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Chinese researchers have developed a technology that sheds light on how the three-dimensional (3D) organization of plant genomes influences gene expression—especially in photosynthesis.

The research, which was led by Prof. Xiao Jun at the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences, in collaboration with BGI Research, is in Science Advances.

The innovative method not only provides a more precise tool for understanding the intricate 3D interactions between genes, but also highlights the critical role of long-range chromatin interactions in gene regulation.

Within plant nuclei, chromatin is not arranged randomly. Instead, chromatin—a combination of DNA and proteins—forms a carefully organized 3D structure that plays a vital role in regulating biological processes.

Although scientists have identified many long-range regulatory elements involved in key agronomic traits, current tools such as Hi-C, ChIA-PET, HiChIP, and OCEAN-C struggle to capture active chromatin interactions at high resolution in a cost-effective and unbiased manner. Moreover, the mechanisms by which these structures form and are maintained—and how they influence gene expression—have largely been unclear.

To overcome these limitations, the researchers integrated ATAC-seq, which detects open (active) chromatin regions, with Hi-C, which maps genome-wide chromatin interactions.

The resulting technique, called Transposase-Accessible Chromosome Conformation Capture (TAC-C), enables targeted capture of interactions in accessible chromatin regions while offering improved resolution and efficiency at lower sequencing depths compared to traditional methods.

The researchers used TAC-C to successfully build high-quality 3D chromatin interaction maps for four major crop species, demonstrating the robustness of the tool.

Their analysis revealed that genomic regions acting as interaction hubs are associated with higher gene expression and reduced sequence variation, suggesting their importance as regulatory elements. These chromatin "anchor" regions are also significantly enriched with quantitative trait loci (QTLs) and expression QTLs (eQTLs), providing strong spatial evidence that 3D chromatin interactions connect distant regulatory elements to their target genes, thereby contributing to phenotypic variation.

In hexaploid wheat, the researchers observed asymmetrical chromatin interactions among the A, B, and D subgenomes, driven by transposable element insertions and sequence variations in anchor regions. This asymmetry led to biased expression of homologous genes across subgenomes.

In animals, chromatin loop formation is regulated by the CTCF/cohesin complex. In contrast, the mechanisms governing chromatin architecture in plants have not been well understood.

In this study, though, the researchers found a concentration of binding sites for the SBP, MYB, Dof, ERF, and GATA transcription factor (TF) families at chromatin interaction anchors. Among these, chromatin loops enriched with SBP-binding motifs showed stronger interactions and were located in functionally active regions.

Further analysis of mutants lacking the SBP TFs TaSPL7 and TaSPL15 revealed loss of chromatin loops associated with several photosynthesis-related genes, including TaCKX11-B, TaSGR-5D, TaNRR-A1, and TaTK-2D. This led to altered gene expression and impacted leaf development and photosynthetic efficiency.

SBP TFs are plant-specific and play essential roles in the development of leaves, flowers, roots, and fruits, as well as the transition between vegetative and reproductive growth. This study suggests that SPL-mediated changes in 3D chromatin architecture may be involved in the regulation of plant development.

In summary, this study offers a clear example of how plant TFs regulate photosynthesis-related genes through 3D organization of the genome. It also shows how the new TAC-C technology opens the door to a deeper understanding of long-range genetic regulation in plants and may guide future crop improvement efforts.