Reorganization of three-dimensional chromatin architecture in Medicago truncatula under phosphorus deficiency


 Emerging evidence reveals that the three-dimensional (3D) chromatin architecture plays a key regulatory role in various biological processes of plants. However, information on the 3D chromatin architecture of legume model plant Medicago truncatula and its potential roles in the regulation of response to mineral nutrient deficiency are very limited. Using Hi-C sequencing, we identified the 3D genome structure of M. truncatula in terms of A/B compartments, topologically associated domains (TADs) and chromatin loops. The gene density, expressional level and active histone modification were higher in A compartments than in B compartments. Moreover, we analyzed the 3D chromatin architecture reorganization in response to phosphorus (P) deficiency. The intra-chromosomal cis-interaction proportion was increased by P deficiency, and a total of 748 A/B compartment switch regions were detected. In these regions, density change of H3K4me3 and H3K27ac modification were associated with expression of P deficiency-responsive genes involved in root system architecture and hormonal response. Further, these genes enhanced the P uptake and mobilization by increasing root surface area and strengthening the signal transduction under P deficiency. These findings advance our understanding of the potential roles of 3D chromatin architecture in responses of plants in general and M. truncatula in particular to P deficiency.