RNA structure is intimately connected to RNA function. Because RNA structure is highly sensitive to the physico-chemical environment, including temperature, crowding, pH, Mg2+ concentration etc., the structure of the same RNA molecule can differ radically in vitro vs. in vivo. We recently developed a method, Structure-seq, that combines chemical probing of RNA structure with high throughput sequencing, thus allowing characterization of RNA structure genome-wide and in vivo1. Our application of Structure-seq to the model plant Arabidopsis has revealed significant correlations between DMS reactivity and alternative polyadenylation, alternative splicing, and gene function1. In particular, we have found that mRNAs of housekeeping genes tend to exhibit features associated with structural stability, while mRNAs of genes encoding proteins with stress-related functions tend to exhibit features associated with structural plasticity. We also found a correlation between protein structure and the corresponding mRNA structure. Currently, we are applying Structure-seq to rice in order to assess genome-wide changes in RNA structure induced by abiotic stressors, to evaluate the hypothesis that such structure changes play significant roles in the regulation of gene expression. 1. Ding, Y., Tang, Y., Kwok, C-K, Zhang, Y., Bevilacqua, P.C., Assmann, S.M. 2014. Nature 505: 696-700.

Revealing RNA structure-function relationships in vivo and genome-wide

251st National Meeting (2016)

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