Dynamic 3D chromatin organization and epigenetic regulation of gene expression in peanut nodules

Root nodules are specialized organs formed by the symbiotic relationship between legumes and soil-borne rhizobia, facilitating an exchange of energy and nutrients essential for both organisms. This process is accompanied by dynamic changes in genomic organization and gene expression. While the three-dimensional (3D) architecture of the genome is known to influence gene regulation, its role in nodulation and symbiotic nitrogen fixation remains largely unexplored. In this study, we present the first high-resolution (40 kb) 3D genomic map of peanut roots and root nodules, generated using a high-throughput/resolution chromosome conformation capture strategy. Compared to roots, ∼2.0% of chromosomal regions in nodules transition from a repressive (B) to an active (A) compartment and exhibit significant alterations in topologically associated domains (TADs). Peanut nodules also show more extensive cis-interactions, with 100s of differentially expressed genes enriched in symbiotic pathways and nitrate metabolism. Additionally, assay for transposase-accessible chromatin with high-throughput sequencing identifies 25,863 and 14,703 open chromatin regions (OCRs) in roots and nodules, respectively. By integrating OCR mapping with epigenomic modifications, we reveal dynamic local OCRs (LoOCRs) and histone modifications associated with nodulation-related genes. Notably, novel TADs and long-range chromatin loops are detected in peanut nodules, including an H3K27me3 modification-mediated loop that may regulate the expression of Nodule Inception. Another altered chromatin loop highlights the nodule highly expressed AhMsrA gene, which positively influences nodulation. Together, these findings shed new light on how chromatin architecture shapes gene expression during legume nodulation and nitrogen fixation.