High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.
High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation.
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DOI：
10.1016/j.devcel.2016.10.012
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发表时间：
2016-11-21
影响因子：
11.8
通讯作者：
Benfey PN
中科院分区：
文献类型：
--
作者：
Li S;Yamada M;Han X;Ohler U;Benfey PN
选择性剪接和长基因间非编码rna （lincRNAs）对器官内细胞特化功能的影响程度尚不清楚。我们从拟南芥根的单个细胞类型中生成了一个全面的基因表达数据集。跨细胞类型的比较表明，选择性剪接倾向于从较长的主要同工异构体中去除编码区域的部分，这为剪接的渐进机制提供了证据。细胞类型特异性内含子保留提示了这种常见形式的选择性剪接的可能起源。跨发育阶段的协调选择性剪接指出了调节分化的作用。与这一假设相一致的是，一种转录因子的不同同种异构体被证明控制着发育转变。LincRNAs在单个细胞类型水平上普遍表达较低，但共表达簇为其功能提供了线索。我们的结果强调了从个体细胞类型水平上的表达分析中获得的见解。Li等人提出了一个综合的基因表达数据集，该数据集使用来自拟南芥根的单个细胞类型和发育区域的短读测序，并辅以长读测序和定量蛋白质组学分析。该资源中的数据表征了细胞类型和发育阶段特异性的选择性剪接和lincRNA表达。
The extent to which alternative splicing and long intergenic noncoding RNAs (lincRNAs) contribute to the specialized functions of cells within an organ is poorly understood. We generated a comprehensive dataset of gene expression from individual cell types of the Arabidopsis root. Comparisons across cell types revealed that alternative splicing tends to remove parts of coding regions from a longer, major isoform, providing evidence for a progressive mechanism of splicing. Cell type-specific intron retention suggested a possible origin for this common form of alternative splicing. Coordinated alternative splicing across developmental stages pointed to a role in regulating differentiation. Consistent with this hypothesis, distinct isoforms of a transcription factor were shown to control developmental transitions. LincRNAs were generally lowly expressed at the level of individual cell types, but co-expression clusters provided clues as to their function. Our results highlight insights gained from analysis of expression at the level of individual cell types. Li et al. present a comprehensive dataset of gene expression generated using short-read sequencing from individual cell types and developmental zones of the Arabidopsis root, complemented by long-read sequencing and quantitative proteomic analyses. The data in this resource characterize cell type and developmental stage-specific alternative splicing and lincRNA expression.