title: The genomic binding sites of a noncoding RNA.
abstract: Long noncoding RNAs (lncRNAs) have important regulatory roles and can function at the level of chromatin. To determine where lncRNAs bind to chromatin, we developed capture hybridization analysis of RNA targets (CHART), a hybridization-based technique that specifically enriches endogenous RNAs along with their targets from reversibly cross-linked chromatin extracts. CHART was used to enrich the DNA and protein targets of endogenous lncRNAs from flies and humans. This analysis was extended to genome-wide mapping of roX2, a well-studied ncRNA involved in dosage compensation in Drosophila. CHART revealed that roX2 binds at specific genomic sites that coincide with the binding sites of proteins from the male-specific lethal complex that affects dosage compensation. These results reveal the genomic targets of roX2 and demonstrate how CHART can be used to study RNAs in a manner analogous to chromatin immunoprecipitation for proteins.
authors.affiliation: Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Simon
authors.forename: Charlotte I
authors.initials: CI
authors.lastname: Wang
authors.forename: Peter V
authors.initials: PV
authors.lastname: Kharchenko
authors.forename: Jason A
authors.initials: JA
authors.lastname: West
authors.forename: Brad A
authors.initials: BA
authors.lastname: Chapman
authors.forename: Artyom A
authors.initials: AA
authors.lastname: Alekseyenko
authors.forename: Mark L
authors.initials: ML
authors.lastname: Borowsky
authors.forename: Mitzi I
authors.initials: MI
authors.lastname: Kuroda
authors.forename: Robert E
authors.initials: RE
authors.lastname: Kingston
mesh_terms: D020816:Amino Acid Motifs; D000818:Animals; D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D004303:Dosage Compensation, Genetic; D004330:Drosophila / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics*; D023281:Genomics; D008297:Male; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization; D022661:RNA, Untranslated / Q000235:genetics*; D016601:RNA-Binding Proteins / Q000235:genetics*; D016914:Ribonuclease H / Q000737:chemistry
chemical_list: D002843:Chromatin; D029721:Drosophila Proteins; C092595:Pabp2 protein, Drosophila; D022661:RNA, Untranslated; D016601:RNA-Binding Proteins; D016914:Ribonuclease H