Phospho-dependent recruitment of the yeast NuA4 acetyltransferase complex by MRX at DNA breaks regulates RPA dynamics during resection

Cheng, Xue; Jobin-Robitaille, Olivier; Billon, Pierre; Buisson, Rémi; Niu, Hengyao; Lacoste, Nicolas; Abshiru, Nebiyu; Côté, Valérie; Thibault, Pierre; Kron, Stephen J.; Sung, Patrick; Brandl, Christopher J.; Masson, Jean‐Yves; Côté, Jacques

doi:10.1073/pnas.1806513115

Cited by 30 publications

(82 citation statements)

References 49 publications

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“…NuA4 has been shown to play an important role for the recruitment of chromatin remodelers such as INO80, SWI/SNF and RSC to DNA repair sites (Bennett & Peterson, 2015;Downs et al, 2004;House et al, 2014). Our recent work indicates that NuA4 is rapidly recruited to a DSB by the MRX complex (Mre11-Rad50-Xrs2) and this is most likely through a DNA damageinduced phospho-dependent interaction with the Xrs2 protein (Cheng et al, 2018). In addition, we have shown that NuA4 directly acetylates RPA to modulates its dynamic association with ssDNA during the repair process (Cheng et al, 2018).…”

Section: Introductionmentioning

confidence: 80%

Antagonistic relationship of NuA4 with the Non-Homologous End-Joining machinery at DNA damage sites

Ahmad

Côté

Cheng

et al. 2021

Preprint

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The NuA4 histone acetyltransferase complex, apart from its known role in gene regulation, has also been directly implicated in the repair of DNA double-strand breaks (DSBs), favoring homologous recombination (HR) in S/G2 during the cell cycle. Here, we investigate the antagonistic relationship of NuA4 with non-homologous end joining (NHEJ) factors. We detect NuA4 at DSBs in G1 when genes for NHEJ factors Rad9, Yku80 and Nej1 are mutated. This is accompanied with the binding of single-strand DNA binding protein RPA, indicating DNA end resection in G1. This NuA4 recruitment to DSBs depends on both Xrs2 and Lcd1/Ddc2. Introducing an acetyltransferase defective allele in these NHEJ mutant backgrounds decreases their hyper-resection phenotype in G1. Interestingly, we identified two novel non-histone acetylation targets of NuA4, Nej1 and Yku80. Acetyl-mimicking mutant of Nej1 inhibits NHEJ, decreases its interaction with other NHEJ factors and favors resection. Altogether, these results establish an antagonistic regulatory function of NuA4 and NHEJ factors in repair pathway choice and suggest a role of NuA4 in alternative repair mechanism that involves DNA-end resection in G1.

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Section: Introductionmentioning

confidence: 80%

Antagonistic relationship of NuA4 with the Non-Homologous End-Joining machinery at DNA damage sites

Ahmad

Côté

Cheng

et al. 2021

Preprint

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“…Acetylation of other proteins, such as p53 (69), Gata-1 (70), and Stat3 (71), all serve as examples of proteins displaying increased binding affinities for specific DNA substrates when acetylated. Interestingly, acetylation of replication protein A (RPA) promotes its displacement from ssDNA during DSB repair (72), and acetylated FEN1 displays lower substrate binding affinity (63). All of these proteins are hypothesized to undergo conformational changes upon acetylation, which may alter their ability to interact with and bind to their cognate substrates.…”

Section: Discussionmentioning

confidence: 99%

Lysine acetylation regulates the activity of nuclear Pif1

Ononye

Sausen

Balakrishnan

et al. 2020

Journal of Biological Chemistry

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In S. cerevisiae, the Pif1 helicase functions in both nuclear and mitochondrial DNA replication and repair processes, preferentially unwinding RNA-DNA hybrids and resolving G-quadruplex structures. We sought to determine how the various activities of Pif1 are regulated in vivo. Here, we report lysine acetylation of nuclear Pif1 and demonstrate that it influences both Pif1’s cellular roles and core biochemical activities. Using Pif1 overexpression toxicity assays, we determined that the acetyltransferase NuA4 and deacetylase Rpd3 are primarily responsible for the dynamic acetylation of nuclear Pif1. Mass spectrometry analysis revealed that Pif1 was modified in several domains throughout the protein’s sequence on the N-terminus (K118, K129), helicase domain (K525, K639, K725), and C-terminus (K800). Acetylation of Pif1 exacerbated its overexpression toxicity phenotype, which was alleviated upon deletion of its N-terminus. Biochemical assays demonstrated that acetylation of Pif1 stimulated its helicase, ATPase, and DNA binding activities while maintaining its substrate preferences. Limited proteolysis assays indicate that acetylation of Pif1 induces a conformational change that may account for its altered enzymatic properties. We propose that acetylation is involved in regulating of Pif1 activities, influencing a multitude of DNA transactions vital to the maintenance of genome integrity.

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“…Interestingly, acetylation of replication protein A (RPA) promotes its displacement from ssDNA during DSB repair [72], and acetylated FEN1 displays lower substrate binding affinity [63]. All of these proteins are hypothesized to undergo conformational changes upon acetylation, which may alter their ability to interact with and bind to their cognate substrates.…”

Section: Discussionmentioning

confidence: 99%

Nuclear Pif1 is Post Translationally Modified and Regulated by Lysine Acetylation

Ononye

Sausen

Balakrishnan

et al. 2020

Preprint

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ABSTRACTIn S. cerevisiae, the Pif1 helicase functions to impact both nuclear and mitochondrial DNA replication and repair processes. Pif1 is a 5’-3’ helicase, which preferentially unwinds RNA-DNA hybrids and resolves G-quadruplex structures. Further, regulation of Pif1 by phosphorylation negatively impacts its interaction with telomerase during double strand break repair. Here, we report that in addition to phosphorylation, Pif1 is also modified by lysine acetylation, which influences both its cellular and core biochemical activities. Using Pif1 overexpression toxicity assays, we determined that the acetyltransferase NuA4 (Esa1) and deacetylase Rpd3 are primarily responsible for dynamically acetylating nuclear Pif1. Mass spectrometry analysis revealed that Pif1 was modified throughout the protein’s sequence on the N-terminus (K118, K129), helicase domain (K525, K639, K725), and C-terminus (K800). Acetylation of Pif1 exacerbated its overexpression toxicity phenotype, which was alleviated upon deletion of its N-terminus. Biochemical assays demonstrated that acetylation of Pif1 stimulated its helicase activity, while maintaining its substrate preferences. Additionally, both the ATPase and DNA binding activities of Pif1 were stimulated upon acetylation. Limited proteolysis assays indicate that acetylation of Pif1 induces a conformational change that may account for its altered enzymatic properties. We propose an acetylation-based model for the regulation of Pif1 activities, addressing how this post translational modification can influence its role as a key player in a multitude of DNA transactions vital to the maintenance of genome integrity.

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Phospho-dependent recruitment of the yeast NuA4 acetyltransferase complex by MRX at DNA breaks regulates RPA dynamics during resection

Cited by 30 publications

References 49 publications

Antagonistic relationship of NuA4 with the Non-Homologous End-Joining machinery at DNA damage sites

Antagonistic relationship of NuA4 with the Non-Homologous End-Joining machinery at DNA damage sites

Lysine acetylation regulates the activity of nuclear Pif1

Nuclear Pif1 is Post Translationally Modified and Regulated by Lysine Acetylation

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