Crosstalk within a functional INO80 complex dimer regulates nucleosome sliding

Abstract

Several chromatin remodellers have the ability to space nucleosomes on DNA. For ISWI remodellers, this involves an interplay between H4 histone tails, the AutoN and NegC motifs of the motor domains that together regulate ATPase activity and sense the length of DNA flanking the nucleosome. By contrast, the INO80 complex also spaces nucleosomes but is not regulated by H4 tails and lacks the AutoN and NegC motifs. Instead nucleosome sliding requires cooperativity between two INO80 complexes that monitor DNA length simultaneously on either side of the nucleosome during sliding. The C-terminal domain of the human Ino80 subunit (Ino80CTD) binds cooperatively to DNA and dimerisation of these domains provides crosstalk between complexes. ATPase activity, rather than being regulated, instead gradually becomes uncoupled as nucleosome sliding reaches an end point and this is controlled by the Ino80CTD. A single active ATPase motor within the dimer is sufficient for sliding.DOI: http://dx.doi.org/10.7554/eLife.25782.001

The Yeast INO80 Complex Operates as a Tunable DNA Length-Sensitive Switch to Regulate Nucleosome Sliding

“…Consistent with recent work with human INO80 (Willhoft et al, 2017), we find by gel remodeling that yeast INO80 mobilizes this 78/78 construct, yielding a distribution of nucleosome positions, some of which are off-center (Figure 3B). Similarly, we find by smFRET that INO80 quickly slides these nucleosomes out of FRET range, as with the end-positioned constructs (Figure 3C).…”

Cryo-EM structures of the human INO80 chromatin-remodeling complex

“…We reasoned that the flat, wheel-like density encapsulated by the RUVBL1-2 barrel (Fig. 3c) corresponds to Ino80-I for the following reasons: (i) biochemical data show that this insertion region contains the main interaction sites for RUVBL1-230, (ii) the Ino80 helicase domains bind to nucleosomes so must be positioned on the periphery of the complex, and (iii) the Ino80 C-terminal domain (Ino80-C) and Ies2 can be deleted without affecting the assembly of the complex9,20. This assignment is also consistent with a recent low-resolution EM study of a complex between the yeast Ino80-I domain bound to a RUVBL1/2 complex32.…”

“…Here we present the structure of a human INO80 core complex9,10,20 at 9.6 Å with portions at 4.1 Å resolution. This core complex was previously shown to have nucleosome sliding activity comparable to the full complex in vitro .…”

Single‐molecule nucleosome remodeling by INO80 and effects of histone tails

“…A consequence of this result is that the structurally heterogeneous INO80 bound state also possesses a lowered energy barrier for initiation of remodeling, thus giving a structural perspective for the previous biochemical results. The INO80 complex is considered to primarily monitor the nucleosome flanking DNA length and the observed increase in remodeling rate in the absence of histone tails is accompanied by an increased ATPase rate . Thus, we assume that studying the INO80 complex activity in the absence of histone tails reports mainly on effects on the active site of the remodeler.…”