Fig. 4: Widespread binding of ZNF729 at GC-rich sequences and promoters in hnPSC.

a, Schematic depicting endogenous tagging of ZNF729, with an FKBPV(F36V) and two HA tags in hnPSCs (ZNF729–FH hnPSCs). Upon addition of dTAG^v-1, ZNF729 is degraded. The protein structure was drawn with IBS 2.0 (ref. ⁵⁷). b, Representative western blot of ZNF729–FH hnPSCs untreated, treated with DMSO as control or treated with dTAG^v-1 for 24 h. The membrane was blotted with an antibody to the HA tag and with α-actin as the loading control blotted on the same membrane. For gel source data, see Supplementary Fig. 1. n = 2 biological replicates. IB, immunoblot. c, Heatmap displaying ZNF729–FH ChIP–seq signal over its bound genomic regions (n = 46,398) in DMSO treated (control) and 24-h dTAG^v-1-treated ZNF729–FH hnPSCs (n = 2 biological replicates). d, Pie charts displaying the genomic features of ZNF729–FH-occupied regions. The pie charts show peak distribution between repetitive or non-repetitive DNA (top) and between promoters, intergenic or intronic DNA regions (bottom). e, Top four DNA sequence motifs obtained when performing motif discovery analysis on the ZNF729–FH ChIP–seq non-repetitive peaks using SeqPos⁵⁸. f, Plot representing GC content at ZNF729–FH-bound (purple line) or unbound (grey line) promoters. TSS, transcription start site. g, Scatter plot displays the odds ratio of ZNF729–FH binding to simple repeats that contain either G or C or both. The vertical dashed line indicates an odds ratio of 1. The horizontal dashed line indicates FDR of 10%. Significantly bound (FDR of 10%) are depicted in red and not bound in grey. h, IGV genome browser capture of the ZNF729–FH ChIP–seq signal (top two tracks, purple) or the TRIM28 ChIP–seq signal (bottom two tracks, turquoise) in DMSO-treated (control) and 24-h dTAG^v-1-treated ZNF729–FH. i, Heatmap displaying the TRIM28 ChIP–seq signal over ZNF729-bound non-repetitive promoters (top), the repetitive regions (middle) or the regions bound by TRIM28 that do not overlap with ZNF729 (bottom). The ChIP–seq signals from control-treated (left) or dTAG^v-1-treated (right) ZNF729–FH hnPSCs are shown (n = 2 biological replicates).