Ait-Mohamed Ouardia, Novák Vanclová Anna M G, Joli Nathalie, Liang Yue, Zhao Xue, Genovesio Auguste, Tirichine Leila, Bowler Chris, Dorrell Richard G
Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
Department of Oceanography, Dalhousie University, Halifax, NS, Canada.
Front Plant Sci. 2020 Oct 16;11:590949. doi: 10.3389/fpls.2020.590949. eCollection 2020.
Transcriptional coordination is a fundamental component of prokaryotic and eukaryotic cell biology, underpinning the cell cycle, physiological transitions, and facilitating holistic responses to environmental stress, but its overall dynamics in eukaryotic algae remain poorly understood. Better understanding of transcriptional partitioning may provide key insights into the primary metabolism pathways of eukaryotic algae, which frequently depend on intricate metabolic associations between the chloroplasts and mitochondria that are not found in plants. Here, we exploit 187 publically available RNAseq datasets generated under varying nitrogen, iron and phosphate growth conditions to understand the co-regulatory principles underpinning transcription in the model diatom . Using WGCNA (Weighted Gene Correlation Network Analysis), we identify 28 merged modules of co-expressed genes in the genome, which show high connectivity and correlate well with previous microarray-based surveys of gene co-regulation in this species. We use combined functional, subcellular localization and evolutionary annotations to reveal the fundamental principles underpinning the transcriptional co-regulation of genes implicated in chloroplast and mitochondrial metabolism, as well as the functions of diverse transcription factors underpinning this co-regulation. The resource is publically available as PhaeoNet, an advanced tool to understand diatom gene co-regulation.
转录协调是原核生物和真核生物细胞生物学的一个基本组成部分，它支撑着细胞周期、生理转变，并促进细胞对环境压力的整体反应。然而，其在真核藻类中的整体动态仍知之甚少。更好地理解转录分配可能为真核藻类的初级代谢途径提供关键见解，这些途径通常依赖于叶绿体和线粒体之间复杂的代谢关联，而这种关联在植物中并不存在。在这里，我们利用在不同氮、铁和磷生长条件下生成的187个公开可用的RNAseq数据集，来了解模式硅藻转录调控的共同调控原则。使用WGCNA（加权基因共表达网络分析），我们在基因组中识别出28个共表达基因的合并模块，这些模块显示出高连通性，并且与该物种先前基于微阵列的基因共调控调查结果相关性良好。我们结合功能、亚细胞定位和进化注释，揭示叶绿体和线粒体代谢相关基因转录共调控的基本原则，以及支撑这种共调控的多种转录因子的功能。该资源作为PhaeoNet公开可用，这是一个用于理解硅藻基因共调控的先进工具。
