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Nat Biotechnol. 2014 Sep;32(9):933-940. doi: 10.1038/nbt.2943. Epub 2014 Jul 6.

Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification.

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Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford CA 94305, USA.
Department of Bioengineering, Stanford University Schools of Medicine and Engineering, Stanford CA 94305, USA.
Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg im Breisgau, Germany.
Contributed equally


Little is known about the functional domain architecture of long noncoding RNAs (lncRNAs) because of a relative paucity of suitable methods to analyze RNA function at a domain level. Here we describe domain-specific chromatin isolation by RNA purification (dChIRP), a scalable technique to dissect pairwise RNA-RNA, RNA-protein and RNA-chromatin interactions at the level of individual RNA domains in living cells. dChIRP of roX1, a lncRNA essential for Drosophila melanogaster X-chromosome dosage compensation, reveals a 'three-fingered hand' ribonucleoprotein topology. Each RNA finger binds chromatin and the male-specific lethal (MSL) protein complex and can individually rescue male lethality in roX-null flies, thus defining a minimal RNA domain for chromosome-wide dosage compensation. dChIRP improves the RNA genomic localization signal by >20-fold relative to previous techniques, and these binding sites are correlated with chromosome conformation data, indicating that most roX-bound loci cluster in a nuclear territory. These results suggest dChIRP can reveal lncRNA architecture and function with high precision and sensitivity.

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