High-resolution gene expression datasets of ontogenetic zones in the root apical meristem. Arabidopsis thaliana

In plants, apical meristems allow continuous growth along the body axis. Within the root apical meristem (RAM), a group of slowly dividing quiescent center (QC) cells is thought to limit stem cell activity to directly neighboring cells (Cowels, 1956; van den Berg et al., 1997), thus endowing them with unique properties, distinct from displaced daughters. This binary identity of the stem cells stands in apparent contradiction with the more gradual changes in cell division potential (Bennett and Scheres, 2010) and differentiation (Yamaguchi et al., 2008; 2010; Furuta et al, 2014; Geldner, 2013; Masucci et al., 1996; Dolan and Costa, 2001) that occur as cells move further away from the QC. To address this paradox and to infer molecular organization of the root meristem, we used a whole-genome approach to determine dominant transcriptional patterns along root ontogeny zones. We found that the prevalent patterns are expressed in two opposing gradients. One is characterized by genes associated with development, the other enriched in differentiation genes. We confirmed these transcript gradients, and demonstrate that these translate to gradients in protein accumulation and gradual changes in cellular properties. We also show that gradients are genetically controlled through multiple pathways. Based on these findings, we propose that cells in the Arabidopsis root meristem gradually transition from ‘stemness’ towards differentiation. Overall design: This study contains high-resolution datasets from cell populations from the enitre root meristem and xylem-specific cell populations. Using fluorescence activated cell sorting, three cell populations were isolated based on their GFP expression intensity. Two-Three replicates were used per sample

在植物中，顶端分生组织（apical meristem）可使植物体沿体轴实现持续生长。在根顶端分生组织（root apical meristem, RAM）内，一群分裂缓慢的静止中心（quiescent center, QC）细胞被认为可将干细胞活性限制在紧邻的邻近细胞中（Cowels, 1956; van den Berg等, 1997），从而赋予这些邻近细胞独特的特性，区别于被位移的子细胞。干细胞的这种二元特性，与细胞远离静止中心后发生的、更为渐进的细胞分裂潜能变化（Bennett与Scheres, 2010）和分化过程（Yamaguchi等, 2008; 2010; Furuta等, 2014; Geldner, 2013; Masucci等, 1996; Dolan与Costa, 2001）看似存在明显矛盾。

为解析这一悖论并推断根分生组织的分子组织架构，我们采用全基因组方法，解析了根发育不同区域的主导转录模式。研究发现，主流转录模式以两种相反的梯度形式表达：一类以发育相关基因为特征，另一类则富集分化相关基因。我们验证了这些转录梯度，并证实它们可转化为蛋白质积累梯度以及细胞特性的渐进性变化。此外，我们还证明这些梯度可通过多条遗传途径进行调控。基于上述发现，我们提出拟南芥（Arabidopsis）根分生组织中的细胞会从‘干细胞态’逐步向分化状态过渡。

实验设计概述：本研究包含来自完整根分生组织与木质部特异性细胞群的高分辨率数据集。我们借助荧光激活细胞分选（fluorescence activated cell sorting），依据绿色荧光蛋白（green fluorescent protein, GFP）的表达强度分离得到三类细胞群。每个样本设置2~3次重复。