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

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.28.969618 doi: bioRxiv preprint Figure 2A but for indicated combinations of remodeler and nucleosome density. "no remodeler" denotes absence of remodeler. "no remodeler" denotes absence of Reb1. Tracks show merged data from replicates shown in Figures S1B, S2A. Reb1 sites were sorted into groups 1 to 3 (number of sites per group indicated) according to orientation of Reb1 sites relative to one or two genes. (B) As Figure 2C , but averages and standard deviation of values for up-and downstream lengths are shown for same groups as in panel A and for all anti-Reb1 SLIM-ChIP sites that contain a Reb1 PWM (light blue). (C) Composite plots (left) and heat maps (right) of MNase-seq analysis of in vivo chromatin or SGD chromatin reconstituted with the indicated nucleosome density and incubated with recombinant WT INO80 complex. Data are aligned at in vivo +1 nucleosome positions and heat maps are sorted from top to bottom by increasing NFR length. Traces with indicated replicate number (n) represent merged data for all replicates. Positions of -1, +1, +2, +3 nucleosomes of the in vivo pattern are labeled. (D) Composite plots as in panel C, right, but for individual replicates and the indicated remodelers. "no remodeler" denotes absence of remodeler. no remodeler author/funder. All rights reserved. No reuse allowed without permission.