Fig. 1

Identification of CLUH interactome by co-immunoprecipitation in both HCT116 cells and mESCs. A–B Schematic representation of the co-IP experimental design. Co-immunoprecipitated proteins from 3xHA-mCLUH sample (IP CLUH) and control sample (IP mock) are identified by LC-MS/MS. A HCT116 cells are transduced with a lentivirus to express the 3xHA-mCLUH protein. B mESCs are genome-edited to express an endogenous 3xHA-CLUH protein. The mESCs knock-in clone G12 is used (see Fig. S1C). C–D Tables summarizing the MS protein identification in HCT116 cells (C) and mESCs (D). Total number of proteins identified by Mascot software with a false discovery rate (FDR) below 1% in IP mock and IP CLUH samples. The five proteins with the highest specific spectral counts in the IP CLUH are shown. Biological replicate samples are numbered from #1 to #3. E–F Volcano plots showing the global enrichment of proteins in IP CLUH versus the IP mock. The x-axis shows the log2 fold change (FC) and the y-axis shows the −log10 of the FDR (n=3), obtained using SAINTexpress software [26]. Significantly enriched proteins are shown in red and are defined by a fold change greater than two and a FDR < 0.1 (shown as dashed red line). Selected proteins with the highest spectral count (shown in D) are labeled and identified with a green circle. The full datasets and analysis are available in Table S1 and S2