Mayer *

MIPS, Institute for Bioinformatics, GSF National Research Center for Environment and Health, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany
Institute of Stem Cell Research, GSF National Research Center for Environment and Health, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany

* Corresponding author; email: Kmayer{at}gsf.de.

The rapidly increasing amount of plant genomic sequences allows for the detection of cis-elements through comparative methods. In addition large-scale gene expression data for Arabidopsis thaliana have recently become available. Co-expression and evolutionarily conserved sequences are criteria, widely used to identify shared cis-regulatory elements. In our study we employ an integrated approach to combine two sources of information, co-expression and sequence conservation. Best candidate orthologous promoter sequences were identified by a bidirectional best blast hit strategy in genome survey sequences from Brassica oleracea. The analysis of 779 microarrays from 81 different experiments provided detailed expression information for Arabidopsis genes co-expressed in multiple tissues and under various conditions and developmental stages. We discovered candidate transcription factor binding sites in 64% of the Arabidopsis genes analyzed. Among them, we detected experimentally verified binding sites and showed strong enrichment of shared cis-elements within functionally related genes. This study demonstrates the value of partially shotgun sequenced genomes and their combinatorial use with functional genomics data to address complex questions in comparative genomics.




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