Nature Reviews Genetics 12, 641-655 (September 2011) | doi:10.1038/nrg3049

Understanding the transcriptome through RNA structure

Yue Wan1, Michael Kertesz2, Robert C. Spitale1, Eran Segal3 & Howard Y. Chang1  About the authors


RNA structure is crucial for gene regulation and function. In the past, transcriptomes have largely been parsed by primary sequences and expression levels, but it is now becoming feasible to annotate and compare transcriptomes based on RNA structure. In addition to computational prediction methods, the recent advent of experimental techniques to probe RNA structure by high-throughput sequencing has enabled genome-wide measurements of RNA structure and has provided the first picture of the structural organization of a eukaryotic transcriptome — the 'RNA structurome'. With additional advances in method refinement and interpretation, structural views of the transcriptome should help to identify and validate regulatory RNA motifs that are involved in diverse cellular processes and thereby increase understanding of RNA function.

Author affiliations

  1. Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
  2. Howard Hughes Medical Institute and Department of Bioengineering, Stanford University, Stanford, California 94305, USA.
  3. Department of Computer Science and Applied Mathematics and Weizmann Institute of Science, Rehovot 76100, Israel.

Correspondence to: Howard Y. Chang1 Email:

Published online 18 August 2011