SHAPE–Seq: High-Throughput RNA Structure Analysis

  1. Stefanie A. Mortimer1,
  2. Cole Trapnell2,6,
  3. Sharon Aviran3,6,
  4. Lior Pachter1,5,
  5. Julius B. Lucks4

Published Online: 1 DEC 2012

DOI: 10.1002/9780470559277.ch120019

Current Protocols in Chemical Biology

Current Protocols in Chemical Biology

How to Cite

Mortimer, S. A., Trapnell, C., Aviran, S., Pachter, L. and Lucks, J. B. 2012. SHAPE–Seq: High-Throughput RNA Structure Analysis. Current Protocols in Chemical Biology. 4:275–297.

Author Information

  1. 1

    Department of Molecular and Cell Biology, University of California, Berkeley, California

  2. 2

    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts

  3. 3

    Center for Computational Biology and the California Institute for Quantitative Biomedical Research, University of California, Berkeley, California

  4. 4

    School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York

  5. 5

    Department of Mathematics, University of California, Berkeley, California

  6. 6

    These authors contributed equally to this work.

Publication History

  1. Published Online: 1 DEC 2012


Knowledge of RNA structure is critical to understanding both the important functional roles of RNA in biology and the engineering of RNA to control biological systems. This article contains a protocol for selective 2′-hydroxyl acylation analyzed by primer extension and sequencing (SHAPE-Seq) that, through a combination of structure-dependent chemical probing and next-generation sequencing technologies, achieves structural characterization of hundreds of RNAs in a single experiment. This protocol is applicable in a variety of conditions, and represents an important tool for understanding RNA biology. The protocol includes methods for the design and synthesis of RNA mixtures for study, and the construction and analysis of structure-dependent sequencing libraries that reveal structural information of the RNAs in the mixtures. The methods are generally applicable to studying RNA structure and interactions in vitro in a variety of conditions, and allows for the rapid characterization of RNA structures in a high-throughput manner. Curr. Protoc. Chem. Biol. 4:275-297 © 2012 by John Wiley & Sons, Inc.


  • RNA structure;
  • next-generation sequencing;
  • chemical probing;
  • high throughput