Fig. 1.

UV irradiation alters the composition of Ku86 macromolecular complexes. A, Protein complexes were purified from parental HeLa-S3 cells or HeLa-S3 cells expressing doubly tagged FLAG-HA Ku86 (supplemental Fig. S1). Representative silver stain analysis of nuclear Ku86 complexes purified before (t = 0, lane 2) or after (t = 0.5 h, 2.5 h, 5 h, lanes 3, 4, and 5, respectively) UV irradiation (300 J/m²), along with a “mock” complex purified from parental HeLa-S3 cells (lane 1). B, Hierarchical clustering of quantitative proteomic data obtained after iTRAQ LC-MS/MS analysis of biological replicates: 118 Ku86 associated proteins detected in two independent experiments (Exp.1 and Exp.2) primarily segregate between two clusters based on their response to UV irradiation. Green and red, respectively, indicate decreased and increased association after UV irradiation (see also supplemental Table S1 Summary of quantitative LC-MS data). (C and D) Functional enrichment analysis of proteins from Cluster 1 and 2. The number of genes represented in (B) for each category is provided on the horizontal axis. The corresponding adjusted p value is indicated within each bar. For clarity, only the first three co-occurrence terms are listed. See supplemental Table S2 Functional enrichment analysis, for the full list of annotations.