The effect of micrococcal nuclease digestion on nucleosome positioning data

Chung, H.R.; Dunkel, I.; Heise, F.; Linke, C.; Krobitsch, S.; Ehrenhofer-Murray, A.E.; Sperling, S.R.; Vingron, M.

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., Dunkel, I., Heise, F., Linke, C., Krobitsch, S., Ehrenhofer-Murray, A.E., 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
ISSN:	1932-6203
Publisher:	Public Library of Science
Volume:	5
Number:	12
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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