Fig. 3: hnRNPK regulates the expression of multi- but not mono-exon 3XTs.

a The C-rich motif is enriched in MTR4-target multi-exon 3XRs. The table shows the results of MEME motif enrichment analysis. E-value; the expected number of motifs with the given log likelihood ratio (or higher), and with the same width and site count that one would find in a similarly sized set of random sequences. Sites; the number of sites contributing to the construction of the motif. b Venn diagram showing the CCWSCC-matched RNA-binding proteins speculated by Tomtom using different distance metrics. Pearson; Pearson correlation coefficient. Euclidean; Euclidean distance. Sandelin; Sandelin-Wasserman similarity. W; A or T. S; G or C. c qRT-PCR analysis of mono- (blue) and multi-exon (red) 3XT expression in HeLa cells transfected with si-hnRNPK. Results are expressed as the mean ± s.d. (n = 3 biologically independent replicates). Paired two-sided Student’s t-test; *p < 0.05. d Lysates from HeLa cells were subjected to immunoprecipitation with an anti-hnRNPK antibody or rabbit IgG, followed by qRT-PCR analysis to detect the indicated RNAs. SNHG9 and SNHG19 RNA were used as negative controls. Results are expressed as the mean ± s.d. (n = 3 biologically independent replicates). Paired two-sided Student’s t-test; *p < 0.05. e hnRNPK associates with MTR4 in vivo. Lysates from HeLa cells were subjected to immunoprecipitation with an anti-MTR4 antibody, an anti-hnRNPK antibody or rabbit IgG followed by immunoblotting analysis with anti-MTR4, anti-hnRNPK or anti-GAPDH antibodies. GAPDH was used as a negative control. This experiment was repeated independently two times with similar results. The exact p-values are c HECTD2 3XT: p = 0.03689 (siCont vs si-hnRNPK#1), p = 0.04965 (siCont vs si-hnRNPK2), SPRED2 3XT: p = 0.01871 (siCont vs si-hnRNPK#1), p = 0.02218 (siCont vs si-hnRNPK#2), KCTD13 3XT: p = 0.01953 (siCont vs si-hnRNPK#1), p = 0.04751 (siCont vs si-hnRNPK#2); d HECTD2 3XT: p = 0.01229 (rabbit IgG vs hnRNPK IP), SPRED2 3XT: p = 0.00157 (rabbit IgG vs hnRNPK IP), KCTD13 3XT: p = 0.01079 (rabbit IgG vs hnRNPK IP). Source data are provided as a Source Data file.