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. Author manuscript; available in PMC: 2013 Apr 29.
Published in final edited form as: Cell Rep. 2012 Aug 16;2(2):372–385. doi: 10.1016/j.celrep.2012.07.009

Figure 3. Ubp10 Interacts with Ribosome Biogenesis Proteins.

Figure 3

(A) FunSpec (http://funspec.med.utoronto.ca/) analysis of the 83 interacting proteins identified by crosslinking coIP MS/MS with Ubp10-3HSV. The p value represents the probability that the intersection of a given list with any functional category occurs by chance. “k” represents the number of genes from the input and “f” represents the total number of genes for that category in the yeast proteome.

(B) Network diagram of the nucleolar-localized proteins identified by crosslinking coIP MS/MS with Ubp10-3HSV. Diagram was generated using Cytoscape (http://www.cytoscape.org/) (Smoot et al., 2011). Thick lines connect interactions discovered by the crosslinking coIP MS/MS analysis. Thin lines mark interactions previously described. RNA polymerase I, BoxC/D snoRNP, and Box H/ACA snoRNP interactions were derived from solved crystal structures (Kuhn et al., 2007; Liang et al., 2009; Rashid et al., 2006; Reichow et al., 2007). UtpA, UtpB, and UtpC interactions were derived from global coIP and Y2H studies (Dragon et al., 2002; Gallagher et al., 2004; Grandi et al., 2002; Krogan et al., 2004; Kuhn et al., 2007; Li and Ye, 2006; Liang et al., 2009; Lim et al., 2011; Rashid et al., 2006;Reichow et al., 2007; Tarassov et al., 2008; Wittmeyer et al., 1999). ◇ and † denote those interactions between Ubp10 and the target proteins that have been previously published (Krogan et al., 2006; Tarassov et al., 2008). # and * denote those interactions between Ubp10 and the target proteins that also occur by coIP in (C) or Y2H in (D).

(C) coIPs between Ubp10-3HSV and the indicated 3HA-tagged target proteins. Ubp10-3HSV was purified with its interacting proteins by immunoprecipitation using anti-HSV antibodies. 1% of lysates and 10% of coIPs were separated by SDS-PAGE and analyzed by anti-HSV and anti-HA western blotting.

(D) Yeast 2-hybrid (Y2H) interactions between cells expressing GBD-Ubp10 and each indicated GAD fusion protein. Cells were spotted onto media plus or minus histidine to measure spotting efficiency and Y2H interaction, respectively.

See also Figure S2.