Going Green: reprogramming roots into shoots using TCP transcription factors

随着细胞的分化，它们改变命运的能力逐渐受到限制，这给修复组织和器官带来了问题。与其他多细胞生物不同，植物以其发育可塑性而闻名。例如，插枝可以使根系再生，反之亦然。在再生过程中，植物细胞有一种独特的能力，通过重新编程它们的命运来改变它们的身份，这是它们再生器官和组织能力的一个关键机制。细胞命运重编程需要基因表达的改变，而基因表达的改变又需要染色质可及性的改变，这样转录机制才能访问不同的基因。至关重要的是，一些被称为先锋因子的转录因子可以结合难以接近的染色质并改变其构象，以便其他因子可以进入DNA启动转录，改变基因表达并导致细胞重编程，从而导致不同的命运。植物转录因子TCP4的异位过表达驱动拟南芥根向茎/茎样器官的转化，表明TCP4在植物细胞重编程中起核心作用。TCP4调控几种染色质重塑因子的表达，这表明TCP4在控制染色质景观方面具有更广泛的作用，可能是一种新的植物先驱因子。为了了解TCP4如何重编程根细胞，将结合下一代测序技术、生物信息学和可诱导的TCP4细胞系的活细胞成像，以获得TCP4诱导的细胞命运转换的全面图景。通过使用染色质颗粒谱分析（CPSA）和染色质免疫沉淀（ChIP-seq），将获得根到茎转化过程中不同时间点的染色质图。这些图谱将与TCP4在同一时间点诱导的基因表达的全局变化（RNA-seq）进行比较，以确定可能已被TCP4进入以启动基因表达的染色质区域。根向芽的转化也将使用荧光标记进行监测，这使我们能够通过共聚焦显微镜识别细胞身份。这将有助于我们理解TCP4对根进行重编程的机制，并有助于建立植物细胞重编程的一般原理。这个项目是一个令人兴奋的学习多学科技能和广泛应用的技术的机会。该项目将在植物转录调控和开拓活动方面带来新的见解，并可能导致从更广泛的组织中开发更有效的植物不育物种繁殖方法，并为改善农业性状和粮食安全提供新的策略。

As cells differentiate, their capacity to switch fate becomes progressively limited, which poses a problem for repairingtissues and organs. Unlike other multicellular organisms, plants are known for their developmental plasticity. Forexample, shoot cuttings can regenerate root systems and vice versa. During regeneration, plant cells have the uniquecapability to change their identity by reprogramming their fate, a key mechanism in their ability to regenerate organs andtissues. Cell fate reprogramming requires changes in gene expression, which in turn requires changes in chromatinaccessibility so that different genes can be accessed by the transcription machinery. Crucially, some transcription factorscalled pioneer factors can bind inaccessible chromatin and change its conformation so that other factors canaccess the DNA to initiate transcription, changing gene expression and causing cell reprogramming to a different fate. Ectopic overexpression of a plant transcription factor, TCP4, drives the conversion of Arabidopsis roots into shoot/stem-like organs, indicating that TCP4 has a central role in plant cell reprogramming. TCP4 regulates the expression ofseveral chromatin remodellers, which suggests that TCP4 has a broader role in controlling the chromatin landscape andmight be a novel plant pioneer factor.To understand how TCP4 reprogrammes root cells, a combination of next generation sequencing techniques,bioinformatics, and live cell imaging in inducible TCP4 lines will be used to obtain a comprehensive picture of the TCP4-induced switch in cell fate. Chromatin maps from different timepoints of the root-to-shoot conversion process will beobtained through the use of chromatin particle spectrum analysis (CPSA) and chromatin immunoprecipitation (ChIP-seq).These maps will be compared to global changes in gene expression (RNA-seq) induced by TCP4 at the same timepoints toidentify regions of the chromatin that may have been made accessible by TCP4 to initiate gene expression. Theconversion of roots into shoots will also be monitored using fluorescent labels that allow us to recognise cell identityby confocal microscopy. This will help us understand the mechanisms that allow TCP4 to reprogramme roots and willcontribute to establishing general principles of plant cell reprogramming.This project is an exciting opportunity to learn multidisciplinary skills and techniques with wide applications. Theproject will lead to new insights in regulation of transcription and pioneering activity in plants and could lead todeveloping more efficient methods of plant propagation for sterile species, from a wider range of tissues, and providenew strategies for improving agricultural traits and food security.