Analyzing the Global Chromatin Structure of Keratinocytes by MNase-Seq

  • Jason M. Rizzo
  • Satrajit SinhaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1195)


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.


MNase-seq Keratinocytes Chromatin Formaldehyde Nucleosomes 



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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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Department of BiochemistryState University of New York at BuffaloBuffaloUSA
  2. 2.Department of Biochemistry, Center of Excellence in Bioinformatics and Life SciencesState University of New YorkBuffaloUSA

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