title: Fuzziness and noise in nucleosomal architecture.
abstract: Nucleosome organization plays a key role in the regulation of gene expression. However, despite the striking advances in the accuracy of nucleosome maps, there are still severe discrepancies on individual nucleosome positioning and how this influences gene regulation. The variability among nucleosome maps, which precludes the fine analysis of nucleosome positioning, might emerge from diverse sources. We have carefully inspected the extrinsic factors that may induce diversity by the comparison of microccocal nuclease (MNase)-Seq derived nucleosome maps generated under distinct conditions. Furthermore, we have also explored the variation originated from intrinsic nucleosome dynamics by generating additional maps derived from cell cycle synchronized and asynchronous yeast cultures. Taken together, our study has enabled us to measure the effect of noise in nucleosome occupancy and positioning and provides insights into the underlying determinants. Furthermore, we present a systematic approach that may guide the standardization of MNase-Seq experiments in order to generate reproducible genome-wide nucleosome patterns.
authors.affiliation: Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028 Barcelona, Spain, Joint IRB-BSC Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain and Department of Biochemistry and Molecular Biology. University of Barcelona, 08028 Barcelona, Spain.
authors.forename: Oscar
authors.initials: O
authors.lastname: Flores
authors.forename: Özgen
authors.initials: Ö
authors.lastname: Deniz
authors.forename: Montserrat
authors.initials: M
authors.lastname: Soler-López
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco
mesh_terms: D004271:DNA, Fungal / Q000737:chemistry; D015870:Gene Expression; D008836:Micrococcal Nuclease; D009707:Nucleosomes / Q000737:chemistry*; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods
chemical_list: D004271:DNA, Fungal; D009707:Nucleosomes; D008836:Micrococcal Nuclease