Research Focus: Elucidation and Determination of the Roles of RNA Structure in Cell Signaling and Environmental Response

RNAs fold into complex secondary and tertiary structures. We are interested in how environmental signals modulate RNA structure-function relationships. Until recently, however, no methods were available to probe the structures of all the RNAs (i.e. 'genome-wide') in a living system. In 2014, the Assmann and Bevilacqua labs developed such a method: 'Structure-seq' (Ding et al., 2014; Ritchey et al., 2019; Tack et. al., 2018). Structure-seq capitalizes on the ability of a membrane-permeant chemical, dimethyl sulfate, to methylate As and Cs in RNA that are not base-paired; accordingly, the presence of DMS reactivity indicates the absence of base pairing. Such methylation imposes a stop to the processivity of reverse transcriptase, and so can be read-out genome-wide by next-gen sequencing techniques. We illustrated the efficacy of our method in the model plant Arabidopsis (Ding et al., 2014). Many abiotic stresses, including temperature, salt, heavy metals, and cellular crowding (desiccation) are known to change RNA structure in the test tube.

We are currently applying our Structure-seq method to investigate how such abiotic stresses change RNA structure genome-wide in vivo in rice, in Arabidopsis, and in the model bacterium Bacillus subtilis in collaboration with Prof. Paul Babitze (Penn State). Our goal is to elucidate how such changes in structure affect mRNA processing (transcription, translation, splicing, stability, etc.) and global RNA function. Most recently, we have shown that heat shock in rice (Su et. al., 2018) and salinity stress in Arabidopsis (Tack et. al., 2020) reshape the RNA structurome and thereby impact RNA abundance. We are also developing (Mitchell et. al., 2018) and incorporating other structure-probing methods (Bevilacqua and Assmann, 2018; Bevilacqua and Assmann, 2018; Mitchell et. al. 2019), which will allow a more complete picture of the dynamic RNA structurome.