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PloS one
Dec 29, 2010;5 (12): e15754.

The effect of micrococcal nuclease digestion on nucleosome positioning data.

Ho-Ryun Chung, Ilona Dunkel, Franziska Heise, Christian Linke, Sylvia Krobitsch, Ann E Ehrenhofer-Murray, Silke R Sperling, Martin Vingron
Author Information
  1. Ho-Ryun Chung: Department of Computational Molecular Biology, MPI für Molekulare Genetik, Berlin, Germany. chung@molgen.mpg.de
PMID: 21206756 DOI: 10.1371/journal.pone.0015754

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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MeSH Term

Algorithms
Chromatin
Codon
Computational Biology
DNA
DNA, Fungal
Databases, Protein
Dimerization
Genome, Fungal
Micrococcal Nuclease
Nucleosomes
Pattern Recognition, Automated
Ribonuclease, Pancreatic
Saccharomyces cerevisiae
Sequence Analysis, DNA

Chemicals

Chromatin
Codon
DNA, Fungal
Nucleosomes
DNA
Ribonuclease, Pancreatic
Micrococcal Nuclease
Journal Article
Article has an altmetric score of 1

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