Extended Data Fig. 9: ZNF729 exerts activator or repressor function at target genes.

a. Low impact of ZNF729-FH depletion on the expression of TEs. MA plot represents TEtranscript⁸⁷-obtained data quantified with DESeq2⁸³. Top ZNF729-bound TE families are labeled. b. Expression from gene promoters bound or unbound by ZNF729. Box plots show basal hnPSC expression (in TPMs) of genes bound or unbound by ZNF729, n = 4 biological replicates. Boxes show the median and the quartile 1 (Q1) to quartile 3 (Q3) range (interquartile range, IQR). Whiskers minimum corresponds to Q1 − 1.5 × IQR, and the maximum to Q3 + 1.5 × IQR. N = 461 bound promoters and n = 13883 unbound promoters. Two-sided Wilcoxon test, P < 2.2e-16. c. Stacked bar plot represents number of down- or upregulated genes upon ZNF729-FH depletion for 24 h with dTAG^v-1 and the percentage of them directly bound by ZNF729 at their promoters (−1kb/+200 bp around the TSS). d. Metagene plots showing TRIM28 ChIP-seq signal over promoters activated or repressed by ZNF729 and over a negative control (TRIM28 bound regions not overlapping with ZNF729). Red represents ZNF729FH DMSO (control) and green dTAG^v-1 treated. e. PCA analysis of bulk transcriptomes from blastoids, dark spheres formed upon high LTR5Hs repression, and DMSO-treated or dTAG^v-1 treated ZNF729-FH hnPSCs. Red shade represents “normal / high” levels of ZNF729 (blastoids, and DMSO treated ZNF729-FH cells). Yellow shade represents “low” ZNF729 levels (dark spheres with high LTR5Hs repression, and dTAG^v-1 treated ZNF729-FH hnPSCs). Note that high ZNF729 and low ZNF729 samples separate along PC3.