The shoot apical meristem (SAM), from which all above-ground tissues of plants are derived, is critical to plant morphology and development. In maize (Zea mays), loss-of-function mutant studies have identified several SAM-related genes, most encoding homeobox transcription factors (TFs), located upstream of hierarchical networks of hundreds of genes. Here, we collect 46 transcriptome and 16 translatome datasets across 62 different tissues or stages from the maize inbred line B73. We construct a dynamic regulome for 27 members of three SAM-related homeobox subfamilies (KNOX, WOX, and ZF-HD) through machine-learning models for the detection of TF targets across different tissues and stages by combining tsCUT&Tag, ATAC-seq, and expression profiling. This dynamic regulome demonstrates the distinct binding specificity and co-factors for these homeobox subfamilies, indicative of functional divergence between and within them. Furthermore, we assemble a SAM dynamic regulome, illustrating potential functional mechanisms associated with plant architecture. Lastly, we generate a wox13a mutant that provides evidence that WOX13A directly regulates Gn1 expression to modulate plant height, validating the regulome of SAM-related homeobox genes. The SAM-related homeobox transcription-factor regulome presents an unprecedented opportunity to dissect the molecular mechanisms governing SAM maintenance and development, thereby advancing our understanding of maize growth and shoot architecture.

中文翻译：

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茎尖分生组织相关同源盒转录因子的动态调节组调节玉米植物结构


茎尖分生组织（SAM）是植物所有地上组织的来源，对植物形态和发育至关重要。在玉米 (Zea mays) 中，功能缺失突变体研究已鉴定出几个 SAM 相关基因，其中大多数编码同源框转录因子 (TF)，位于数百个基因的分层网络的上游。在这里，我们收集了来自玉米自交系 B73 的 62 个不同组织或阶段的 46 个转录组和 16 个翻译组数据集。我们通过机器学习模型为 3 个 SAM 相关同源盒亚家族（KNOX、WOX 和 ZF-HD）的 27 个成员构建了动态调节组，通过结合 tsCUT&Tag、ATAC-seq 和表达分析。这种动态调节组展示了这些同源盒亚家族的独特结合特异性和辅助因子，表明它们之间和内部的功能差异。此外，我们组装了 SAM 动态调节组，说明了与植物结构相关的潜在功能机制。最后，我们生成了一个 wox13a 突变体，该突变体提供了 WOX13A 直接调节 Gn1 表达以调节植物高度的证据，从而验证了 SAM 相关同源盒基因的调节组。 SAM 相关同源盒转录因子调节组提供了前所未有的机会来剖析控制 SAM 维持和发育的分子机制，从而增进我们对玉米生长和芽结构的理解。