The effect of micrococcal nuclease digestion on nucleosome positioning data
Authors
- H.R. Chung
- I. Dunkel
- F. Heise
- C. Linke
- S. Krobitsch
- A.E. Ehrenhofer-Murray
- S.R. Sperling
- M. Vingron
Journal
- PLoS ONE
Citation
- PLoS ONE 5 (12): e15754
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.