MNase_control
The effect of MNase on nucleosome positioning data
Micrococcal nuclease (MNase) is frequently used to determine nucleosome positions both in vitro and in vivo. This is achieved by digesting chromatin by MNase and selecting nucleosomal sized DNA fragments (~150 base pairs). To check to what extend the resulting data is biased by the use MNase and the size selection, a control experiment was performed, where naked yeast DNA was digested with MNase and fragments of 150 base pairs were selected. The MNase data shows a good correspondence to the data obtained by digesting chromatin assembled in vitro as well as chromatin isolated in vivo.
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 sequence-dependent models for nucleosome positioning based on such data. Thus, sequencing data generated after MNase digestion of chromatin requires a control experiment in order to determine nucleosome positions.