Fig. 7: Evf2 RNP regulation and HiC inter-chr and intra-chr loops across RCDs. | Nature Communications

Fig. 7: Evf2 RNP regulation and HiC inter-chr and intra-chr loops across RCDs.

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

Fig. 7: Evf2 RNP regulation and HiC inter-chr and intra-chr loops across RCDs.The alternative text for this image may have been generated using AI.

A Evf2 regulated RNP binding across chr6 RCDs, based on Cut&Run results of single RNP binding to <120 bp fragments (SOX2, DLX, SMARCA44, NONO, SMARCC2), the numbers of Evf2 positively regulated sites (+, gray) and negatively regulated (-, red) sites across chr6 and in each RCD, fold changes for each RNP and RCD relative to the expected number set to 1 (dashed line, E). Pvals and χ² statistic values are indicated for each RNP. gray triangle (decreased gradient of positive-regulated Dlx sites in the proximal-distal direction). B Evf2-regulated RNP binding across RCDs in a gradient (defined as ≥4 consecutive RCDs) is shown. C. Evf2 regulated RNP binding across chrX-RBS-defined domains: Evf2(+, red) and (-, gray) Pval and χ² values are indicated for each RNP; χ² values are not calculated for RNPs that are not regulated (zero sites, SMARCA4, DLX). D Evf2 (+) regulated RNP binding across chr11 RBS-defined domains, the chromosome with the highest number of RCDs (17). Chi-square analysis, Evf2 (+) regulated (p = 0, all RNPs): SOX2, χ²=1947, SMARCA4, χ²= 14387, NONO, χ²= 2712, SMARCC2, χ²= 4055; χ² values are not calculated for RNPs that are not regulated at one of the RCDs (zero sites, Evf2 (+) reg. DLX, Evf2 (-) reg. SMARCA4, Evf2 (-) reg. SMARCC2). E JASPAR analysis of Sox2, Dlx2, and Dlx5 consensus DNA binding homeobox motif enrichment at Evf2 regulated sites, 120 fragment Cut&Run peaks in Evf2TS/TS ÷ Evf2+/+. F Chr6: Top-ranked PWMEnrich DNA motif analysis identified TF DNA motif enrichment at Evf2-regulated NONO or SMARCC2 sites (pval<1E-04, FDR < 0.05, ≥2 domains). Only motifs identified in 2 or more domains are marked. RCDs 1 and 2 are combined (gray region= domains 1 + 2), expected number of motifs for each domain based on proportional domain size. G, H Chr-RCD mapping of frequencies of HiC intra-chr (light gray) and inter-chr (dark gray) interaction sites in E13.5 wildtype GEs. E = 1 (expected number, dashed line). HiC, 6-8 wildtype embryos (12-16 E13.5GEs), n = 2 pools, FDR < 0.01, and qval<0.02 determined between biological replicates.

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