Abstract
Historically, the simplest method to robustly identify active gene regulatory elements has been enzymatic digestion of nuclear DNA by nucleases such as DNaseI. Regions of extreme chromatin accessibility to DNaseI, commonly known as DNaseI hypersensitive sites, have been repeatedly shown to be markers for all types of active cis-acting regulatory elements, including promoters, enhancers, silencers, insulators, and locus control regions. However, the original classical method, which for over 25 years relied on Southern blot, was limited to studying only small regions of the genome. Here we describe the detailed protocol for DNase-chip, a high-throughput method that allows for a targeted or genome-wide identification of cis-acting gene regulatory elements.
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Acknowledgments
We would like to thank Lingyun Song for her technical assistance and helpful discussions.
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© 2009 Humana Press, a part of Springer Science+Business Media, LLC
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Shibata, Y., Crawford, G.E. (2009). Mapping Regulatory Elements by DNaseI Hypersensitivity Chip (DNase-Chip). In: Pollack, J. (eds) Microarray Analysis of the Physical Genome. Methods in Molecular Biology™, vol 556. Humana Press. https://doi.org/10.1007/978-1-60327-192-9_13
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DOI: https://doi.org/10.1007/978-1-60327-192-9_13
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