Abstract
Identification of genomic binding sites and proteins associated with noncoding RNAs will lead to more complete mechanistic characterization of the regulatory activities of noncoding RNAs. Capture hybridization analysis of RNA targets (CHART) is a powerful technique wherein specific RNA molecules are isolated from cross-linked nuclear extracts using complementary, biotinylated capture oligonucleotides, allowing subsequent identification of genomic DNA and proteins cross-linked to the RNA of interest. Here, we describe the procedure for CHART and list strategies to optimize nuclear extract preparation, capture oligonucleotide design, and isolation of nucleic acids and proteins enriched through CHART.
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Acknowledgment
C.P.D. is supported by a graduate research fellowship from the National Science Foundation.
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Davis, C.P., West, J.A. (2015). Purification of Specific Chromatin Regions Using Oligonucleotides: Capture Hybridization Analysis of RNA Targets (CHART). In: Nakagawa, S., Hirose, T. (eds) Nuclear Bodies and Noncoding RNAs. Methods in Molecular Biology, vol 1262. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2253-6_10
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DOI: https://doi.org/10.1007/978-1-4939-2253-6_10
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Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2252-9
Online ISBN: 978-1-4939-2253-6
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