Conservation of noncoding microsatellites in plants: implication for gene regulation

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.

Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes

“…And we found that the introns didn′t contain more hexanucleotide P-SSRs than exons, which was inconsistent with previous reports [2]. It has been reported that CDSs are preferentially selected with tri- and hexanucleotide SSR motifs [3, 28,30,43,46], which can reduce potential translational frameshift mutations [47]. This evidence can help to explain why tri-fold nucleotide SSR motifs are more frequent in CDSs than other genomic regions.…”

Development and Application of Microsatellites in Candidate Genes Related to Wood Properties in the Chinese White Poplar (Populus tomentosa Carr.)

“…For example, SSRs in coding regions that result in amino acid changes can cause either loss or gain of function, SSRs in the 5′UTR can affect gene transcription or translation, SSRs in the 3′UTR can be responsible for gene silencing or transcription slippage, and SSRs in introns might act as transcriptional enhancers of gene expression. 8,32,40 Previous study that phenylalanine ammonia-lyase (PAL) transcripts have been localized to develop xylem cells in aspen ( P. tremuloides ) stem, was consistent with its involvement in lignin biosynthesis. 41 This report supported the identification of a single-marker non-coding association in PtoPAL 2 that explained 4.6% of the phenotypic variation in lignin content (Table 5).…”

Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping

“…The expansion and contraction of microsatellite repeats in the 5′ UTRs of genes have significance in regulating gene expression for many traits including amylose content in rice, 71 quality protein in maize 72 and light and salicylic responses in Brassica . 73 These findings thus inferred the significant correlation between the number of microsatellite repeat units in the different sequence components (functional domain and 5′ UTR) of seed weight/size trait-specific TFFDMS and TFGMS associated TF genes and their differential expression in the genes preferentially with regard to seed development in contrasting chickpea genotypes. Understanding the adaptive and evolutionary significance of such TFFDMS and TFGMS repeat expansion/contraction in the functional domain and 5′ UTRs of TF genes, respectively, is of relevance that needs further systematic experimentation by assaying a large number of contrasting chickpea genotypes of different tissues and/or stages (embryogenesis to maturation) of seed development.…”