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Updated: Nov 5, 2025
RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE
Lu Chen1,2,3, Howard Y Chang4,5, Steven E Artandi1,2,3
1Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
None:
The majority of the mammalian genome is transcribed into non-coding RNAs, many of which co-evolve with RNA-binding proteins (RBPs) to function as biochemically defined and tractable ribonucleoproteins (RNPs). Here, we applied icSHAPE- a robust and versatile RNA structural probing pipeline- to endogenous RNPs purified from nuclei, providing base-resolution structural rationale for RNP activity and subcellular localization. Combining with genetic and biochemical reconstitutions, structural and functional alternations can be directly attributed to a given RBP without ambiguity. For complete details on the use and execution of this protocol, please refer to Chen et al. (2018).
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