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

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.

Source: Springer protocols feed by Genetics/Genomics - January 1, 2015 Category: Genetics & Stem Cells Source Type: news