Focus on RNA Secondary Structure

In parallel to the genetic code for protein synthesis, a second layer of information is embedded in all RNA transcripts in the form of RNA structure. RNA structure influences practically every step in the gene expression program. However, the nature of most RNA structures or effects of sequence variation on structure are not known. In a recent study, researchers from Stanford University School of Medicine report the initial landscape and variation of RNA secondary structures (RSSs) in a human family trio (mother, father and their child)1. These results highlight the potentially broad contribution of RNA structure and its variation to gene regulation.


RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. In a second study, researchers from Pennsylvania State University present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing2. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.


  1. Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY. (2014) Landscape and variation of RNA secondary structure across the human transcriptome. Nature 505(7485), 706-9. [abstract]
  2. Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM. (2014) In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 505(7485), 696-700. [abstract]