title: In situ dissection of RNA functional subunits by domain-specific chromatin isolation by RNA purification (dChIRP).
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.
authors.affiliation: Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, CCSR 2130, 269 Campus Drive, Stanford, CA, 94305-5168, USA.
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Quinn
authors.forename: Howard Y
authors.initials: HY
authors.lastname: Chang
mesh_terms: D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry* / Q000235:genetics / Q000302:isolation & purification*; D029721:Drosophila Proteins / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D004331:Drosophila melanogaster / Q000235:genetics* / Q000378:metabolism; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D002843:Chromatin; D029721:Drosophila Proteins; D062085:RNA, Long Noncoding; D014157:Transcription Factors; C454144:roX1 protein, Drosophila