Genome‐scale, single‐cell‐type resolution of microRNA activities within a whole plant organ

First author: Christopher Andrew Brosnan; Affiliations: Swiss Federal Institute of Technology (瑞士联邦理工学院): Zürich, Switzerland

Corresponding author: Olivier Voinnet

Loaded into ARGONAUTE(AGO) proteins, eukaryotic micro(mi)RNAs regulate gene expression via cleavage, translational repression, and/or accelerated decay of sequence‐complementary target transcripts. Despite their importance in development, cell identity maintenance and stress responses, how individual miRNAs contribute to spatial gene regulation within the complex cell mosaics formed in tissues/organs has remained inaccessible in any organism to date. We have developed a non‐invasive methodology to examine, at single‐cell‐type resolution, the AGO‐loading and activity patterns of entire miRNA cohorts in intact organs, applied here to the Arabidopsis root tip. A dual miRNAome–targetome analytical interface allowing intuitive data integration/visualization was developed as the basis for in‐depth investigations via single‐cell‐type experimentation. These uncovered an array of so far speculative or hitherto unknown types of spatial miRNA‐mediated gene regulation schemes, including via widespread cell‐to‐cell movement between contiguous layers of distinct identities. This study provides the proof of principle that minimally invasive, genome‐scale analysis of miRNA activities within and between single‐cell types of whole organs is achievable.

能够被载入AGO蛋白的真核miRNA通过剪切、转录抑制以及促进序列互补靶转录本的衰退来调控基因的表达。目前除了知道miRNA在发育、细胞特性维持以及胁迫响应过程中具有非常重要的作用，但在形成于组织/器官的复杂细胞类型中，单个的miRNA如何作用于空间上基因表达的调控还不清楚。作者开发了一套非侵入性方法来从单细胞水平上研究一个完整器官中所有miRNA的AGO载入和活性模式，本文中主要应用于拟南芥的根尖组织。作者开发了一个双向的miRNA组-靶基因组分析界面用于直观的数据整合和可视化，作为单细胞类型试验的深度分析基础。本文的研究发现了一系列迄今为止推测性的、或是未知类型空间上miRNA介导的基因表达调控体系，包括不同类型细胞相连层之间的细胞-细胞迁移。本文的研究证明了通过微创对整个器官单个细胞类型之内或之间miRNA活性在基因组范围上分析是可行的。

通讯：Olivier Voinnet (http://www.impb.ethz.ch/research/research-rb.html)

研究方向：小RNA：miRNA + siRNA。

doi: 10.15252/embj.2018100754

Journal: The EMBO Journal

Published date: June 12, 2019