Elia Andrew E H, Boardman Alexander P, Wang David C, Huttlin Edward L, Everley Robert A, Dephoure Noah, Zhou Chunshui, Koren Itay, Gygi Steven P, Elledge Stephen J
Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA.
Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
Mol Cell. 2015 Sep 3;59(5):867-81. doi: 10.1016/j.molcel.2015.05.006. Epub 2015 Jun 4.
Execution of the DNA damage response (DDR) relies upon a dynamic array of protein modifications. Using quantitative proteomics, we have globally profiled ubiquitination, acetylation, and phosphorylation in response to UV and ionizing radiation. To improve acetylation site profiling, we developed the strategy FACET-IP. Our datasets of 33,500 ubiquitination and 16,740 acetylation sites provide valuable insight into DDR remodeling of the proteome. We find that K6- and K33-linked polyubiquitination undergo bulk increases in response to DNA damage, raising the possibility that these linkages are largely dedicated to DDR function. We also show that Cullin-RING ligases mediate 10% of DNA damage-induced ubiquitination events and that EXO1 is an SCF-Cyclin F substrate in the response to UV radiation. Our extensive datasets uncover additional regulated sites on known DDR players such as PCNA and identify previously unknown DDR targets such as CENPs, underscoring the broad impact of the DDR on cellular physiology.
DNA损伤反应（DDR）的执行依赖于一系列动态的蛋白质修饰。我们运用定量蛋白质组学技术，全面分析了紫外线和电离辐射诱导下的泛素化、乙酰化和磷酸化情况。为了改进乙酰化位点分析，我们开发了FACET-IP策略。我们关于33500个泛素化位点和16740个乙酰化位点的数据集，为蛋白质组DDR重塑提供了有价值的见解。我们发现，K6和K33连接的多聚泛素化在DNA损伤反应中大量增加，这表明这些连接方式可能主要负责DDR功能。我们还表明，Cullin-RING连接酶介导了10%的DNA损伤诱导的泛素化事件，并且EXO1是紫外线辐射反应中SCF-Cyclin F的底物。我们广泛的数据集揭示了已知DDR相关蛋白（如PCNA）上的其他调控位点，并鉴定出了以前未知的DDR靶点（如着丝粒蛋白），强调了DDR对细胞生理学的广泛影响。
