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.
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Acknowledgment
I would like to thank Dr. Mike Clark (Oxford) and Dr Lovorka Stojic (Cambridge) for critically reading the manuscript.
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Vance, K.W. (2017). Mapping Long Noncoding RNA Chromatin Occupancy Using Capture Hybridization Analysis of RNA Targets (CHART). In: Ørom, U. (eds) Enhancer RNAs. Methods in Molecular Biology, vol 1468. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-4035-6_5
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DOI: https://doi.org/10.1007/978-1-4939-4035-6_5
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Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-4033-2
Online ISBN: 978-1-4939-4035-6
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