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

Quinn, J. J., Ilik, I. A., Qu, K., Georgiev, P., Chu, C., Akhtar, A., et al. (2014). Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nature biotechnology, 32, 933-940.

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Quinn, Jeffrey J., Author
Ilik, Ibrahim A.1, Author              
Qu, Kun, Author
Georgiev, Plamen1, Author              
Chu, Ci, Author
Akhtar, Asifa1, Author              
Chang, Howard Y., Author
Affiliations:
1Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Max Planck Society, ou_2243643              

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 Abstract: 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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Language(s): eng - English
 Dates: 2014
 Publication Status: Published in print
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 Rev. Type: Peer
 Identifiers: eDoc: 701878
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Title: Nature biotechnology
  Alternative Title : Nat. Biotechnol.
Source Genre: Journal
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Pages: - Volume / Issue: 32 Sequence Number: - Start / End Page: 933 - 940 Identifier: -