Abstract：
Higher-order chromatin structure is critical for regulation of gene expression. In plants, light profoundly affects the morphogenesis of emerging seedlings as well as global gene expression to ensure optimal adaptation to environmental conditions. However, the changes and functional significance of chromatin organization in response to light during seedling development are not well documented. We constructed Hi-C contact maps for the cotyledon, apical hook and hypocotyl of soybean subjected to dark and light conditions. The resulting high-resolution Hi-C contact maps identified chromosome territories, A/B compartments, A/B sub-compartments, TADs (Topologically Associated Domains) and chromatin loops in each organ. We observed increased chromatin compaction under light and we found that domains that switched from B sub-compartments in darkness to A sub-compartments under light contained genes that were activated during photomorphogenesis. At the local scale, we identified a group of TADs constructed by gene clusters consisting of different numbers of Small Auxin-Upregulated RNAs (SAURs), which exhibited strict co-expression in the hook and hypocotyl in response to light stimulation. In the hypocotyl, RNA polymerase II (RNAPII) regulated the transcription of a SAURs cluster under light via TAD condensation. Our results suggest that the 3D genome is involved in the regulation of light-related gene expression in a tissue-specific manner.
摘要：
高级染色质结构对于基因表达的调节至关重要。在植物中,光深刻地影响新兴幼苗的形态发生以及全球基因表达，以确保对环境条件的最佳适应。然而,在幼苗发育过程中，染色质组织响应光的变化和功能意义尚不清楚。我们为子叶构建了Hi-C接触图，大豆的顶端钩和下胚轴受到黑暗和光照条件的影响。由此产生的高分辨率Hi-C接触图确定了染色体区域，A/B舱,A/B子隔间，每个器官中的TAD（拓扑关联域）和染色质环。我们观察到在光照下染色质压缩增加，并且我们发现在光照下从B子区室切换到A子区室的结构域包含在光形态发生过程中被激活的基因。在局部尺度上,我们确定了一组由不同数量的小生长素上调RNA（SAURs）组成的基因簇构建的TADs，响应光刺激，在钩和下胚轴中表现出严格的共表达。在下胚轴，RNA聚合酶II（RNAPII）通过TAD缩合在光照下调节SAURs簇的转录。我们的结果表明，3D基因组以组织特异性方式参与光相关基因表达的调节。
