Ruler elements in chromatin remodelers set nucleosome array spacing and phasing

Elisa Oberbeckmann; Vanessa Niebauer; Shinya Watanabe; Lucas Farnung; Manuela Moldt; Andrea Schmid; Patrick Cramer; Craig L. Peterson; Sebastian Eustermann; Karl-Peter Hopfner; Philipp Korber

Remodeler rulers regulate nucleosome sliding direction bias in response to nucleosome environment. We propose an overarching framework for this relay that amounts to a widely applicable remodeler ruler principle (Figure 7) . A remodeler may slide a nucleosome either to the left or to the right from a given position. If there is no bias for sliding in either direction, the nucleosome will experience a random walk along the DNA (regions C in in three hypothetical examples Figure 7A ). Net nucleosome movement in one direction (Gangaraju and Bartholomew, 2007; Langst et al., 1999; McKnight et al., 2011; Stockdale et al., 2006; Udugama et al., 2011; Yang et al., 2006; Zhou et al., 2018) requires an overall sliding direction bias in this direction. We conceptualize a remodeler ruler as a remodeler-intrinsic feature that generates an overall sliding direction bias in response to the (epi)genetic information in the environment of the nucleosome that the remodeler is remodeling. The bias may originate from differences, e.g., in binding orientation, ATPase activity, sliding rate or processivity and is regulated by interaction of the ruler with a generalized "barrier". This may be a GRF, a DSB, a neighboring nucleosome, or a DNA sequence element. Histone modifications/ variants may modulate as well. While the microscopic details may differ for different remodelers and information author/funder. All rights reserved. No reuse allowed without permission.