Chung, Ho-Ryun; Dunkel, Ilona; Heise, Franziska; Linke, Christian; Krobitsch, Sylvia; Ehrenhofer-Murray, Ann; Sperling, Silke R.; Vingron, Martin:
The effect of micrococcal nuclease digestion on nucleosome positioning data
2010
In: PLoS ONE, ohne Seitenagabe
Artikel/Aufsatz in Zeitschrift / Fach: Biologie
Fakultät für Biologie » Genetik
Titel:
The effect of micrococcal nuclease digestion on nucleosome positioning data
Autor(in):
Chung, Ho-Ryun; Dunkel, Ilona; Heise, Franziska im Online-Personal- und -Vorlesungsverzeichnis LSF anzeigen; Linke, Christian; Krobitsch, Sylvia; Ehrenhofer-Murray, Ann im Online-Personal- und -Vorlesungsverzeichnis LSF anzeigen; Sperling, Silke R.; Vingron, Martin
Erscheinungsjahr
2010
Erschienen in:
PLoS ONE, ohne Seitenagabe
WWW URL

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.