BL-Hi-C reveals the 3D genome structure of Brassica crops with high efficiency and sensitivity

High-throughput chromatin conformation capture (Hi-C) technologies can be used to investigate the three-dimensional genomic structure of plants. However, complex protocol and high background noise in Hi-C hinder its practical application in plant 3D genomics. Here, we took the approach of modified Bridge Linker Hi-C technology (BL-Hi-C) to explore plant 3D landscape. We modified the BL-Hi-C method by simplifing nuclei extraction step. By using Brassica rapa and Brassica oleracea, BL-Hi-C showed higher signal value and lower background noise than Hi-C. The high sensitivity of BL-Hi-C was further demonstrated by its capacity to identify gene loops involving BrFLC1, BrFLC2 and BrFLC3 which were undetectable in Hi-C. BL-Hi-C also showed promising performance with input as low as 100 mg leaf tissue. By analyzing of the generated data from BL-Hi-C, we found that the simulated 3D genome structure of B. rapa leaf cells was Bouquet configuration. Our results showed that the modified BL-Hi-C is a powerful tool for the investigation of plants genomic organization, gene regulation, and genome assembly. IN A NUTSHELL Background3D genome structure play a critical role in regulating spatiotemporal gene expression. However, there is a lack of simple, efficient and sensitive Hi-C technique in plants. QuestionHow to study plant 3D genomics more simple and efficientHow to detect plant chromatin loops more sensitive? FindingsWe showed that BL-Hi-C is more simple, efficient and sensitive than coventional Hi-C by using Brassica rapa and Brassica oleracea. Furthermore, BL-Hi-C demonstrated its high sensitivity by detecting gene loops involving BrFLC1, BrFLC2, and BrFLC3 which could not be detected by Hi-C. In addition, BL-Hi-C demonstrated promising performance with inputs as low as 100 mg leaf tissue. By analyzing BL-Hi-C data, we found that the simulated 3D genome structure of B. rapa leaf cells was Bouquet configuration. Next stepsHow chromatin loops are formed and regulated gene expression are key questions to be answered in plants. Our dataset of BL-Hi-C will enable future investigations to improve our understanding of chromatin loops.