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ID: 548585.0, MPI für molekulare Genetik / Department of Computational Molecular Biology
The effect of MNase on nucleosome positioning data.
Authors:Chung, Ho-Ryun; Dunkel, Ilona; Heise, Franziska; Linke, Christian; Krobitsch, Sylvia; Ehrenhofer-Murray, Ann E.; Sperling, Silke R.; Vingron, Martin
Language:English
Date of Publication (YYYY-MM-DD):2010-12-29
Title of Journal:PLoS ONE
Journal Abbrev.:PLOS One
Volume:5
Issue / Number:12
Start Page:e15754
End Page:e15754
Full name of Issue-Editor(s):Michael J. Pazin, National Institute on Aging, National Institutes of Health, United States of America
Copyright:© 2010 Chung et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Review Status:not specified
Audience:Experts Only
Abstract / Description: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.
Comment of the Author/Creator:E-mail: chung@molgen.mpg.de
External Publication Status:published
Document Type:Article
Version Comment:Automatic journal name synchronization
Communicated by:Martin Vingron
Affiliations:MPI für molekulare Genetik
External Affiliations:1.Abteilung für Genetik, ZMB, Universität Duisburg-Essen, Essen, Germany.
Identifiers:URL:http://www.plosone.org/article/info%3Adoi%2F10.137...
ISSN:1932-6203
DOI:10.1371/journal.pone.0015754
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