Mapping long noncoding RNA chromatin occupancy using capture hybridization analysis of RNA targets (CHART)

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Abstract

Capture Hybridization Analysis of RNA Targets (CHART) has recently been developed to map the genome-wide binding profile of chromatin-associated RNAs. This protocol uses a small number of 22-28 nucleotide biotinylated antisense oligonucleotides, complementary to regions of the target RNA that are accessible for hybridization, to purify RNAs from a cross-linked chromatin extract. RNA-chromatin complexes are next immobilized on beads, washed, and specifically eluted using RNase H. Associated genomic DNA is then sequenced using high-throughput sequencing technologies and mapped to the genome to identify RNA-chromatin associations on a large scale. CHART-based strategies can be applied to determine the nature and extent of long noncoding RNA (long ncRNA) association with chromatin genome-wide and identify direct long ncRNA transcriptional targets.

Original languageEnglish
Title of host publicationEnhancer RNAs
Subtitle of host publicationMethods and Protocols
EditorsU Andersson Orom
Place of PublicationNew York, U. S. A.
PublisherSpringer
Pages39-50
Number of pages12
ISBN (Print)9781493940332
DOIs
Publication statusPublished - 24 Sep 2016

Publication series

NameMethods in Molecular Biology
Volume1468

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  • Cite this

    Vance, K. W. (2016). Mapping long noncoding RNA chromatin occupancy using capture hybridization analysis of RNA targets (CHART). In U. Andersson Orom (Ed.), Enhancer RNAs: Methods and Protocols (pp. 39-50). (Methods in Molecular Biology; Vol. 1468). Springer. https://doi.org/10.1007/978-1-4939-4035-6_5