Li Mengyao, Fan Xiaoxing, Li Xiaohan, Zhang Mingyue, Liu Yuting, Ni Yuqing, Li Yanjun, Jiang Yi, Gao Xiang, Zhao Yajie, Zhou Chao, Yang Xuerong, Zhao Xiang Yu, Zhang Xian Sheng, Shi Junpeng, Wang Jiechen, Liu Hongjun
State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Agriculture and Biotechnology, The Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China.
Plant J. 2025 Jul;123(2):e70316. doi: 10.1111/tpj.70316.
The early development of maize kernels plays a crucial role in determining yield and grain quality. Deciphering chromatin accessibility dynamics can further advance our understanding of tissue-specific regulatory networks. In this study, we performed an integrated multiomics analysis to explore chromatin accessibility dynamics during cell fate transitions in early kernel development. Endosperm and seed coat samples collected at 4-10 days after pollination (DAP) are chosen for the assay for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) data, which reveal that chromatin accessibility undergoes stage-specific remodeling during early endosperm differentiation (4-10 DAP). Differences in distal accessible chromatin regions (dACRs) and expression patterns highlight distinct regulatory mechanisms for the zein and starch synthesis pathways, differing from recognized transcriptional co-regulation. Novel transcription factors (TF) and downstream genes were identified and validated, including DOF36, ZmNAC128, and ZmbZIP3. Notably, similar accessible chromatin regions (ACRs) patterns and expression profiles were observed for the marker genes between maternal placenta chalaza (PC) fusion zone and basal endosperm transfer layer (BETL) region of the offspring, suggesting potential co-regulatory modules. In conclusion, we generated a time-course atlas of ACRs and transcriptome to analyze specific expression regulation, construct cell differentiation trajectories, and develop cell-type-specific gene regulatory networks.
玉米籽粒的早期发育在决定产量和籽粒品质方面起着至关重要的作用。解析染色质可及性动态变化能够进一步增进我们对组织特异性调控网络的理解。在本研究中，我们进行了一项综合多组学分析，以探索早期籽粒发育过程中细胞命运转变期间的染色质可及性动态变化。选取授粉后4 - 10天（DAP）收集的胚乳和种皮样本用于转座酶可及染色质测序（ATAC-seq）和RNA测序（RNA-seq）分析，结果显示在胚乳早期分化阶段（4 - 10 DAP）染色质可及性经历了阶段特异性重塑。远端可及染色质区域（dACRs）和表达模式的差异突出了醇溶蛋白和淀粉合成途径独特的调控机制，这与公认的转录共调控不同。鉴定并验证了新的转录因子（TF）和下游基因，包括DOF36、ZmNAC128和ZmbZIP3。值得注意的是，在子代的母体胎盘合点（PC）融合区和胚乳基部转运层（BETL）区域之间，标记基因观察到相似的可及染色质区域（ACRs）模式和表达谱，表明存在潜在的共调控模块。总之，我们生成了ACRs和转录组的时间进程图谱，以分析特定的表达调控、构建细胞分化轨迹并建立细胞类型特异性基因调控网络。
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