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Sequence-dependent Nucleosome Positioning.


Chung,  Ho-Ryun
Computational Epigenetics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society;

Vingron,  Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Chung, H.-R., & Vingron, M. (2009). Sequence-dependent Nucleosome Positioning. Journal of Molecular Biology, 386(5), 1411-1422. doi:10.1016/j.physletb.2003.10.071.

Eukaryotic DNA is organized into a macromolecular structure called chromatin. The basic repeating unit of chromatin is the previous termnucleosome,next term which consists of two copies of each of the four core histones and DNA. The nucleosomal organization and the positions of previous termnucleosomesnext term have profound effects on all DNA-previous termdependentnext term processes. Understanding the factors that influence previous termnucleosome positioningnext term is therefore of general interest. Among the many determinants of previous termnucleosome positioning,next term the DNA previous termsequencenext term has been proposed to have a major role. Here, we analyzed more than 860,000 nucleosomal DNA previous termsequencesnext term to identify previous termsequencenext term features that guide the formation of previous termnucleosomesnext term in vivo. We found that both a periodic enrichment of AT base pairs and an out-of-phase oscillating enrichment of GC base pairs as well as the overall preference for GC base pairs are determinants of previous termnucleosome term The preference for GC pairs can be related to a lower energetic cost required for deformation of the DNA to wrap around the histones. In line with this idea, we found that only incorporation of both signal components into a previous termsequencenext term model for previous termnucleosomenext term formation results in maximal predictive performance on a genome-wide scale. In this manner, one achieves greater predictive power than published approaches. Our results confirm the hypothesis that the DNA previous termsequencenext term has a major role in previous termnucleosome positioningnext term in vivo.