Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE

Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE

Summary: 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-...

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Main Authors: Lu Chen, Howard Y. Chang, Steven E. Artandi
Format: Article
Language:English
Published: Elsevier 2021-06-01
Series:STAR Protocols
Subjects:
Cell separation/fractionation
Sequencing
RNA-seq
Molecular Biology
Gene Expression
CRISPR
Online Access:http://www.sciencedirect.com/science/article/pii/S2666166721001842
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spelling doaj-fc70a519090b4034b994595c8788deed2021-06-21T04:25:20ZengElsevierSTAR Protocols2666-16672021-06-0122100477Analysis of RNA conformation in endogenously assembled RNPs by icSHAPELu Chen0Howard Y. Chang1Steven E. Artandi2Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Corresponding authorCenter for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USAStanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Corresponding authorSummary: 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).http://www.sciencedirect.com/science/article/pii/S2666166721001842Cell separation/fractionationSequencingRNA-seqMolecular BiologyGene ExpressionCRISPR
collection DOAJ
language English
format Article
sources DOAJ
author Lu Chen
Howard Y. Chang
Steven E. Artandi
spellingShingle Lu Chen
Howard Y. Chang
Steven E. Artandi
Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE
STAR Protocols
Cell separation/fractionation
Sequencing
RNA-seq
Molecular Biology
Gene Expression
CRISPR
author_facet Lu Chen
Howard Y. Chang
Steven E. Artandi
author_sort Lu Chen
title Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE
title_short Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE
title_full Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE
title_fullStr Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE
title_full_unstemmed Analysis of RNA conformation in endogenously assembled RNPs by icSHAPE
title_sort analysis of rna conformation in endogenously assembled rnps by icshape
publisher Elsevier
series STAR Protocols
issn 2666-1667
publishDate 2021-06-01
description Summary: 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).
topic Cell separation/fractionation
Sequencing
RNA-seq
Molecular Biology
Gene Expression
CRISPR
url http://www.sciencedirect.com/science/article/pii/S2666166721001842
work_keys_str_mv AT luchen analysisofrnaconformationinendogenouslyassembledrnpsbyicshape
AT howardychang analysisofrnaconformationinendogenouslyassembledrnpsbyicshape
AT steveneartandi analysisofrnaconformationinendogenouslyassembledrnpsbyicshape
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