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The effect of micrococcal nuclease digestion on nucleosome positioning data

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Item Type:Article
Title:The effect of micrococcal nuclease digestion on nucleosome positioning data
Creators Name:Chung, H.R. and Dunkel, I. and Heise, F. and Linke, C. and Krobitsch, S. and Ehrenhofer-Murray, A.E. and Sperling, S.R. and Vingron, M.
Abstract:Eukaryotic genomes are packed into chromatin, whose basic repeating unit is the nucleosome. Nucleosome positioning is a widely researched area. A common experimental procedure to determine nucleosome positions involves the use of micrococcal nuclease (MNase). Here, we show that the cutting preference of MNase in combination with size selection generates a sequence-dependent bias in the resulting fragments. This strongly affects nucleosome positioning data and especially sequence-dependent models for nucleosome positioning. As a consequence we see a need to re-evaluate whether the DNA sequence is a major determinant of nucleosome positioning in vivo. More generally, our results show that data generated after MNase digestion of chromatin requires a matched control experiment in order to determine nucleosome positions.
Keywords:Algorithms, Automated Pattern Recognition, Chromatin, Codon, Computational Biology, Dimerization, DNA, DNA Sequence Analysis, , Fungal DNA, Fungal Genome, Micrococcal Nuclease, Nucleosomes, Pancreatic Ribonuclease, Protein Databases, Saccharomyces Cerevisiae
Source:PLoS ONE
Publisher:Public Library of Science
Page Range:e15754
Date:29 December 2010
Official Publication:https://doi.org/10.1371/journal.pone.0015754
PubMed:View item in PubMed

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