Fig 1.

(A) Experimental workflow. Nuclear extracts were prepared from HeLa wild-type-protein- or GFP-fusion protein-expressing cells. GFP pulldowns were performed in triplicate and analyzed separately by mass spectrometry. Raw data were analyzed by MaxQuant, and specific interactors were selected from background using label-free quantification in Perseus. iBAQ intensities were used to calculate the relative abundance of interaction partners. (B and C) Identification of interacting proteins for Ash2l (B) and Rbbp5 (C) by volcano plots (left) and the stoichiometry (>0.01) of these interactors presented by bar graphs (right). In the volcano plots, the ratio of GFP to WT in label-free quantification are plotted against the −log₁₀ of the false discovery rate (FDR) calculated by a permutation-based FDR adapted t test. Significant outliers are labeled. Bar graphs indicate the stoichiometry of interacting proteins (indicated at the bottom) relative to Set1/Mll proteins. The dashed line indicates a ratio to the total Mll/Set1 protein of 1. Error bars indicate the standard deviations of the biochemical triplicate for each experiment.