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Nuclear Bodies and Noncoding RNAs

Volume 1262 of the series Methods in Molecular Biology pp 199-213

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In Situ Dissection of RNA Functional Subunits by Domain-Specific Chromatin Isolation by RNA Purification (dChIRP)

  • Jeffrey J. QuinnAffiliated withHoward Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of MedicineDepartment of Bioengineering, Stanford University Schools of Medicine and Engineering
  • , Howard Y. ChangAffiliated withHoward Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine Email author 

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Abstract

Here we describe domain-specific chromatin isolation by RNA purification (dChIRP), a technique for dissecting the functional domains of a target RNA in situ. For an RNA of interest, dChIRP can identify domain-level intramolecular and intermolecular RNA–RNA, RNA–protein, and RNA–DNA interactions and maps the RNA’s genomic binding sites with higher precision than domain-agnostic methods. We illustrate how this technique has been applied to the roX1 lncRNA to resolve its domain-level architecture, discover its protein- and chromatin-interacting domains, and map its occupancy on the X chromosome.

Key words

RNA Long noncoding RNA ChIRP Chromatin RNA-binding protein RNA domains