FSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
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ABSTRACT:
SUBMITTER: Corley M
PROVIDER: S-EPMC8406031 | biostudies-literature | 2021 Sep
REPOSITORIES: biostudies-literature
Publications
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
Corley Meredith M Flynn Ryan A RA Blue Steven M SM Yee Brian A BA Chang Howard Y HY Yeo Gene W GW
STAR protocols 20210825 3
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein to identify RNA bases that hydrogen-bond with protein. SHAPE or fSHAPE coupled with enhanced crosslinking and immunoprecipitation (SHAPE-eCLIP or fSHAPE-eCLIP) pulls down RNAs bound by any protein ...[more]
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