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RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs
Published on: July 11, 2020
Conservation of noncoding microsatellites in plants: implication for gene regulation
Lida Zhang1, Kaijing Zuo, Fei Zhang
1Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200030, China. zhangld@sjtu.edu.cn <zhangld@sjtu.edu.cn>
BMC Genomics
|December 26, 2006
Summary
Ancient conserved noncoding microsatellites (CNMSs) in plant genomes regulate gene expression. These microsatellites are involved in plant responses to light and salicylic acid, offering insights into plant-specific gene regulation.
Area of Science:
- Plant genomics
- Molecular biology
- Bioinformatics
Background:
- Microsatellites are abundant in plant genomes, particularly in 5' noncoding regions.
- While some microsatellites regulate genes, their general properties as regulatory elements remain largely unknown.
- This study investigates conserved noncoding microsatellites (CNMSs) in plant 5' noncoding regions.
Purpose of the Study:
- To identify and characterize conserved noncoding microsatellites (CNMSs) in the 5' noncoding regions of Arabidopsis and Brassica genomes.
- To determine the regulatory roles of these CNMSs in gene expression.
- To explore the evolutionary conservation and potential functions of microsatellites in plant gene regulation.
Main Methods:
- Inter- and intragenomic phylogenetic footprinting were used to identify CNMSs in Arabidopsis and Brassica.
- Computational scans identified known cis-regulatory elements within CNMSs.
- Gene expression patterns were analyzed to correlate CNMSs with specific regulatory responses.
Main Results:
- 247 orthologous and 122 paralogous CNMSs were identified, including CT/GA and CTT/GAA repeats.
- 18 microsatellites showed high conservation in regulatory regions of orthologous and paralogous genes, with some found in more distant homologs.
- Light-responsive elements were associated with CT/GA repeats, and salicylic acid-responsive elements with (CTT)n/(GAA)n repeats, with 70-80% of associated genes showing salicylic acid regulation.
Conclusions:
- Noncoding microsatellites can be ancient and conserved across plant species.
- Identified CNMSs function as regulatory elements involved in light and salicylic acid responses.
- These findings highlight the role of over-represented microsatellites in plant-specific gene regulation.
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