This study presents the application of Micro-C-XL, a high-throughput chromosome conformation capture technology, to map nucleosome-resolution chromatin organization and enhancer-promoter loops in Arabidopsis. Micro-C-XL uses micrococcal nuclease instead of restriction enzymes and long cross-linkers, enabling high-resolution analysis of chromatin structure. The method identified over 14,000 chromatin boundaries, which are associated with chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL revealed associations between RNA polymerases and local chromatin organization, suggesting that gene transcription contributes to the establishment of local chromatin domains. By perturbing Pol II genetically and chemically, the study confirmed its role in regulating chromatin organization. Visible loops and stripes were assigned to super-enhancers and their target genes, providing insights into the identification and mechanisms of distal CREs in plants. The study also investigated factors regulating these chromatin loops and expanded Micro-C-XL to soybean and rice. The results show that Micro-C-XL provides high-resolution insights into chromatin organization and enhancer-promoter loops in plants, revealing the three-dimensional genome structure. The study highlights the importance of chromatin organization in gene expression, genome stability, and function. It also demonstrates the role of gene transcription in local chromatin domain formation and the influence of Pol II on chromatin organization. The study identifies chromatin loops associated with super-enhancers and their target genes, suggesting that Micro-C-XL combined with other omics can provide robust analyses of regulatory relationships between CREs and genes. The study also shows that Micro-C-XL can be applied to other plants, such as rice and soybean, confirming its utility in analyzing chromatin organization in diverse plant species. The findings contribute to the understanding of chromatin organization and transcriptional regulation in plants.This study presents the application of Micro-C-XL, a high-throughput chromosome conformation capture technology, to map nucleosome-resolution chromatin organization and enhancer-promoter loops in Arabidopsis. Micro-C-XL uses micrococcal nuclease instead of restriction enzymes and long cross-linkers, enabling high-resolution analysis of chromatin structure. The method identified over 14,000 chromatin boundaries, which are associated with chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL revealed associations between RNA polymerases and local chromatin organization, suggesting that gene transcription contributes to the establishment of local chromatin domains. By perturbing Pol II genetically and chemically, the study confirmed its role in regulating chromatin organization. Visible loops and stripes were assigned to super-enhancers and their target genes, providing insights into the identification and mechanisms of distal CREs in plants. The study also investigated factors regulating these chromatin loops and expanded Micro-C-XL to soybean and rice. The results show that Micro-C-XL provides high-resolution insights into chromatin organization and enhancer-promoter loops in plants, revealing the three-dimensional genome structure. The study highlights the importance of chromatin organization in gene expression, genome stability, and function. It also demonstrates the role of gene transcription in local chromatin domain formation and the influence of Pol II on chromatin organization. The study identifies chromatin loops associated with super-enhancers and their target genes, suggesting that Micro-C-XL combined with other omics can provide robust analyses of regulatory relationships between CREs and genes. The study also shows that Micro-C-XL can be applied to other plants, such as rice and soybean, confirming its utility in analyzing chromatin organization in diverse plant species. The findings contribute to the understanding of chromatin organization and transcriptional regulation in plants.