Oncogenic chromodomain mutations allosterically impair TIP60 acetyltransfearse function preventing activation of DNA repair genes under genotoxic stress

Abstract

TIP60 is a tumor suppressor with histone acetyltransferase activity that regulates chromatin accessibility in diverse processes including DNA repair, apoptosis, mitosis, transcription, and autophagy. Structurally TIP60 contains a C-terminal MYST domain that mediates its HAT activity, while the N-terminal chromodomain are conserved modules that facilitate its association with chromatin by recognizing histone modifications. Mutations within the chromodomain have been implicated in various cancers, yet their functional consequences remain poorly understood, particularly with respect to TIP60s role in maintaining genomic integrity. Here, we uncover a novel allosteric mechanism whereby cancer-associated chromodomain mutations impair TIP60s catalytic activity without disrupting its chromatin binding, underscoring critical interdomain communication between the chromodomain and the MYST domain. Through structural modelling and molecular dynamics simulations, we identified two missense mutations (R53H and R62W) in TIP60s chromodomain that not only altered TIP60s conformation but also destabilized its trimeric assembly, thereby impairing acetyl-CoA docking. Importantly, we found that TIP60 engages acetyl-CoA exclusively in its trimeric state, and the R62W mutation perturbs the trimeric interface, thereby altering the docking sites for acetyl-CoA. Consistent with these structural changes, biochemical assays revealed that chromodomain mutant TIP60 variants, while retaining chromatin loading, exhibited markedly reduced autoacetylation and histone acetyltransferase activity. Moreover, these mutants failed to activate the p21 gene in response to DNA damage, thereby predisposing the genome to the accumulation of mutations and leaving cells unable to arrest the cell cycle for repair of genomic lesions. Together, our findings establish that distal chromodomain mutations allosterically destabilize TIP60 oligomerization, impair acetyl-CoA utilization, and compromise DNA damage responses. The mechanism establishes a link between chromodomain mutations and genomic instability, shedding light on how reader domain alterations may underlie cancer progression.