Fig. 4: Enhanced HyPro-MS enables specific labeling of the PNCTR-proximal proteome.
From: Enhanced hybridization-proximity labeling discovers protein interactomes of single RNA molecules
A Principal component analysis shows tight clustering of the PNCTR, ACTB and negative control (Ctrl) HyPro-MS samples. B Volcano plot for the PNCTR-proximal proteins known to localize to the nucleus based on the Human Protein Atlas data (https://www.proteinatlas.org/). Significant hits are shown in red. Known PNC markers and proteins localizing to the nucleolar rim compartment are labeled. C Metascape annotation of PNCTR-proximal proteome reveals enrichment for RNA and DNA metabolism functions, alongside aspects of ribosome biogenesis. D PNCTR-proximal proteomes identified by both the enhanced (this study) and the original28 versions of HyPro-MS are significantly enriched for physical protein-protein interactions from the STRING database48 (score > 0.7), as compared to simulated (n = 100) controls, which are presented as box plots. However, the enrichment is markedly more robust for the enhanced HyPro-MS. The comparisons were made using a two-sided Wilcoxon signed rank test. E The PNCTR-proximal proteome identified by enhanced HyPro-MS is significantly enriched for nucleolar-rim proteins. F The PNCTR-proximal proteome mapped by the original HyPro-MS shows no significant enrichment for nucleolar-rim proteins. In (E, F), enrichment was assessed using a two-sided Fisher’s exact test.
