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.
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Quinn, J.J., Chang, H.Y. (2015). In Situ Dissection of RNA Functional Subunits by Domain-Specific Chromatin Isolation by RNA Purification (dChIRP). In: Nakagawa, S., Hirose, T. (eds) Nuclear Bodies and Noncoding RNAs. Methods in Molecular Biology, vol 1262. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2253-6_12
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DOI: https://doi.org/10.1007/978-1-4939-2253-6_12
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