Transcriptional landscaping in plant stem cells: from chromatin to gene regulatory networks

所有的陆地生命最终都依赖于植物分生组织--一小群未分化的细胞，它们产生所有主要的植物器官，如叶子和花。在高等植物如拟南芥的茎顶端分生组织（SAM）中，基因调控网络（GRNs）控制细胞生长、命运和身份，以平衡新器官如叶和花的形成与分生组织完整性的维持，确保生长所需的多能细胞的可持续供应。转录因子，特别是同源结构域蛋白SHOOT MERISTEMLESS（STM），通过调节靶基因表达在SAM功能中发挥关键作用。然而，STM GRN的组成和结构并不完全清楚。该项目旨在全面了解SAM中的STM基因调控网络。STM编码一个Knotted 1样TALE同源域转录因子，该因子仅在分生组织中表达。STM功能的丧失导致分生组织的发育或维持失败，而STM过表达抑制叶细胞分化并促进异位芽分生组织的从头形成。这些显著的表型变化表明STM在调控分生组织发育和功能的GRN中起着核心作用。为了了解STM如何运作，以及它的作用是如何与更广泛的分生组织GRN整合，将进行一个多层次的转录美化方法。首先，将使用可诱导的STM过表达和RNAi（基因沉默），然后进行全基因组RNA-seq分析来鉴定推定的STM靶基因。为了确定这些STM响应基因中的哪些直接受STM调节，将进行全局染色质免疫沉淀（ChIP-seq）以鉴定STM结合的基因组区域。由于STM也会影响染色质结构以控制细胞的分化状态，因此染色质粒子谱分析（CPSA）将用于分析STM结合的基因组区域中的染色质结构，将推定的STM结合位点置于核小体和其他DNA结合因子的更广泛范围内。贝叶斯网络分析将被用来推断GRN结构和STM靶基因之间的关系。该项目是令人兴奋的机会，在分生组织生物学的两个既定专家的监督下进行培训，并学习多学科技能和技术，包括分子遗传学，植物细胞和组织培养，生物信息学和发育生物学。该项目将导致对控制分生组织发育的网络的新见解，并可能导致操纵植物生长，结构和产量的新策略。

All terrestrial life ultimately depends on plant meristems - small groups of undifferentiated cells that produce all major plant organs such as leaves and flowers. In the shoot apical meristem (SAM) of higher plants such as Arabidopsis, gene regulatory networks (GRNs) control cell growth, fate and identity to balance the formation of new organs, such as leaves and flowers, with maintenance of meristem integrity, ensuring the sustainable supply of pluripotent cells necessary for growth. Transcription factors, particularly the homeodomain protein SHOOT MERISTEMLESS (STM), play critical roles in SAM function through regulation of target gene expression. However, the components and structure of the STM GRN are not fully understood. This project aims to develop a comprehensive understanding of the STM gene regulatory network in the SAM. STM encodes a Knotted1-like TALE homeodomain transcription factor that is expressed only in the meristem. Loss of STM function leads to failure to develop or maintain the meristem, while STM overexpression inhibits leaf cell differentiation and promotes the de novo formation of ectopic shoot meristems. These dramatic phenotypic changes suggest a central role for STM in the GRN(s) that regulate meristem development and function. To understand how STM operates and how its role is integrated with the wider meristem GRNs, a multi-layered transcriptional landscaping approach will be undertaken. First, putative STM target genes will be identified using inducible STM overexpression and RNAi (gene silencing) followed by genome-wide RNA-seq analysis. In order to determine which of these STM-responsive genes are directly regulated by STM, global chromatin immunoprecipitation (ChIP-seq) will be performed to identify genomic regions to which STM is bound. Since STM also affects the chromatin structure to control the differentiation status of cells, chromatin particle spectrum analysis (CPSA) will be used to analyse the chromatin structure in the genomic regions bound by STM, placing the putative STM binding sites within the wider landscape of nucleosomes and other DNA-bound factors. Bayesian network analysis will then be used to infer GRN structure and relationships among the STM target genes. This project is exciting opportunity to train under the supervision of two established experts in meristem biology, and to learn multidisciplinary skills and techniques including molecular genetics, plant cell and tissue culture, bioinformatics and developmental biology. The project will lead to new insights into networks controlling meristem development and could lead to novel strategies for the manipulation of plant growth, architecture and yield.