Abstract
Eukaryotic DNA is wrapped around histone octamers, known as nucleosomes, in an orderly fashion that provides the primary structure of chromatin organization. The compaction of DNA into nucleosomal repeats not only allows the tight packaging of the large eukaryotic genomes into the nucleus, it also dictates the accessibility of genetic information. Thus, in order to understand how nucleosomes can affect the dynamics of DNA–protein interactions, such as those associated with transcriptional regulatory mechanisms, it is important to define nucleosomal positioning and occupancy along genomic DNA. Here we describe a method that relies on the enzymatic activity of micrococcal nuclease (MNase) to determine nucleosomal footprints and boundaries. By pairing this technique with next generation sequencing techniques (i.e., MNase-seq), it is possible to generate a genome-wide detailed map of chromatin architecture.
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Acknowledgments
This work is partially supported by grants R21DE021137 and R03HD073891 to SS. We thank Dr. Michael Buck and Dr. Maria Tsompana for their help and advice with the MNase-seq experiments.
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Rizzo, J.M., Sinha, S. (2014). Analyzing the Global Chromatin Structure of Keratinocytes by MNase-Seq. In: Turksen, K. (eds) Epidermal Cells. Methods in Molecular Biology, vol 1195. Springer, New York, NY. https://doi.org/10.1007/7651_2014_77
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DOI: https://doi.org/10.1007/7651_2014_77
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