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Fig. 3 | BMC Biology

Fig. 3

From: ASC proneural factors are necessary for chromatin remodeling during neuroectodermal to neuroblast fate transition to ensure the timely initiation of the neural stem cell program

Fig. 3

Proneural mediated chromatin changes correlate with transcriptional output during early neurogenesis. A A schematic representation of the strategy used to generate H3K27Ac ChIP-seq datasets and RNA-seq profiling. B Heatmaps of H3K27Ac ChIP-seq signal centered on Class I and Class II proneural peaks. C Genomic snapshots at the nvy and wor loci. D Boxplots of normalized H3K27Ac signal in stage 9 DHS sites from modENCODE. 2090 DHSs with proneural binding (left), not proneural-bound DHS 14,127 (right). Statistics performed with Wilcoxon rank-sum tests. E Differentially expressed genes from RNA-seq in scAPAA versus NΔE embryos FDR 0.2 (n = 4). F Gene Set Enrichment Analysis (GSEA) of RNA-seq data reveal enrichment for BDGP “VNC neuroblasts” with scAPAA>NΔΕ genes and “ventral epidermis” classes with the scAPAA<NΔΕ genes. G GSEA of differentially acetylated st.9 DHSs in scAPAA. vs. NΔΕ embryos (scAPAA> NΔΕ left, scAPAA<NΔΕ (right) with the ranked genes from the RNA-seq of the same comparison. H A Venn diagram of the GSEA Core Enrichment Genes from G (left panel) with potential target genes of the proneural consensus binding events. H List of selected 40 genes from the intersection in H with proneural binding and combined RNA-seq and differential acetylation. Differential acetylation testing on stage 9 DHS regions in wt bibG4, bib>UscAPAA, and U-NΔE embryos (n = 2) is provided in Additional file 2: Table S4. RNA-seq edgeR analysis output provided in Additional file 2: Table S5

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