Fig. 7. Patient-derived ADNP Y719* hiPSCs display R-loop accumulation and CTCF increase at ADNP targets.

a Schematic of the human ADNP gene showing exons and location of ADNP mutation relative to the cDNA sequence (top). Zinc fingers (blue) and homeodomain (red) are present in WT ADNP protein, while ADNP Y719* lacks the homeodomain (bottom). b Western blot for ADNP and Actin in control and ADNP Y719* hiPSCs. ADNP was detected using both C- and N-terminus recognizing ADNP antibodies as indicated. c Pie chart displaying distribution of 36,746 hiPSC ADNP peaks across genomic features. d MA plot of RNA-Seq expression for 13,057 genes between control and ADNP Y719* hiPSCs. Blue dots indicate differentially expressed genes (adjusted p-value <=0.05; p-values computed by edgeR with Benjamini–Hochberg adjustment for multiple comparisons). Red dots indicate differentially expressed genes with an ADNP CUT&RUN peak within 3 kb of the gene body. e Top 10 most significantly enriched processes (obtained from Enrichr) in differentially expressed ADNP targets (red dots in d) that are up- or downregulated in ADNP Y719*. Neurologically relevant processes are shown in red. f Scatterplot of CTCF signal (RPM) in control and ADNP Y719* hiPSCs across 36,746 ADNP CUT&RUN peaks called in control hiPSCs. g Genome browser view of the COL22A1 gene showing CTCF CUT&RUN signal (RPM) in control and ADNP Y719* hiPSCs and ADNP CUT&RUN signal (RPM) in control hiPSCs. h Signal plot of normalized MapR signal in control and ADNP Y719* hiPSCs over 36,746 ADNP CUT&RUN peaks called in control hiPSCs. i Genome browser view of the SC5D gene showing MapR signal (RPM) in control and ADNP Y719* hiPSCs and ADNP CUT&RUN signal (RPM) in control. j Genome browser view of the CALCOCO1 gene showing CTCF CUT&RUN and MapR signal (RPM) in control and ADNP Y719* hiPSCs and ADNP CUT&RUN signal (RPM) in control. Source data underlying (b) are provided as a Source data file.