Figure 4.

Promoter-enhancer interaction regulation in gene expression during spermatogonial differentiation.A, the numbers of PEIs in Un-SG and Di-SG samples. The number in the overlapped region refers to PEIs present in both populations. B, the numbers of promoters that interact with at least one enhancer in Un-SG and Di-SG samples. C, left, distribution of PEI distance in Un-SG and Di-SG samples. Right, the average PEI distance in Un-SG and Di-SG samples. D, composition of skipping and nonskipping enhancers in PEIs. E, the proportions of PEIs in or out of TADs. F, the average numbers of enhancers that interact with each promoter in Un-SG and Di-SG samples. P: Mann-Whitney U test, one-tailed. G, the average expression levels of genes with or without PEIs. P: Mann-Whitney U test, one-tailed. H, more interacting enhancers are associated with higher proportions of genes in top gene expression intervals. The numbers in columns refer to the proportions of genes in each gene expression interval. I, heatmaps of expression levels and RP indices of two clusters of genes that were expressed in either or both spermatogonial subpopulations (TPM > 1) and that exhibited a fold change of ≥4. J, gene ontology-biological process analysis of genes with differential RP indices during spermatogonial differentiation. K, heatmaps of representative genes, with differential RP indices and expression levels during spermatogonial differentiation. L, the average expression levels of genes regulated by Un-SG- or Di-SG-exclusive PEIs. P: Mann-Whitney U test, one-tailed. Di-SG, differentiating spermatogonia; PEI, promoter-enhancer interaction; RP, regulatory potential; TADs, topologically associating domains; TPM, transcripts per million; Un-SG, undifferentiated spermatogonia.