Light Control of Soybean Three-dimensional Chromatin Organization

Chromatin three-dimensional conformation inside the eukaryotic nucleus is critical for regulating gene expression in many biological processes. Light has a profound effect on emerging seedling morphogenesis and genome expression, to ensure optimal adaptation to the surrounding light condition. To examine the alteration and possible function of chromatin organization during the process of seedling development in response to changing light conditions, we constructed the Hi-C contact maps for the cotyledon, apical hook, and hypocotyl of soybean subjected to constant darkness and constant light treatments. The resulting Hi-C contact maps revealed distinct euchromatin and heterochromatin domains, corresponding to A and B compartments, respectively. The chromatin condensation increased after light illumination. Furthermore, we found the more defined A and B sub-compartments, derived from A/B compartments, are positively related to transcriptional activity. The genes within the domains in which a B sub-compartment in darkness switched to A sub-compartment under light, were mainly activated during photomorphogenesis. At the local scale, the TADs (Topologically Associated Domain)-like domains were successfully identified in the cotyledon, apical hook and hypocotyl. The light-induced dynamics of TADs-like domains, constructed by Small Auxin-Upregulated (SAUR) gene clusters, were mediated by the H3K27me3 modification, and these SAUR gene clusters exhibit strict co-expression in hook and hypocotyl for light stimulation responses. Thus, regulation of the 3D genome contributes to the tissue-specific regulation of light-related gene expression in soybean seedlings during photomorphogenesis.