Genetics, Development and Cell Biology Department, Iowa State University, Ames, IA 50011, USA.
Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08901-8520, USA.
Plant Cell. 2023 Dec 21;36(1):19-39. doi: 10.1093/plcell/koad247.
NAKED ENDOSPERM1 (NKD1), NKD2, and OPAQUE2 (O2) are transcription factors important for cell patterning and nutrient storage in maize (Zea mays) endosperm. To study the complex regulatory interrelationships among these 3 factors in coregulating gene networks, we developed a set of nkd1, nkd2, and o2 homozygous lines, including all combinations of mutant and wild-type genes. Among the 8 genotypes tested, we observed diverse phenotypes and gene interactions affecting cell patterning, starch content, and storage proteins. From ∼8 to ∼16 d after pollination, maize endosperm undergoes a transition from cellular development to nutrient accumulation for grain filling. Gene network analysis showed that NKD1, NKD2, and O2 dynamically regulate a hierarchical gene network during this period, directing cellular development early and then transitioning to constrain cellular development while promoting the biosynthesis and storage of starch, proteins, and lipids. Genetic interactions regulating this network are also dynamic. The assay for transposase-accessible chromatin using sequencing (ATAC-seq) showed that O2 influences the global regulatory landscape, decreasing NKD1 and NKD2 target site accessibility, while NKD1 and NKD2 increase O2 target site accessibility. In summary, interactions of NKD1, NKD2, and O2 dynamically affect the hierarchical gene network and regulatory landscape during the transition from cellular development to grain filling in maize endosperm.
裸胚乳 1（NKD1）、NKD2 和不透明 2（O2）是玉米（Zea mays）胚乳中细胞模式和营养物质储存的重要转录因子。为了研究这 3 个因子在共同调控基因网络中的复杂调控相互关系，我们开发了一套 NKD1、NKD2 和 O2 纯合系，包括突变体和野生型基因的所有组合。在测试的 8 种基因型中，我们观察到了影响细胞模式、淀粉含量和储存蛋白的多种表型和基因相互作用。授粉后约 8 至 16 天，玉米胚乳经历从细胞发育到为灌浆积累营养物质的转变。基因网络分析表明，NKD1、NKD2 和 O2 在这段时间内动态调节一个层次化的基因网络，早期指导细胞发育，然后过渡到限制细胞发育，同时促进淀粉、蛋白质和脂质的生物合成和储存。调节这个网络的遗传相互作用也是动态的。转座酶可及染色质的测定（ATAC-seq）表明，O2 影响全局调控景观，降低 NKD1 和 NKD2 靶位点的可及性，而 NKD1 和 NKD2 增加 O2 靶位点的可及性。总之，NKD1、NKD2 和 O2 的相互作用在玉米胚乳从细胞发育到灌浆的转变过程中动态影响层次化的基因网络和调控景观。
