Fig. 6: ATAC-sequencing shows changes in the CM4 subcluster and changes in chromatin access near TFs.

A Visualization of ATAC-Seq reads of open chromatin around the Nppa locus in each of the CM subclusters. CM4 cluster has more open chromatin compared to other clusters (see arrow). B Visualization of ATAC-Seq reads of open chromatin around the Nppa locus in the CM4 cluster from PMIS-miR-200 samples. The Nppa locus appears more open in PMIS-miR-200 samples compared to WT (see arrows). C Open chromatin of the CM4 cluster was analyzed for enrichment of TF binding motifs. Shown are the top 10 enriched motifs. Motifs are enriched for T-Box family members, with Tbx5 being the most enriched. D UMAP feature blot of RNA expression (Upper) and motif enrichment (chromVAR) (lower) for Tbx5, Mef2c, Gata4, and Nkx2.5. E Heatmap of enriched topics across the CM cell states. CM4 cells are enriched for Topic 9 which contains TBX5 as the topic ranked as a differentially enriched motif (Supplemenatary File 7). F Heatmap of the TFs predicted to bind enriched eRegulons regions based on RNA expression of the TFs. G Nppa-Luciferase activity in AC16 cells stably expressing PMIS-miR-200 or a non-targeting control (PMIS-Scramble) showing activation of the Nppa promoter in PMIS-miR-200 cells. The statistic test performed was one-way ANOVA with multiple comparisons. N = 4. Data are presented as mean values ± SEM.