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

Part of the Methods in Molecular Biology book series (MIMB, volume 1262)

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 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Howard Hughes Medical Institute and Program in Epithelial BiologyStanford University School of MedicineStanfordUSA
  2. 2.Department of BioengineeringStanford University Schools of Medicine and EngineeringStanfordUSA

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