Unique structural features of the human NuA4/TIP60 acetyltransferase and chromatin remodeling complex [ChIP-seq]

The human NuA4/TIP60 co-activator complex, a fusion of the yeast SWR1 and NuA4 complexes, both incorporates the histone variant H2A.Z into nucleosomes and acetylates histones H4/H2A/H2A.Z to play crucial roles regulating gene expression and maintaining genome stability. Our cryo-EM studies show that within the NuA4/TIP60 complex, the EP400 subunit serves as an architectural scaffold holding the different functional modules in specific positions and giving rise to a novel arrangement of the ARP module. EP400 interacts with the TRRAP subunit using a footprint that overlaps with that of the SAGA acetyltransferase complex, thereby preventing the formation of a hybrid complex. Loss of the TRRAP subunit leads to mislocalization of NuA4/TIP60, resulting in the redistribution of H2A.Z and its acetylation across the genome, emphasizing the dual functionality of NuA4/TIP60 as a single macromolecular assembly. To investigate the effect of the Delta-TRRAP mutation in the EP400 subunit of TIP60, we generated clonal K562 cell lines with the inducible acute degradation tag (dTAG) at the endogenous EP400 locus, rescued by stable exogenous expression of either WT (control) or Delta-TRRAP EP400. We degraded the endogenous EP400 and evaluated genome-wide the effect of the EP400 mutation compared to the WT control on H2A.Z incorporation and acetylation by ChIP-seq. We generated a total of 12 libraries, including 2 biological replicates of inputs (controls), H2A.Z and H2A.Zacetyl pull-downs for each rescue condition (WT or Delta-TRRAP EP400).