(A) Flow chart of BioID experiments. mCherry-BirA*-HA expressing ES cells were used as control to subtract the effect of promiscuous biotinylation activity of BirA*. (B) Localization of bait proteins (mCherry or HA) and biotin-tagged proteins (Streptavidin-FITC) in mCherry-BirA*-HA control ES cells and Aire-BirA*-HA ES cells shown by immunofluorescence staining. Scale bars: 1 μm. Bottom panel for each group shows magnified views of a mitotic cell, marked by arrows in top panel. Scale bars: 4 μm for mCherry-BirA*-HA, 2 μm for Aire-BirA*-HA. (C) List of proximity partners of AIRE identified by SAINT analysis (n = 3, 1%FDR) of BioID/mass spectrometry data and annotations of functional categories.