Fig. 6

TF-associated chromatin topology and its transcriptional function. a Illustration of chromatin hub model of chromatin interactions using the contact frequency (degree >  = 5). The total number of H3K4me3-associated chromatin hubs is 7180. b Distribution of the number of MYC2 target genes and randomly selected genes in chromatin hubs. ***p < 2.2e-16 from Wilcoxon test. c Expression levels of genes in different categories based on active mark-associated chromatin interaction models and MYC2 occupancy. ***p < 0.001 from Wilcoxon test. d Log2 fold change in expression of looping genes associated with lost loops in myc2 mutant compared to the wild-type. Fold-changes represent the expression changes of each gene in myc2 mutant relative to the wild-type. The lost loops were divided into three categories based on the MYC2 occupancy model. *p < 0.05 from Wilcoxon test. e Changes of MYC2 target-associated chromatin hubs in myc2 mutant compared to wild-type. These hubs were classified into four categories: stable, entirely and partially disassembled, and others. The number and proportion of hubs included in each category were given. f Representative examples of stable, partially, and entirely disassembled hubs in myc2 and wild-type. g Percentages of shared connecting genes in the indicated hub categories between myc2 and wild-type. ***p < 0.001 from Wilcoxon test. h Browser screenshot showing the chromatin connectivity and gene transcription within AtPUB19-centric hub. Light orange box indicates reduction of chromatin connectivity within the AtPUB19-centric hub and downregulation of AtPUB19 gene expression. Each MYC2 binding site, chromatin interaction, H3K4me3 peak, and RNA-seq track represent the normalized loops and read coverage in myc2 and wild-type. i A proposed model for the impacts of MYC2 in 3D genome organization and gene transcription. In the MYC2 dominated chromatin hub, MYC2 coupled with other TFs and mediators to create microenvironment that facilitates gene transcription in the wild-type. As MYC2 activity is abolished, the MYC2-centric hub is disassembled and the gene expression decreases. More red wavy lines indicate higher expression