Conservation of noncoding microsatellites in plants: implication for gene regulation

Lida Zhang,Fei Zhang,Xiaofen Sun,Yidong Zhang,Jiang Wang,Kaijing Zuo,Kexuan Tang,Youfang Cao

doi:10.1186/1471-2164-7-323

Lida Zhang, Fei Zhang + Show 6 more

Open Access

https://doi.org/10.1186/1471-2164-7-323

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Abstract

BackgroundMicrosatellites 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.ResultsWe 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.ConclusionOur 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.

Highlights

Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions
In Arabidopsis thaliana, this feature is mostly attributable to the fact that complementary sequences to (CT)/GA and CTT/GAA repeats are more frequently found in 5'-flanks than in other genomic regions, suggesting that they can potentially function as factors in regulating gene expression [7]
We identified 247 Arabidopsis-Brassica orthologous conserved noncoding microsatellite sequences (CNMSs) and 122 Arabidopsis paralogous CNMSs [see Additional file 1], involving 491 CT/GA and CTT/GAA repeats respectively (Table 1), which accounted for 10.6% of these types located in the 500-bp regions upstream of coding sequences in the Arabidopsis genome

Summary

Introduction

Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. The (GA)n sequences in regulatory regions of some plant genes can be recognized by GAGA-binding factors [12,13,14], and more generally, the GA-rich element, a more complex 9 base pairs (bp) based (GA)n repeat, has been shown to have protein-binding affinity [15]. Another major microsatellite in plants, the trinucleotide repeat sequence (GAA)n presented within 5'UTR of ntp303 was found important in the modulation of transcription and translation efficiency [16]. The mechanism is still unclear, the microsatellite length polymorphism is thought to affect the expression of the related genes of amylose synthesis

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