Genome-Wide Approaches for RNA Structure Probing

  • Ian M. Silverman
  • Nathan D. Berkowitz
  • Sager J. Gosai
  • Brian D. Gregory
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 907)


RNA molecules of all types fold into complex secondary and tertiary structures that are important for their function and regulation. Structural and catalytic RNAs such as ribosomal RNA (rRNA) and transfer RNA (tRNA) are central players in protein synthesis, and only function through their proper folding into intricate three-dimensional structures. Studies of messenger RNA (mRNA) regulation have also revealed that structural elements embedded within these RNA species are important for the proper regulation of their total level in the transcriptome. More recently, the discovery of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) has shed light on the importance of RNA structure to genome, transcriptome, and proteome regulation. Due to the relatively small number, high conservation, and importance of structural and catalytic RNAs to all life, much early work in RNA structure analysis mapped out a detailed view of these molecules. Computational and physical methods were used in concert with enzymatic and chemical structure probing to create high-resolution models of these fundamental biological molecules. However, the recent expansion in our knowledge of the importance of RNA structure to coding and regulatory RNAs has left the field in need of faster and scalable methods for high-throughput structural analysis. To address this, nuclease and chemical RNA structure probing methodologies have been adapted for genome-wide analysis. These methods have been deployed to globally characterize thousands of RNA structures in a single experiment. Here, we review these experimental methodologies for high-throughput RNA structure determination and discuss the insights gained from each approach.


PARS FragSeq ds/ssRNA-seq DMS-seq Structure-seq CIRS-seq MOD-seq hSHAPE SHAPE-CE SHAPE-seq 



We thank past and present members of the Gregory lab for helpful discussions, especially Qi Zheng, Fan Li, and Lee Vandivier. This work was supported by an NSF Career Award MCB-1053846 and NSF grant MCB-1243947 to BDG. We declare no competing financial interests.


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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Ian M. Silverman
    • 1
    • 2
  • Nathan D. Berkowitz
    • 1
    • 3
  • Sager J. Gosai
    • 1
  • Brian D. Gregory
    • 1
    • 2
    • 3
  1. 1.Department of BiologyUniversity of PennsylvaniaPhiladelphiaUSA
  2. 2.Cell and Molecular Biology Graduate GroupUniversity of PennsylvaniaPhiladelphiaUSA
  3. 3.Genomics and Computational Biology Graduate GroupUniversity of PennsylvaniaPhiladelphiaUSA

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