High Throughput Data Analysis Of RNA Secondary Structure In Arabidopsis Thaliana

RNA structure plays a crucial role in gene maturation, regulation and function. Determining the form and frequency of RNA folds is essential for a better understanding of how RNA exerts its functions in vivo. With the recent advent of high-throughput technologies, which combined with chemical modification or strand-specific enzymes cleavage, it is realistic to begin analyzing RNA structures on a genome-wide scale.The dimethyl sulphate (DMS) modification based high-throughput sequencing data in Arabidopsis thaliana were analyzed by two different computational methods (PARS and Structure-seq methods). The result reveals that these two methodologies show no significant difference when dealing with the same data set. Moreover, a novel INDEX was proposed to reflect the extent of DMS modification in each transcript. The Gene Ontology annotations of those transcripts in the Top 10% of the Index distribution are enriched in three processes:(a) annotations of biological functions related to stress and stimulus responses; (b) transport process; (c) energy metabolic process. Lastly, analysis the structure patterns of miRNA target sites shows that the target sites have higher average DMS score compared with the flanking regions (50 nt), indicating that the miRNA target sites in transcripts are less structured than their flanking regions in A. thaliana. Probing RNA secondary structure by high-throughput sequencing will enable us to better understand the relationship between RNA secondary structure and functions in diverse cellular processes.