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Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE.

ABSTRACT: 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).

SUBMITTER: Chen L

PROVIDER: S-EPMC8102169 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE.

Chen Lu L Chang Howard Y HY Artandi Steven E SE

STAR protocols 20210428 2

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 fun ...[more]

PMID: 33997809

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