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Background  Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. Although some 5' noncoding microsatellites involved in gene regulation have been described, the general properties of microsatellites as regulatory elements are still unknown. To address the question of microsatellites associated with regulatory elements, we have analyzed the conserved noncoding microsatellite sequences (CNMSs) in the 5' noncoding regions by inter- and intragenomic phylogenetic footprinting in the  Arabidopsis  and  Brassica  genomes.    Results  We identified 247  Arabidopsis-Brassica  orthologous and 122  Arabidopsis  paralogous CNMSs, representing 491 CT/GA and CTT/GAA repeats, which accounted for 10.6% of these types located in the 500-bp regions upstream of coding sequences in the  Arabidopsis  genome. Among these identified CNMSs, 18 microsatellites show high conservation in the regulatory regions of both orthologous and paralogous genes, and some of them also appear in the corresponding positions of more distant homologs in  Arabidopsis , as well as in other plants. A computational scan of CNMSs for known  cis -regulatory elements showed that light responsive elements were clustered in the region of CT/GA repeats, as well as salicylic acid responsive elements in the (CTT) n /(GAA) n  sequences. Patterns of gene expression revealed that 70–80% of CNMS (CTT) n /(GAA) n  associated genes were regulated by salicylic acid, which was consistent with the prediction of regulatory elements  in silico .    Conclusion  Our analyses showed that some noncoding microsatellites were conserved in plants and appeared to be ancient. These CNMSs served as regulatory elements involved in light and salicylic acid responses. Our findings might have implications in the common features of the over-represented microsatellites for gene regulation in plant-specific pathways.

Conservation of noncoding microsatellites in plants: implication for gene regulation