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

In this context, we also tested if Fun30 positions in vivo-like +1/-1 nucleosomes on its own, but it did not ( Figure S3D ). In contrast to nucleosome peak heights, nucleosome peak positions and therefore corresponding phasing and spacing distances were not significantly affected across groups 1 to 3 for all remodelers, including INO80 ( Figure S3B ). Therefore, all remodelers symmetrically generated phasing and spacing distances at Reb1 and BamHI sites, which warranted averaging over the up-and downstream values. Resulting values were plotted in different ways to The copyright holder for this preprint (which was not peer-reviewed) is the .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 facilitate multi-dimensional comparisons ( Figure 2C -E). As all remodelers generated linker lengths independently of the barrier type, we combined linker length values for both barriers (Reb1 and BamHI, Figure 2C ). Linker length determination relied on nucleosome peak calling, which was often not possible beyond the -1/+1 nucleosomes at low nucleosome density ( Figure S2A ), so that linker length data for low density conditions were more sparse, even absent for ISW1a.