Fig. 3: Pre-configuration with feature histone modifications precedes chromatin loop dynamics.

a Heatmap showing clusters of top 1000 variable loops among enhancers and promoters by loop strengths (normalized CPM). Loops contained E–E, E–P, or P–P loops. b Heatmaps showing cognate H3K4me3, H3K27ac, and gene expression on anchors of each loop. Only reads on ChIP-seq peaks were used to calculate normalized signals of H3K4me3 and H3K27ac. The eAEC and HEC scRNA-seq data were from GSE139389. Pre-HSC and LT-HSC scRNA-seq data were from GSE67120 and GSE66954. Gene expression values were calculated and normalized with log2(TPM/10 + 1). c Percentages of genes in three loop clusters with down-regulated, transient, and up-regulated expression from eAECs to LT-HSCs. Transient genes meant those whose expression was up-regulated in some cases and down-regulated in others. d Biological process analysis of looping regions in three clusters. The inputs were these looping anchor regions for GO term analysis with GREAT. The −log10(FDR) values were shown after BH correction. e Track views showing the loop change trend among enhancers and promoters at the Ets1, Cebpg, and Meis1 loci. f Violin plots showing expression of representative genes in three clusters with log2(TPM/10 + 1). The scRNA-seq data contain 42 eAECs, 33 HECs, 50 pre-HSCs and 16 LT-HSCs. Box-and-whiskers plots represented the maxima, 75th percentile, median, 25th percentile, and minima. Wilcoxon Rank Sum test (two-sided) was performed between two adjacent stages. *P-value < 0.05, **P-value < 0.01, ***P-value < 0.001, ****P-value < 0.0001, “ns” not significant. eAEC early AEC, pre pre-HSC, LT LT-HSC.