title: RNA antisense purification (RAP) for mapping RNA interactions with chromatin.
abstract: RNA-centric biochemical purification is a general approach for studying the functions and mechanisms of noncoding RNAs. Here, we describe the experimental procedures for RNA antisense purification (RAP), a method for selective purification of endogenous RNA complexes from cell extracts that enables mapping of RNA interactions with chromatin. In RAP, the user cross-links cells to fix endogenous RNA complexes and purifies these complexes through hybrid capture with biotinylated antisense oligos. DNA loci that interact with the target RNA are identified using high-throughput DNA sequencing.
authors.affiliation: Broad Institute of Harvard and MIT, 415 Main St., Cambridge, MA, 02142, USA, engreitz@mit.edu.
authors.forename: Jesse
authors.initials: J
authors.lastname: Engreitz
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.forename: Mitchell
authors.initials: M
authors.lastname: Guttman
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D002843:Chromatin / Q000378:metabolism*; D004247:DNA / Q000378:metabolism*; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D051379:Mice; D016372:RNA, Antisense / Q000302:isolation & purification*; D017423:Sequence Analysis, RNA; D012984:Software
chemical_list: D002843:Chromatin; D016372:RNA, Antisense; D004247:DNA