Extended Data Fig. 9: TNRC18 binds corepressors, mediating transcriptional repression.

a. Scatter plots of the indicated TNRC18-interacting proteins identified by BioID in HEK293 (x-axis) and HeLa cells (y-axis). The mass spectrometry data following BioID in HeLa cells is shown in Supplementary Table 5. b. Pearson correlation plot using the IF signals of the indicated protein in HEK293 cells. c. Structural model of the Sin3A’s PAH domain (green) in complex with the TNRC18 peptide (cyan). The structure was predicted via PHYRE2 (http://www.sbg.bio.ic.ac.uk/~phyre2/html/page.cgi?id=index). The model of the complex was generated by the Coot program, using the structure of mouse Sin3A PAH1-SAP25 SID complex (PDB 2RMS) as template. d. Sanger sequencing (top) and Western blot (bottom) for the TNRC18 L760A KI mutation introduced into HEK293 cells. Vinculin is the sample processing control. e. Scatter plot showing the indicated TE families that exhibit significant expression change, based on RNA-seq profiles of HEK293 cells with the TNRC18 L760A mutation versus WT controls. Adjusted P value is calculated by negative binomial model-based methods (DESeq2). f. RT-qPCR of the indicated TEs in HEK293 cells with TNRC18 L760A mutation versus WT controls (n = 3 independent experiments; **P < 0.01; ***P < 0.001; ****P < 0.0001, two-sided t-test). Data were plotted as the mean ±s.d. after normalization to signals of GAPDH and then to those of WT. The exact P value is shown in Supplementary Table 8. g. GSEA revealed enrichment for the indicated pathways in HEK293 cells with the TNRC18 L760A mutation versus WT controls. Immunity-related gene sets are labelled in red. The P value was calculated by a two sided empirical phenotype-based permutation test; the false discovery rate q-value is adjusted for geneset size and several hypotheses testing whereas the P value is not. h. RT-qPCR of the indicated immunity-related genes in WT and TNRC18-L760A-mutated HEK293 cells (n = 3 independent experiments; *P < 0.05; ***P < 0.001; ****P < 0.0001, two-sided t-test). Data were plotted as the mean ±s.d. after normalization to signals of GAPDH and then to those of WT. The exact P value is shown in Supplementary Table 8. i. Heatmap of CUT&RUN signals for TNRC18, HDAC2, TRIM28 and SETDB1 in HEK293 cells, across ±5 kb from the TNRC18 peaks (n = 7545; defined as the common peaks of TNRC18 and GFP-TNRC18, based on CUT&RUN in HEK293 cells). j. IGV tracks showing the CUT&RUN signals of the indicated protein at the reported TRIM28 target gene in HEK293 cells. k. The motif search analysis revealed the binding motifs of KRAB-ZnF proteins to be enriched at the TNRC18 peaks.