Fig. 3: Evf2 guidance of Dlx5/6UCE to gene bodies (±5 kb) align with transcriptional regulation and Evf2-RNP recruitment. | Nature Communications

Fig. 3: Evf2 guidance of Dlx5/6UCE to gene bodies (±5 kb) align with transcriptional regulation and Evf2-RNP recruitment.

From: Single-cell transcriptomics of ventral forebrain progenitors identifies Evf2 enhancer lncRNA-enhancer gene guidance through direct RNA binding and RNP recruitment domains

Fig. 3: Evf2 guidance of Dlx5/6UCE to gene bodies (±5 kb) align with transcriptional regulation and Evf2-RNP recruitment.The alternative text for this image may have been generated using AI.

Differential scRNAseq analysis of Evf2 regulated genes located on chr6 (Evf2TS/TS÷ Evf2+/+) identifies cell type specificity, represented according to color (VZ, SVZ, Isl1, Lhx6). A Evf2-EGG-GB plots align Dlx5/6UCE shifts at each chr6 transcriptionally regulated gene target and distances of associated Evf2 regulated Evf2-RNP binding sites. Colored loops highlight Evf2 differentially regulated scRNAseq gene targets on chr6 (Evf2TS/TS÷ Evf2+/+) in E13.5GE subpopulations (VZ, SVZ, Isl1, Lhx6) coincident with Evf2-Dlx5/6UCE guidance: Top panel (Evf2 positively regulated RNPs). Bottom panel (Evf2 negatively regulated RNPs), chr6: 0-150 Mb. B Panel focus is zoomed on chr6 proximal region (X-axis, chr6: 3.2-9.1 Mb). Evf2 positively and negatively regulated RNP binding are shown in one panel, with red rings around negatively regulated RNPs. Legend in (A) is also used in (B), individual RNPs. In both (A) and (B): Dlx5/6UCE distances are plotted on the Y-axis (X 1 Mb up (upstream) and down (downstream) distances from gene (0)). Evf2(+)regulated Dlx5/6UCE position (yellow dots), Evf2(℃)regulated Dlx5/6UCE position (blue dots). Transcriptional effects of Evf2 loss (Evf2TS/TS): shifts associated with decreased gene expression (red rings), shifts associated with increased gene expression (gray rings). Right Y axis (gene expression): log2 (fold change in gene expression), black diamonds (−3 to +3), red diamonds (<−3). Y-axis Evf2-regulated RNP binding sites (X10kb distances from gene (0)) (SMARCC2, SMARCA4, DLX, SOX2, NONO, SMC1): solid ovals (Evf2(+) regulated binding), red rings around solid ovals (Evf2(ȓ) regulated binding). Blue line indicates location of Dlx5/6UCE/Evf1/2 on chr6. Results are based on previously published datasets (4,5: Evf2 regulated Dlx5/6UCE-4Cseq, Cut&Run [Evf2 regulated RNP binding, SMARCA4, DLX, SOX2], ChIPseq [Evf2 regulated RNP binding, Smc1/Smc3], this work: scRNAseq, Cut&Run [Evf2 regulated RNP binding, NONO. SMARCC2]).

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