Understanding the transcriptome through RNA structure

Abstract

In addition to carrying information in their linear sequences of nucleotides (primary structure), RNA molecules fold into intricate shapes. Pairing of local nucleotides can create secondary structures such as hairpins and stem–loops, and interactions among distantly located sequences can create tertiary structures. RNA structures are involved in a wide range of cellular processes, including transcriptional and post-transcriptional regulation and sensing metabolites. Structures can occur in coding or non-coding RNAs, and learning more about RNA structure will improve our understanding of the transcriptome. Computational predictions of RNA structures have been important and continue to be refined and also combined with experimental methods. Experimental methods, which can involve enzymes or chemicals, to differentiate single- or double-stranded RNAs are now being scaled-up through coupling to next-generation sequencing.