Comprehensive Hi-C Data Analysis and Multi-Omics Integration. (A) Global Interaction Map: A Circos plot visualizing genome-wide trans (inter-chromosomal) interactions. (B) TAD Identification: A Hi-C interaction heatmap (Chr7) revealing Topologically Associating Domains (TADs) outlined in dashed black lines. The deep red diagonal indicates high contact frequency. (C) High-Resolution Loop Calling: A zoomed-in view of a specific chromatin loop (off-diagonal peak). The arc above illustrates the physical connection between two distal loci. (D) Structure-Function Correlation: Integration of the loop anchors from (C) with 1D genomics tracks. The left anchor coincides with an active enhancer mark (ChIP-seq H3K27ac), and the right anchor aligns with an actively transcribed gene (RNA-seq), demonstrating a functional enhancer-promoter interaction detected by Hi-C.Cotton fiber quality is regulated by a complex gene network during rapid cell elongation. The researchers aimed to decode the "black box" of how dynamic 3D chromatin architecture drives this differentiation process in a single-cell model.
A comprehensive Multi-Omics approach was applied across four key developmental stages:
- Hi-C Sequencing: To map genome-wide chromatin interactions (TADs and A/B compartments).
- RNA-Seq: To track dynamic gene expression changes.
- ChIP-Seq (H3K27ac/H3K4me3): To identify active regulatory elements.
- Compartment Switching: The study revealed that chromatin compartment status (A/B) changes significantly during development, directly correlating with the activation or silencing of fiber-related genes.
- TAD Dynamics: While TAD boundaries were largely stable, internal interaction frequencies shifted, facilitating stage-specific regulation.
- Subgenome Coordination: In the allotetraploid genome, the two subgenomes displayed distinct 3D packing strategies to coordinate fiber elongation.
Figure 1. Dynamic 3D Chromatin Architecture. High-resolution Hi-C interaction heatmaps showing clear Topologically Associating Domains (TADs) and A/B compartment tracks in the cotton genome. The data quality allows for precise boundary identification.
Figure 2. Integrated Multi-Omics Analysis (Hi-C + RNA-seq + ChIP-seq). Visualization of a functional chromatin loop (purple arc) connecting a distal enhancer (ChIP-seq peak) to its target gene promoter. This structural interaction directly correlates with the gene's high expression level (RNA-seq track).
This study demonstrates that the 3D genome dynamically remodels to regulate cell differentiation. Integrating Hi-C with RNA-seq successfully linked spatial chromatin changes to phenotypic traits, offering new targets for molecular breeding.
