Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response

• Published in: Molecular cell 2015-09, Vol.59 (5), p.867-881
• Main Authors: 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.
• Format: Article
• Language: English
• Subjects: Acetylation - radiation effects; Cullin Proteins - metabolism; Databases, Protein; DNA Damage; DNA Repair; DNA Repair Enzymes - metabolism; Exodeoxyribonucleases - metabolism; HeLa Cells; Humans; Phosphorylation - radiation effects; Proteasome Endopeptidase Complex - metabolism; Protein Array Analysis - statistics & numerical data; Proteome - metabolism; Proteome - radiation effects; Proteomics - methods; Proteomics - statistics & numerical data; Spindle Apparatus - metabolism; Ubiquitination - radiation effects
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2015.05.006

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. [Display omitted] •Proteomic discovery of DNA damage-regulated ubiquitination and acetylation sites•FACET-IP approach improves acetylation site detection•Atypical K6- and K33-polyubiquitin linkages increase in response to UV radiation•SCF-Cyclin F mediates EXO1 ubiquitination in response to UV radiation Elia et al. have globally profiled ubiquitination, acetylation, and phosphorylation in the DNA damage response (DDR). Their valuable datasets of 33,500 ubiquitination and 16,740 acetylation sites implicate K6- and K33-linked polyubiquitination in the DDR, demonstrate that CRLs mediate 10% of DDR ubiquitination events, and reveal that EXO1 is an SCF-Cyclin F substrate.