Fig. 4: Experimental validation of predicted DUBs (USP11 and USP20) for FOXP3. | Nature Communications

Fig. 4: Experimental validation of predicted DUBs (USP11 and USP20) for FOXP3.

From: A protein sequence-based deep transfer learning framework for identifying human proteome-wide deubiquitinase-substrate interactions

Fig. 4: Experimental validation of predicted DUBs (USP11 and USP20) for FOXP3.The alternative text for this image may have been generated using AI.

a Prediction results of DUBs for both FOXP3 and upstream regulators (SMAD3/4) in the TGF-β pathway. SMAD3/4 and NFAT cooperate to induce FOXP3 expression through binding to FOXP3 enhancer30. Scores in the figure are assigned by TransDSI. The red pentagram indicates validation by our subsequent experiments. b Experimental validation of the USP11-FOXP3 interaction using Co-immunoprecipitation (IP) assay. HEK293T cells were transfected with Myc-USP11 and Flag-FOXP3, after 36 h, cells lysates were immunoprecipitated with indicated antibody and analyzed by western blot. c USP11 was found to remove ubiquitin modifications from FOXP3. HEK293T cells were transfected with HA-Ub, Myc-USP11, control vector or Flag-FOXP3, and cells were treated with MG132 for 8 h before collection. Ubiquitinated FOXP3 was immunoprecipitated with anti-Flag antibody and detected by immunoblotting with anti-HA antibody. d The USP20-FOXP3 interaction was validated by the same experimental validation protocol as the USP11-FOXP3 interaction in (b). e Like USP11 in (c) USP20 was also found to remove ubiquitin modifications from FOXP3, as determined by the same procedure. Source data are provided as a Source Data file.

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