Figure 6. The TAZ-CAMTA1 and YAP-TFE3 interactomes are enriched for transcriptional regulators and chromatin modifiers.

(A) Overview of BioID method. (B) Summary of YAP-TFE3 and TAZ-CAMTA1 interactomes. (C) Dot plot representation of chromatin modifiers shared by YAP-TFE3 and TAZ-CAMTA1 interactomes. (D) Table of chromatin modifiers shared by YAP-TFE3 and TAZ-CAMTA1 interactomes. (E) Classification of prey proteins shared between TAZ-CAMTA1 and YAP-TFE3 interactomes. (F) Algorithm to prioritize the TAZ-CAMTA1 and YAP-TFE3 interactomes for the subsequent RNAi screen. For BioID mass spectrometry, two biological replicates were made for each cell line. Affinity purification and proximity biotinylation coupled to mass spectrometry were performed as described in Lambert et al., 2015. SAINT (significance analysis of interactome) analysis (Choi et al., 2011) was performed on the mass spectrometry data, using 10 controls compressed to 5. Only proteins with iProphet protein probability ≥ 0.95 were used. Results are expressed in dotplot format. Each prey protein is represented as a dot, with color signifying average spectral count, the darkness indicating average spectral count between the two biological replicates (the darker the dot, the higher the average spectral count), and the size represents the relative abundance. Darkness of the ring indicates the Bayesian False Discovery Rate (BFDR); black (FDR ≤ 0.01), blue (FDR ≤ 0.05), light blue (FDR > 0.05). The data was filtered so that each prey had a minimum of 10 spectral counts in at least one of the biological replicates.

Figure 6—figure supplement 1. BioID Mass Spectrometry shows that YAP-TFE3 and TAZ-CAMTA1 have an altered interactome compared to YAP and TAZ.

Group (A) prey proteins often demonstrated a loss of interaction with the fusion proteins. Group (B) prey proteins demonstrated enhanced interaction with the fusion proteins relative to TAZ and YAP and generally consisted of epigenetic modifiers and also interacted with CAMTA1 and TFE3. Group (C) prey proteins predominantly demonstrated enhanced interactions with TAZ-CAMTA1 relative to TAZ, and predominantly represented epigenetic modifiers. (D) Protein quantification table for YAP-TFE3 and YAP control showing similar expression levels. Biological replicates are represented. (E) Protein quantification table for TAZ-CAMTA1 and TAZ control showing similar expression levels. Biological replicates are represented. Results demonstrated in dot plot form. Size of dot is proportionate to relative abundance. Darkness of dot is proportionate to the spectral count. Darkness of the ring indicates the Bayesian False Discovery Rate (BFDR); black (FDR ≤ 0.01), blue (FDR ≤ 0.05), light blue (FDR > 0.05).