title: The effect of micrococcal nuclease digestion on nucleosome positioning data.
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.
authors.affiliation: Department of Computational Molecular Biology, MPI für Molekulare Genetik, Berlin, Germany. chung@molgen.mpg.de
authors.forename: Ho-Ryun
authors.initials: HR
authors.lastname: Chung
authors.forename: Ilona
authors.initials: I
authors.lastname: Dunkel
authors.forename: Franziska
authors.initials: F
authors.lastname: Heise
authors.forename: Christian
authors.initials: C
authors.lastname: Linke
authors.forename: Sylvia
authors.initials: S
authors.lastname: Krobitsch
authors.forename: Ann E
authors.initials: AE
authors.lastname: Ehrenhofer-Murray
authors.forename: Silke R
authors.initials: SR
authors.lastname: Sperling
authors.forename: Martin
authors.initials: M
authors.lastname: Vingron
mesh_terms: D000465:Algorithms; D002843:Chromatin / Q000737:chemistry; D003062:Codon; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000737:chemistry; D004271:DNA, Fungal / Q000235:genetics; D030562:Databases, Protein; D019281:Dimerization; D016681:Genome, Fungal; D008836:Micrococcal Nuclease / Q000378:metabolism*; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism / Q000648:ultrastructure; D010363:Pattern Recognition, Automated / Q000379:methods; D012259:Ribonuclease, Pancreatic / Q000737:chemistry; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D002843:Chromatin; D003062:Codon; D004271:DNA, Fungal; D009707:Nucleosomes; D004247:DNA; D012259:Ribonuclease, Pancreatic; D008836:Micrococcal Nuclease