A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.
A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants.
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DOI：
10.1016/j.devcel.2022.01.008
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发表时间：
2022-02-28
影响因子：
11.8
通讯作者：
Ohler, Uwe
中科院分区：
文献类型：
--
作者：
Shahan, Rachel;Hsu, Che-Wei;Nolan, Trevor M.;Cole, Benjamin J.;Taylor, Isaiah W.;Greenstreet, Laura;Zhang, Stephen;Afanassiev, Anton;Vlot, Anna Hendrika Cornelia;Schiebinger, Geoffrey;Benfey, Philip N.;Ohler, Uwe
在所有多细胞生物中，转录网络协调器官发育。拟南芥的根，因其结构简单且具有无限生长的特性，是研究发育轨迹背后时空转录特征的理想模型。为了绘制根细胞类型和发育时间上的基因表达动态，我们构建了一个单细胞分辨率的全面的器官尺度图谱。除了在拟时间中估计发育进程外，我们还运用最优运输的数学概念来推断发育轨迹并确定其潜在的调控因子。为了证明该图谱在解释新数据集方面的实用性，我们对两个关键转录调控因子SHORTROOT和SCARECROW进行了单细胞分辨率的突变体分析。我们报道了SCARECROW中混合细胞身份表型背后组织转分化的转录组学和体内证据。我们的研究结果支持该图谱作为一种丰富的社区资源，用于揭示确定和维持细胞身份以调控时空器官发育的转录程序。
转录网络如何调控器官发育？沙汉和许等人利用单细胞RNA测序技术制作了一个拟南芥根图谱，揭示了细胞类型分化背后基因表达的渐进变化以及细胞命运的候选调控因子。该图谱能够解释较小的单细胞RNA测序数据集，并揭示了发育突变体中的新表型。
In all multicellular organisms, transcriptional networks orchestrate organ development. The Arabidopsis root, with its simple structure and indeterminate growth, is an ideal model to investigate the spatiotemporal transcriptional signatures underlying developmental trajectories. To map gene expression dynamics across root cell types and developmental time, we built a comprehensive, organ-scale atlas at single cell resolution. In addition to estimating developmental progressions in pseudotime, we employed the mathematical concept of optimal transport to infer developmental trajectories and identify their underlying regulators. To demonstrate the utility of the atlas to interpret new datasets, we profiled mutants for two key transcriptional regulators at single cell resolution, shortroot and scarecrow. We report transcriptomic and in vivo evidence for tissue trans-differentiation underlying a mixed cell identity phenotype in scarecrow. Our results support the atlas as a rich community resource for unraveling the transcriptional programs that specify and maintain cell identity to regulate spatiotemporal organ development. How do transcriptional networks regulate organ development? Using scRNA-seq, Shahan and Hsu et al. produced an Arabidopsis root atlas, revealing gradual gene expression changes underlying differentiation of cell types and candidate regulators of cell fate. The atlas enabled interpretation of smaller scRNA-seq datasets and revealed new phenotypes in developmental mutants.
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影响因子：
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