Abstract
Upon DNA damage, the ALC1/CHD1L nucleosome remodeling enzyme (remodeler) is activated by binding to poly(ADP-ribose). How activated ALC1 recognizes the nucleosome, as well as how this recognition is coupled to remodeling, is unknown. Here, we show that remodeling by ALC1 requires a wild-type acidic patch on the entry side of the nucleosome. The cryo-electron microscopy structure of a nucleosome-ALC1 linker complex reveals a regulatory linker segment that binds to the acidic patch. Mutations within this interface alter the dynamics of ALC1 recruitment to DNA damage and impede the ATPase and remodeling activities of ALC1. Full activation requires acidic patch-linker segment interactions that tether the remodeler to the nucleosome and couple ATP hydrolysis to nucleosome mobilization. Upon DNA damage, such a requirement may be used to modulate ALC1 activity via changes in the nucleosome acidic patches.
Highlights
Packaging into chromatin creates a barrier to DNA transactions (Lorch and Kornberg, 2017)
Nucleosome Remodeling by ALC1 Requires the EntrySide acidic patch’’ (AP) To probe whether the nucleosome AP (Figure 1A) might regulate ALC1, we constructed end-positioned nucleosomes with AP mutations (APMs; alanine substitutions on H2A E61A, E64A, D90A, and E92A) on both faces of the octamer (APM/APM nucleosomes)
To compare the remodeling of WT nucleosomes with intact APs (WT/WT) and APM/APM nucleosomes under saturating concentrations of ALC1fl R860W and ATP, we first used an ensemble fluorescence resonance energy transfer (FRET) assay (Yang et al, 2006)
Summary
Packaging into chromatin creates a barrier to DNA transactions (Lorch and Kornberg, 2017). Previous studies have identified interactions between the AP and several remodelers, including SWR1 (Willhoft et al, 2018), INO80 (Eustermann et al, 2018; Ayala et al, 2018), BAF (He et al, 2020), and RSC (Valencia et al, 2019; Wagner et al, 2020; Ye et al, 2019). These structures suggested that the remodeler-AP interaction acts as a physical tether in the assembly of the nucleosome-remodeler complex. The AP has been implicated in the activation of imitation-switch (ISWI)-family remodelers and chromodomain helicase DNA-binding protein 1 (Chd1) (Dann et al, 2017; Dao et al, 2020; Gamarra et al, 2018; Goldman et al, 2010; Levendosky and Bowman, 2019), and an AP-interacting basic motif was shown to be essential for remodeling by the ISWI remodeler SNF2h (Dao et al, 2020)
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