Extended Data Fig. 3: PABPC4 acts in concert with HNRNPC to control alternative polyadenylation and directs its target mRNAs to AGO2-dependent translational repression.
From: An mRNA processing pathway suppresses metastasis by governing translational control from the nucleus

(a) Significant depletion of selected gene ontology (GO) terms in the HNRNPC interactome in MDA-LM2 compared to MDA-MB-231 cells, as determined by coIP-MS. Also reported are the associated empirical p-values from permutation tests. (b) Enrichment of PABPC4 in HNRNPC coIP-MS data in MDA-MB-231 and MDA-LM2 cells. n = 3 biological replicates. Individual data points and mean values are shown, error bars indicating SEM; p-value calculated using parametric linear model controlling for input abundances. (c-d) Comparison of alternative polyadenylation ratio (logAPAR) in PABPC4 knockdown (sgPABPC4) (c) or PABPN1 knockdown (sgPABPN1) (d) and control (sgControl) cells, as in Fig. 2d. Below, cumulative density plots as in Extended Data Fig. 2e are shown. (e) Heatmaps showing the enrichment of canonical poly(A) signals in the vicinity of PABPC4 binding peaks (as determined by PAPER-CLIP). The bolded border denotes a statistically significant enrichment (hypergeometric test, corrected p < 0.05; red). MI values and associated z-scores are shown. (f) Cumulative density plot of logAPAR comparing sgHNRNPC/sgPABPC4 (double knockdown) to sgControl/sgPABPC4 cells, for HNRNPC 3′ UTR target and non-target mRNAs, as in (c). (g) Relative RNA quantity in cytoplasmic versus nuclear fraction, as determined by RTqPCR. (h-i) Cumulative density plot of logAPAR comparing MDA-MB-231 and MDA-LM2 (h) or MDA-MB-231 sgControl and sgHNRNPC (i) cells, in nuclear versus cytoplasmic fractions, for HNRNPC 3′ UTR target and non-target mRNAs, as in (c). (j-k) Comparison of logAPAR from cytoplasmic RNAs, in MDA-LM2 and MDA-MB-231 (j) or MDA-MB-231 sgControl and sgHNRNPC (k) cells, as in (c). (l-m) Enrichment patterns of HNRNPC target mRNAs in the cytoplasm as a function of logTER between MDA-LM2 and MDA-MB-231 (l) or MDA-MB-231 sgControl and sgHNRNPC (m) cells, as in Fig. 1d.