The effect of micrococcal nuclease digestion on nucleosome positioning data


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


  • PLoS ONE


  • PLoS ONE 5 (12): e15754


  • 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.