DNA的雙股斷裂對於基因體的完整性是非常嚴重的傷害，若是雙股斷裂的修復路徑失去功能則會導致基因體的不穩定(genomic instability)以及癌症。在酵母Saccharomyces cerevisiae中，NuA4會被召引到雙股斷裂上，並且對H2A以及H4做乙醯化(acetylation)，乙醯化可以讓染色體結構變的鬆散並且讓修復蛋白能夠結合到斷裂點。NuA4包含兩個次蛋白(subunit) YNG2以及EAF3，其中Yng2包含 plant homeodomain(PHD domain)，而Eaf3包含Chromodomain，分別能夠和甲基化的組蛋白H3K4me3以及H3K36me相互作用，先前的實驗顯示Chromodomain (eaf3-chromoW84/88A)以及PHD domain (yng2-PHD)雙突變酵母在生長和雙股斷裂的修復上有缺陷。在這裡，我們發現組蛋白修飾H3K4me2以及H3K4me3在DNA雙股斷裂處有大量上升，說明PHD domain以及chromodomain能夠和H3K4me2以及H3K4me3相互作用，因此召引NuA4到雙股斷裂處。此外我們觀察到eaf3-chromoW84/88A yng2-∆PHD雙突變酵母在生長上有缺陷，我們也發現在eaf3-chromoW84/88A yng2-∆PHD雙突變酵母中核醣體蛋白(ribosomal protein)有表現量下降的情況。由於在細胞中，合成核糖體(ribosome)會用掉大約90%的能量，這結果說明我們觀察到eaf3-chromoW84/88A /yng2-∆PHD雙突變酵母有生長缺陷可能是因為轉錄核糖體蛋白的功能受到影響，而導致核糖體蛋白表現量下降，進而造成生長上的缺陷。我們的結果證明PHD domain以及chromodomain和甲基化的H3K4有相互作用，且甲基化的H3K4不管是在轉錄還是修復雙股斷裂的功能上都扮演非常重要的角色。
自從我們發現組蛋白修飾(histone modifiction)包含H2A-S129p、H3K4me2、H3K4me3、H3K36me2以及H4K12ac，這些組蛋白修飾會特別出現在雙股斷裂附近，因此我們測試另外一條修復路徑"複製後修復"(post-replication repair, PRR)是否也會有組蛋白的修飾。PRR路徑是一條能夠讓細胞在複製碰到錯誤時可以先通過這些錯誤(bypass)，先完成複製後再去修復錯誤。PRR可以分成兩條路徑，translesion synthesis (TLS)以及template-switching (TS)。在先前研究顯示DOT1能夠對TLS路徑進行負調控(negatively regulates)，然而在TS路徑中組蛋白的修飾卻仍然不清楚。在這裡我們證明在rad5酵母中在將SET1、SET2、DOT1進行基因剔除後，再用UV、MMS、HU處裡並不影響TS路徑，說明組蛋白的修飾在TS路徑並不是必須的。
總結以上結果，組蛋白修飾包含H2A-S129p、H3K4me2、H3K4me3、H3K36me2以及H4K12ac，這些修飾對於雙股斷裂都扮演很重要的角色。H2A-S129p以及H3K4能夠和NuA4的actin-related、PHD domain以及Chromodomain相互作用，因此NuA4能夠被召引到雙股斷裂處並促進雙股斷裂的修復。相反的，這些組蛋白的修飾對於PRR路徑的TS路徑並不是必需的，雖然先前有文獻指出DOT1有參與在TLS路徑中。

DNA double strand breaks (DSBs) are the most dangerous lesions that threat the integrity of genome. Failure to repair DSBs properly can lead to genomic instability and cancer. In yeast Saccharomyces cerevisiae, the histone acetyltransferase, NuA4 complex is recruited to DSBs where it acetylate H2A and H4. This modification can relax chromatin structure and allow the access of repair proteins to DSBs. Two subunit of NuA4, YNG2 and EAF3, that contain the plant homeodomain (PHD) and chromodomain can interact with trimethylated K4 of histone H3 (H3K4me3) and methylated K36 of histone H3 (H3K36me) respectively in vitro. Previous studies have shown that mutations both in the chromodomain (eaf3-chromodW84/88A) and PHD (yng2-PHD) after defective in cell growth and the DSB repair. Here, we demonstrated that high level of H3K4me2 and H3K4me3 are enriched at HO cleavage site, suggesting the induced H3K4me2 and H3K4me3 can be docking site for the PHD and chromodomain, thus recruiting NuA4 at the DSB site. Since the eaf3-chromoW84/88A yng2-∆PHD double mutant strain defective in cell growth, we discover that the transcription level of several ribosomal protein is dramatically reduced in the eaf3-chromoW84/88A yng2-∆PHD double mutant strain. Given that ribosome synthesis utilizes~90% of the energy in the cell, the growth defect conferred by the eaf3-chromoW84/88A yng2-∆PHD double mutant strain could be due to the low transcription of ribosome protein. Our result demonstrated that the combined interaction of the PHD and chromodomain with methylated H3K4 plays important roles both in transcription and DSB repair.
Since we discovered that histone modifications including H2A-S129p, H3K4me2, H3K4me3, H3K36me2, and H4K12ac are specifically induced around the DSB site, we tested whether the other repair pathway, postreplication repair (PRR), require histone modification.
PRR is the damage bypass mechanism that allows cells to complete DNA replication in presence of DNA lesions. PRR can be divided into two subpathways, translesion synthesis (TLS) and template-switching (TS) pathways. Previous studies have demonstrated that Dot1 negatively regulates TLS in response to replication stress, however, it remains unclear whether histone modifications are involved in the TS pathway. Here we demonstrated that deletion of SET1, SET2, and DOT1 has no significant effect on the TS pathway, suggesting histone modifications are dispensable for the TS pathway.
In summary, histone modifications including H2A-S129p, H4K12ac, H3K4me2, and H3K4me3 play an important role in DSB repair. The modified histone H2A-S129p and methylated H3K4 serves as the binding sites for the actin-related, PHD and chromodomain of NuA4 complexes, thus recruiting NuA4 complex at the DSB sits to facilitate DSB repair. By contrast, these histone modifications are dispensable for the TS pathway of PRR, despite of the involvement of DOT1 in the TLS pathway of PRR.

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