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

Functional and structural identification of remodeler rulers. The protein ruler model was first proposed for ISW1a (Yamada et al., 2011) . It suggested that ISW1a shortens the linker until its ruler contacts the neighboring nucleosome, but did not conceptualize why this would lead to a stable nucleosome position. We built on and expanded this model, identified remodeler rulers via their functionality and pinpointed the INO80 ruler also in structural terms. On the functional level, a ruler is revealed if a) the same remodeler generates the same phasing and/or spacing distances although it works on chromatin with varying nucleosome density (clamping activity), or b) different remodelers/different mutant versions of the same remodeler generate different phasing and/or spacing distances although they all work on the same chromatin (remodeler-specific phasing/spacing). For the INO80 complex, we found that the Nhp10 module, especially the Ino80 N-terminus, as well as the Arp8 module, especially the Ino80-HSA-helix, contributed to the ruler function. Lack of the Ino80 N-terminus, concomitant with lacking the Nhp10 module, allowed INO80, e.g., to slide nucleosomes closer to DNA ends, maybe for steric reasons, while impaired DNA traction during remodeling due to compromised Ino80-HSA helix-DNA interactions had the opposite effect. It remains to be elucidated how exactly such modules within the multi-subunit organisation relay barrier information to the core ATPase.