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Analyzing Targeted Nucleosome Position and Occupancy in Cancer, Obesity, and Diabetes

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Epigenetics and Gene Expression in Cancer, Inflammatory and Immune Diseases

Part of the book series: Methods in Pharmacology and Toxicology ((MIPT))

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Abstract

Chromatin structure plays an integral role in regulation of gene transcription. Studying nucleosome position and occupancy at key regulatory regions within DNA is important to understanding the potential epigenetic mechanisms of gene regulation during various environmental exposures and diseased states. Targeted nucleosome mapping is a convenient method to map nucleosome positions at a specific genomic locus. In this method, mononucleosomal DNA is isolated using micrococcal nuclease. This is followed by qPCR, which uses the mononucleosomal DNA, or the DNA bound by the nucleosome, as the template and overlapping primers that span the target region of genome. qPCR products are analyzed by gel electrophoresis and densitometry to yield a map of nucleosomes along specific, targeted genomic loci.

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Author information

Authors and Affiliations

  1. Department of Nutrition Science, Purdue University, 700 W. State Street, West Lafayette, IN, 47907, USA

    Prasad P. Devarshi & Tara M. Henagan

Authors
  1. Prasad P. Devarshi
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  2. Tara M. Henagan
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Corresponding author

Correspondence to Tara M. Henagan .

Editor information

Editors and Affiliations

  1. Department of Nutrition Science, Purdue University, West Lafayette, Indiana, USA

    Barbara Stefanska

  2. Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine University of Liverpool, Liverpool, United Kingdom

    David J. MacEwan

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Devarshi, P.P., Henagan, T.M. (2017). Analyzing Targeted Nucleosome Position and Occupancy in Cancer, Obesity, and Diabetes. In: Stefanska, B., MacEwan, D. (eds) Epigenetics and Gene Expression in Cancer, Inflammatory and Immune Diseases. Methods in Pharmacology and Toxicology. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6743-8_4

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  • DOI: https://doi.org/10.1007/978-1-4939-6743-8_4

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6741-4

  • Online ISBN: 978-1-4939-6743-8

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