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 type, barrier type and nucleosome density determine distance to barrier. The findings for the distance to barrier were more complex than for lengths of linker 1 ( Figure 2C -E). First, the distance to barrier depended on the barrier type ( Figure 2C ). It was always longer for Reb1 than for BamHI generated DNA ends, with the largest difference for ISW1a and the smallest for Chd1. The DNA footprint size of S. cerevisiae Reb1 is not known, possibly 20 bp as for the S. pombe Reb1 DNA binding domain (Jaiswal et al., 2016) . This would contribute 10 bp to the distance to barrier ( Figure 2B ) and could explain the differences between distance to Reb1 vs. BamHI sites for Chd1, but not for the other remodelers. Therefore, INO80, ISW2 and ISW1a, but not Chd1, aligned nucleosomes differently at Reb1 versus at DSBs. Second, the distance to DNA ends was mostly similar to linker lengths for INO80, ISW2 and ISW1a, arguing that these remodelers, but not Chd1, used a DNA end in a similar way as a neighboring nucleosome for nucleosome alignment. Third, distances to barriers depended on nucleosome density in a similar way as linker lengths for all remodelers but INO80, where distances to both barriers varied less between low and medium density than linker length. We concluded that there are remodeler-specific differences in how a nucleosome is positioned next to another nucleosome versus next to a barrier like Reb1 versus next to a DNA end and how this depends on nucleosome density. This is again a clear case of different remodelers generating different nucleosome positioning, although starting from the same SGD chromatin, which argues for remodelerspecific rulers governing nucleosome positioning. 2D), which we interpreted as processive spacing activity along the arrays as long as nucleosomes were sufficiently provided. At low density, ISW2, Chd1 and especially INO80 still generated high +1/-1 nucleosome peaks ( Figure S2A ), in contrast to ISW1a, for which these peaks were less pronounced and +2/-2 nucleosome peaks could not be discerned. We suggest that ISW1a is less processive than other remodelers in bringing nucleosomes next to barriers at low densities. distance to barrier site / bp normalized dyad density Remodelers generate similar arrays on all but more effectively on eukaryotic DNA sequences. The same linker lengths in arrays at BamHI and Reb1 sites ( Figure 2C ), at Reb1 sites in groups 1 to 3 and the symmetry of nucleosome distances to Reb1 sites in groups 1 to 3 ( Figure S3A ,B) suggested that remodeler rulers position nucleosomes independently of DNA sequence flanking the barriers. Nonetheless, there are evolved DNA features at promoters, especially for INO80 (accompanying paper Oberbeckmann & Krietenstein et al.) , that affected occupancies (peak heights, not positions, Figure S3A ), which may also be true for evolved nucleosome-favoring dinucleotide periodicities (Satchwell et al., 1986) in gene bodies.