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Mapping Long Noncoding RNA Chromatin Occupancy Using Capture Hybridization Analysis of RNA Targets (CHART)

  • Keith W. VanceEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1468)

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.

Key words

CHART Long noncoding RNA Chromatin Genome-wide binding Oligonucleotide capture 

Notes

Acknowledgment

I would like to thank Dr. Mike Clark (Oxford) and Dr Lovorka Stojic (Cambridge) for critically reading the manuscript.

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Copyright information

© Springer Science+Business Media New York 2017

Authors and Affiliations

  1. 1.Department of Biology and BiochemistryUniversity of BathBathUK

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