New Era of Studying RNA Secondary Structure and Its Influence on Gene Regulation in Plants.

Xiaofei Yang,Minglei Yang,Hongjing Deng,Yiliang Ding

doi:10.3389/fpls.2018.00671

Abstract

The dynamic structure of RNA plays a central role in post-transcriptional regulation of gene expression such as RNA maturation, degradation, and translation. With the rise of next-generation sequencing, the study of RNA structure has been transformed from in vitro low-throughput RNA structure probing methods to in vivo high-throughput RNA structure profiling. The development of these methods enables incremental studies on the function of RNA structure to be performed, revealing new insights of novel regulatory mechanisms of RNA structure in plants. Genome-wide scale RNA structure profiling allows us to investigate general RNA structural features over 10s of 1000s of mRNAs and to compare RNA structuromes between plant species. Here, we provide a comprehensive and up-to-date overview of: (i) RNA structure probing methods; (ii) the biological functions of RNA structure; (iii) genome-wide RNA structural features corresponding to their regulatory mechanisms; and (iv) RNA structurome evolution in plants.

Highlights

The dynamic structure of RNA plays a central role in post-transcriptional regulation of gene expression such as RNA maturation, degradation, and translation
Advances in probing methods has enabled the highly-conserved plant long non-coding RNA (lncRNA) COOLAIR structure to be determined by chemical profiling with capillary electrophoresis (CE) (Hawkes et al, 2016)
A recent study combining genome-wide RNA binding protein (RBP) profiling and RNA secondary structure profiling shows that RBP binding sites tend to be more single-stranded (Gosai et al, 2015)