title: Understanding RNA-Chromatin Interactions Using Chromatin Isolation by RNA Purification (ChIRP).
abstract: ChIRP is a novel and easy-to-use technique for studying long noncoding RNA (lncRNA)-chromatin interactions. RNA and chromatin are cross-linked in vivo using formaldehyde or glutaraldehyde, and purified using biotinylated antisense oligonucleotides that hybridize to the target RNA. Co-precipitated DNA is then purified and analyzed by quantitative PCR (qPCR) or high-throughput sequencing.
authors.affiliation: Center for Personal Dynamic Regulomes, Stanford University, 269 Campus Drive, Stanford, CA, 94305, USA.
authors.forename: Ci
authors.initials: C
authors.lastname: Chu
authors.affiliation: Center for Personal Dynamic Regulomes, Stanford University, 269 Campus Drive, Stanford, CA, 94305, USA. howchang@stanford.edu.
authors.forename: Howard Y
authors.initials: HY
authors.lastname: Chang
mesh_terms: D019921:Biotinylation; D002843:Chromatin / Q000235:genetics / Q000302:isolation & purification*; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D009693:Nucleic Acid Hybridization / Q000235:genetics; D016133:Polymerase Chain Reaction / Q000379:methods; D012313:RNA / Q000235:genetics / Q000302:isolation & purification*; D062085:RNA, Long Noncoding / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D002843:Chromatin; D062085:RNA, Long Noncoding; D012313:RNA; D004247:DNA
keywords: Chromatin; Cross-linking; High-throughput sequencing; lncRNA