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Methods Mol Biol. 2015;1262:199-213. doi: 10.1007/978-1-4939-2253-6_12.

In situ dissection of RNA functional subunits by domain-specific chromatin isolation by RNA purification (dChIRP).

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Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2130, 269 Campus Drive, Stanford, CA, 94305-5168, USA.


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.

[Indexed for MEDLINE]

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