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Related Experiment Video

Updated: Oct 21, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
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RNA Secondary Structure Prediction Using High-throughput SHAPE

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fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.

Meredith Corley1, Ryan A Flynn2,3, Steven M Blue1

  • 1Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, UCSD Stem Cell Program, University of California San Diego, La Jolla, CA 92093, USA.

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|September 6, 2021
PubMed
Summary
This summary is machine-generated.

Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) and footprinting SHAPE (fSHAPE) methods, when combined with enhanced crosslinking and immunoprecipitation (eCLIP), reveal RNA secondary structures and protein interactions. These protocols advance RNA biology research.

Keywords:
AntibodyGenomicsMolecular BiologyRNAseq

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Structural Biology

Background:

  • RNA secondary structure is crucial for molecular functions and interactions.
  • Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a key technique for probing RNA structure.
  • Understanding RNA-protein interactions is vital for deciphering gene regulation and cellular processes.

Purpose of the Study:

  • To detail protocols for SHAPE-enhanced crosslinking and immunoprecipitation (SHAPE-eCLIP).
  • To describe protocols for footprinting SHAPE-enhanced crosslinking and immunoprecipitation (fSHAPE-eCLIP).
  • To present an analysis protocol for fSHAPE for identifying RNA bases interacting with proteins.

Main Methods:

  • Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) for RNA structure probing.
  • Footprinting SHAPE (fSHAPE) to detect RNA-protein hydrogen bonds.
  • Enhanced crosslinking and immunoprecipitation (eCLIP) to isolate protein-bound RNAs.
  • Combined SHAPE-eCLIP and fSHAPE-eCLIP methodologies.

Main Results:

  • Detailed protocols for SHAPE-eCLIP and fSHAPE-eCLIP are provided.
  • An analysis protocol for fSHAPE is described.
  • These methods enable simultaneous characterization of RNA structure and protein binding.

Conclusions:

  • SHAPE-eCLIP and fSHAPE-eCLIP are powerful techniques for studying RNA structure and protein interactions.
  • The described protocols facilitate comprehensive analysis of RNA regulatory mechanisms.
  • These advancements aid in understanding RNA's role in biological functions.