Structure and regulation of the human INO80–nucleosome complex

Abstract

Access to DNA within nucleosomes is required for a variety of processes in cells including transcription, replication and repair. Consequently, cells encode multiple systems that remodel nucleosomes. These complexes can be simple, involving one or a few protein subunits, or more complicated multi-subunit machines . Biochemical studies have placed the motor domains of several chromatin remodellers in the superhelical location 2 region of the nucleosome. Structural studies of yeast Chd1 and Snf2-a subunit in the complex with the capacity to remodel the structure of chromatin (RSC)-in complex with nucleosomes have provided insights into the basic mechanism of nucleosome sliding performed by these complexes. However, how larger, multi-subunit remodelling complexes such as INO80 interact with nucleosomes and how remodellers carry out functions such as nucleosome sliding , histone exchange and nucleosome spacing remain poorly understood. Although some remodellers work as monomers , others work as highly cooperative dimers. Here we present the structure of the human INO80 chromatin remodeller with a bound nucleosome, which reveals that INO80 interacts with nucleosomes in a previously undescribed manner: the motor domains are located on the DNA at the entry point to the nucleosome, rather than at superhelical location 2. The ARP5-IES6 module of INO80 makes additional contacts on the opposite side of the nucleosome. This arrangement enables the histone H3 tails of the nucleosome to have a role in the regulation of the activities of the INO80 motor domain-unlike in other characterized remodellers, for which H4 tails have been shown to regulate the motor domains.

Transient kinetic analysis of SWR1C-catalyzed H2A.Z deposition unravels the impact of nucleosome dynamics and the asymmetry of stepwise histone exchange

“…Recently, two studies have reported cryo-EM reconstructions of the yeast and human INO80C remodeling enzyme bound to an end-positioned nucleosome (Eustermann et al, 2018;Ayala et al, 2018). INO80C is highly related to SWR1C, having a similar subunit module organization and sharing several subunits, such as the Rvb1/Rvb2 heterohexomeric ring assembly.…”

Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA

“…We believe that the predictions of our simulations, such as the existence of distinct twist defect patters induced by the remodeler, could be potentially tested via Cryo-EM, which is becoming more and more accurate in the characterization of the structural heterogeneity of biomolecular complexes (Bilokapic et al, 2018;Fernandez-Leiro & Scheres, 2016). Finally, our computational methods may be readily employed for investigating the activity of different remodelers with known structural information, such as Chd1 (Farnung et al, 2017) and INO80 (Ayala et al, 2018;Eustermann et al, 2018), and for studying remodeling in the biologicallyrelevant context of multi-nucleosome chromatin fiber (Nikitina, Norouzi, Grigoryev, & Zhurkin, 2017).…”

“…While in vitro the nucleosome locations are solely determined by DNA mechanics Morozov et al, 2009), precise positioning in vivo is largely controlled by chromatin remodelers (Lai & Pugh, 2017;Struhl & Segal, 2013), which are ATPdependent molecular machines (Clapier, Iwasa, Cairns, & Peterson, 2017;Zhou, Johnson, Gamarra, & Narlikar, 2016). High-resolution structures of some of these remodelers bound to nucleosomes were obtained very recently by cryo-EM (Ayala et al, 2018;Eustermann et al, 2018;Farnung, Vos, Wigge, & Cramer, 2017;Liu, Li, Xia, Li, & Chen, 2017). While these static structures provide crucial insights, currently missing are the dynamic aspects of how these molecular machines work, on which the current study focus by molecular dynamics simulations.…”

“…This may represent a shared fundamental mechanism at the basis of most remodeling activities; the interactions with the additional domains would then confer specificity to the remodeler, allowing for substrate recognition and determining whether the final outcome is nucleosome repositioning, histone ejection or histone exchange (Clapier et al, 2017). For instance, recent experiments suggested that the INO80 remodeler causes histone exchange by sliding nucleosomal DNA from its translocase binding site around SHL 6 (Ayala et al, 2018;Brahma et al, 2017;Eustermann et al, 2018). Therefore, the detailed characterization of active nucleosome sliding by the translocase domain would represent a significant step forward in our understanding of chromatin remodeling.…”

The INO80 ATP-dependent chromatin remodelling complex alleviates stalled Polymerase II to promote non-coding RNA transcription termination

“…Recent reports suggest that the interaction between H3 and linker DNA is dictated by the H3 N-terminal tail (Rhee et al, 2014). This is intriguing as in vitro evidence suggest that the N-terminal tail of H3 obstructs RNAPII progression if unacetylated, (Bintu et al, 2012), whilst it also regulates the remodelling activity of INO80 (Ayala et al, 2018). Indeed, our findings that loss of the HDAC component Rco1 alleviates pausing of RNAPII and increases productive transcription elongation from a compromised NNS-dependent termination site (Figure 7) suggest that coordination between premature termination and elongation is regulated by the acetylation status of histone H3 N-terminal tail.…”