the effect of micrococcal nuclease digestion on nucleosome positioning data核小体定位数据的影响微球菌的核酸酶消化.pdfVIP

The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data 1 2 3 4 4 Ho-Ryun Chung *, Ilona Dunkel , Franziska Heise , Christian Linke , Sylvia Krobitsch , Ann E. 3 2 1 Ehrenhofer-Murray , Silke R. Sperling , Martin Vingron ¨ 1 Department of Computational Molecular Biology, MPI fur Molekulare Genetik, Berlin, Germany, 2 Group Cardiovascular Genetics, Department of Vertebrate Genomics, ¨ ¨ ¨ MPI fur Molekulare Genetik, Berlin, Germany, 3 Abteilung fur Genetik, ZMB, Universitat Duisburg-Essen, Essen, Germany, 4 Neurodegenerative Disorder Group, Otto ¨ Warburg Laboratory, MPI fur Molekulare Genetik, Berlin, Germany 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 experime