Fig. 8

Differential regulatory networks mediated by chromatin loops between the At and Dt subgenomes. a Bar plot showing the proportion of different types of loops. G-G means that both loop anchors contain genes. G-N means that one of loop anchors contains genes. N-N means that both loop anchors do not contain genes. b Bar plot showing the number of different histone modifications in non-gene regions connected by three types of loops between the At and Dt subgenomes. c The density distribution of HG-HG loop anchors at the TAD-like structure level during fiber development. d The HG-HG loop-mediated interaction networks for homoeologous genes in chromosomes A05 and D05. The Dt-subgenomic network is mirror-symmetric to the At subgenome network. The position of each node in the At subgenomic network is consistent with that in the Dt-subgenome; the node size and network edges may be different. Each node represents a homoeologous gene and each line represents a loop (homoeologous loops in purple, non-homoeologous loops in gray) between two homoeologous genes. The node size is scaled to the number of loops associated with each gene. The purple line refers to homoeologous loops. The zoom-in plot shows the loop interactions of homoeologous gene pairs within 100 kb around At subgenomic RDL1 (a) and Dt-subgenomic RDL1' (a'). The red lines represent loops associated with RDL and RDL'. e A proposed model showing the dynamic 3D chromatin organization during fiber development. Dynamic changes include the decreased proportion of A compartment, interactions between active TAD-like structure and chromatin loops. The bar plot shows dynamics at different scales: proportions of compartment and TAD-like structure relative to genome length, and loop number