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  The effect of MNase on nucleosome positioning data.

Chung, H.-R., Dunkel, I., Heise, F., Linke, C., Krobitsch, S., Ehrenhofer-Murray, A. E., et al. (2010). The effect of MNase on nucleosome positioning data. PLoS ONE, 5(12), e15754-e15754. doi:10.1371/journal.pone.0015754.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-79BB-4 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-79BC-2
Genre: Journal Article
Alternative Title : PLOS One

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 Creators:
Chung, Ho-Ryun1, Author              
Dunkel, Ilona1, Author              
Heise, Franziska, Author
Linke, Christian2, Author              
Krobitsch, Sylvia2, Author              
Ehrenhofer-Murray, Ann E.3, Author              
Sperling, Silke R.4, Author
Vingron, Martin5, Author              
Affiliations:
1Computational Epigenetics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479658              
2Neurodegenerative Disorders (Sylvia Krobitsch), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479661              
3Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433554              
4Max Planck Society, ou_persistent13              
5Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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 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.

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Language(s): eng - English
 Dates: 2010-12-29
 Publication Status: Published in print
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Title: PLoS ONE
  Alternative Title : PLOS One
Source Genre: Journal
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Pages: - Volume / Issue: 5 (12) Sequence Number: - Start / End Page: e15754 - e15754 Identifier: ISSN: 1932-6203