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Microarray analysis of wild-type (WT; Ler-0) and smn2-90 mutants to identify SMN2-regulated defense-related genes

ABSTRACT: Transcriptome analysis to identify genes up- and down-regulated genes in smn2-90 mutant compared with WT plants with or without flg22 elicitation.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE143778 | GEO | 2023/01/16

REPOSITORIES: GEO

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RNA-Seq of wild-type (WT) and smn2 mutants for quantitative analysis of transcriptomes and mapping SMN2-dependent degraded regions

Project description:To compare expression of defense-related genes between WT and smn2 mutant, we performed the RNA-seq analysis using the total RNA prepared from Arabidopsis WT and smn2 seedlings. RNA-seq profiling showed 250 Differentially Expressed Genes (DEGs) detected in smn2 compared to WT. Genome-wide mapping of DEG regions was also performed to elucidate SMN2-dependent degraded regions in defense-related genes.

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Project description:Small molecule splicing modifiers have been extensively described which target the generic splicing machinery and thus have low target specificity. We have identified potent splicing modifiers with unprecedented high selectively, correcting the splicing deficit of the SMN2 (survival motor neuron 2) gene in Spinal Muscular Atrophy (SMA). Here we show that they directly bind to two sites of the SMN2 pre-mRNA, thereby stabilizing a novel ribonucleoprotein (RNP) complex in the SMN2 gene that is critical for the high target specificity of these small molecules over other genes. In addition to the therapeutic potential of these molecules for treatment of SMA, our work may have wide-ranging consequences for further research to identify small molecules that target splicing correction of specific genes by interacting with tertiary RNA structures.

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Expression analysis of Arabidopsis mpk11 mutant treated with flg22

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