RT Journal Article
SR Electronic
T1 Emergence of robust nucleosome patterns from an interplay of positioning mechanisms
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 431445
DO 10.1101/431445
A1 Johannes Nuebler
A1 Michael Wolff
A1 Benedikt Obermayer
A1 Wolfram Möbius
A1 Ulrich Gerland
YR 2018
UL http://biorxiv.org/content/early/2018/10/01/431445.abstract
AB Proper positioning of nucleosomes in eukaryotic cells is determined by a complex interplay of factors, including nucleosome-nucleosome interactions, DNA sequence, and active chromatin remodeling. Yet, characteristic features of nucleosome positioning, such as gene-averaged nucleosome patterns, are surprisingly robust across perturbations, conditions, and species. Here, we explore how this robustness arises despite the underlying complexity. We leverage mathematical models to show that a large class of positioning mechanisms merely affects the quantitative characteristics of qualitatively robust positioning patterns. We demonstrate how statistical positioning emerges as an effective description from the complex interplay of different positioning mechanisms, which ultimately only renormalize the model parameter quantifying the effective softness of nucleosomes. This renormalization can be species-specific, rationalizing a puzzling discrepancy between the effective nucleosome softness of S. pombe and S. cerevisiae. More generally, we establish a quantitative framework for dissecting the interplay of different nucleosome positioning determinants.