FIGURE 2.

(A) Western blot for degradation of endogenous DDX3X tagged with mini-AID (mAID) upon treatment with an auxin (indole-3-acetic acid) in HCT-116 human colorectal carcinoma cell line expressing OsTIR1 under the control of a CMV promoter (DDX3^degr). (B) Experimental schematic for ribosomal profiling after replacement of endogenous DDX3X with exogenous DDX3X or 3Y. (C) Western blot for expression of exogenous FLAG-tagged DDX3X and DDX3Y in HCT-116 cells after degradation of endogenous DDX3X. (D, left) Full and (right) zoomed in plots of differential expression analysis of RNA and ribosome profiling changes upon complementation of DDX3X with either DDX3Y or DDX3X. Point size indicates P-value of differential translation (two biological replicates, each condition). (E) Fold-change in TE between DDX3Y and DDX3X expression in mRNAs classified based on DDX3 sensitivity (as in Supplemental Fig. S2A). (F) The fold-change of the riboskew, or ratio in ribosome occupancy in the 5′ UTR versus the coding sequence under DDX3 depletion (left) or the ratio between complementation with DDX3Y or DDX3X (right). Effect size (Cliff's delta) between the “Not_significant” and “TE_down” groups is indicated.