Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density

Abstract

Arrays of regularly spaced nucleosomes are a hallmark of chromatin, but it remains unclear how they are generated. Recent genome-wide studies, in vitro and in vivo, showed constant nucleosome spacing even if the histone concentration was experimentally reduced. This counters the long-held assumption that nucleosome density determines spacing and calls for factors keeping spacing constant regardless of nucleosome density. We call this a clamping activity. Here, we show in a purified system that ISWI- and CHD1-type nucleosome remodelers have a clamping activity such that they not only generate regularly spaced nucleosome arrays but also generate constant spacing regardless of nucleosome density. This points to a functionally attractive nucleosome interaction that could be mediated either directly by nucleosome-nucleosome contacts or indirectly through the remodelers. Mutant Drosophila melanogaster ISWI without the HAND-SANT-SLIDE (HSS) domain had no detectable spacing activity even though it is known to remodel and slide nucleosomes. This suggests that the role of ISWI remodelers in generating constant spacing is not just to mediate nucleosome sliding; they actively contribute to the attractive interaction. Additional factors are necessary to set physiological spacing in absolute terms.

ACKNOWLEDGMENTS

This work was supported by grants from the German Research Community (DFG) (MU3613/1-1, MU3613/3-1, and SFB1064-A07 to F.M.-P. and SFB/TR5-M6, SFB1064-A04, and KO 2945/1-1 to P.K.) and the Bavarian Research Network for Molecular Biosystems (BioSysNet; to U.G. and P.K.).

We thank Henrike Klinker for providing purified ACF remodeling complex, help with fluorescence labeling, critical reading of the manuscript, and very helpful discussions; Nicola Hepp for cloning pFMP233; Steven Völker for help with Chd1 purification; and Peter Becker for critical comments on the manuscript.