Yan Haidong, Mendieta John P, Zhang Xuan, Luo Ziliang, Marand Alexandre P, Liang Yan, Minow Mark A A, Zhong Yun, Jin Yarong, Jang Hosung, Li Xiang, Zhang Xinxin, Roulé Thomas, Wagner Doris, Tu Xiaoyu, Wang Yonghong, Jiang Daiquan, Zhong Silin, Huang Linkai, Wessler Susan R, Schmitz Robert J
Department of Genetics, University of Georgia, Athens, GA, USA.
College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China.
Nat Plants. 2025 Sep 17. doi: 10.1038/s41477-025-02106-6.
Cis-regulatory elements (CREs) are essential for regulating gene expression, yet their evolutionary dynamics in plants remain elusive. Here we constructed a single-cell chromatin accessibility atlas for Oryza sativa from 103,911 nuclei representing 126 cell states across nine organs. Comparative genomics between O. sativa and 57,552 nuclei from four additional grass species (Zea mays, Sorghum bicolor, Panicum miliaceum and Urochloa fusca) revealed that chromatin accessibility conservation varies with cell-type specificity. Epidermal accessible chromatin regions in the leaf were less conserved compared to other cell types, indicating accelerated regulatory evolution in the L1-derived epidermal layer of O. sativa relative to other species. Conserved accessible chromatin regions overlapping the repressive histone modification H3K27me3 were identified as potentially silencer-like CREs, as deleting these regions led to up-regulation of gene expression. This study provides a comprehensive epigenomic resource for the rice community, demonstrating the utility of a comparative genomics approach that highlights the dynamics of plant cell-type-specific CRE evolution.
顺式调控元件（CREs）对于调节基因表达至关重要，但其在植物中的进化动态仍不清楚。在这里，我们从代表九个器官中126种细胞状态的103,911个细胞核构建了水稻的单细胞染色质可及性图谱。水稻与另外四种禾本科物种（玉米、高粱、黍和黑麦草）的57,552个细胞核之间的比较基因组学表明，染色质可及性保守性随细胞类型特异性而变化。与其他细胞类型相比，叶片中的表皮可及染色质区域保守性较低，这表明水稻L1衍生的表皮层相对于其他物种的调控进化加速。与抑制性组蛋白修饰H3K27me3重叠的保守可及染色质区域被鉴定为潜在的类似沉默子的CREs，因为删除这些区域会导致基因表达上调。本研究为水稻群体提供了全面的表观基因组资源，证明了比较基因组学方法的实用性，该方法突出了植物细胞类型特异性CRE进化的动态。
