Ducloy Amélie, Azzopardi Marianne, Ivsic Caroline, Cueff Gwendal, Sourdeval Delphine, Charif Delphine, Cacas Jean-Luc
University Paris-Saclay, INRAE, AgroParisTech, Institute Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
School of biological Sciences, University of Western Australia, Australia.
Data Brief. 2024 Feb 28;53:110243. doi: 10.1016/j.dib.2024.110243. eCollection 2024 Apr.
The Unfolded Protein Response (UPR) is a retrograde, ER-to-nucleus, signalling pathway which is conserved across kingdoms. In plants, it contributes to development, reproduction, immunity and tolerance to abiotic stress. This RNA sequencing (RNA-seq) dataset was produced from 14-day-old seedlings challenged by tunicamycin (Tm), an antibiotic inhibiting Asn-linked glycosylation in the endoplasmic reticulum (ER), causing an ER stress and eventually activating the UPR. Wild-type (WT) and a double mutant deficient for two main actors of the UPR ( and ) were used as genetic backgrounds in our experimental setup, allowing to distinguish among differentially-expressed genes (DEGs) which ones are dependent on or independent on IRE1s. Also, shoots and roots were harvested separately to determine organ-specific transcriptomic responses to Tm. Library and sequencing were performed using DNBseq™ technology by the Beijing Genomics Institute. Reads were mapped and quantified against the Arabidopsis genome. Differentially-expressed genes were identified using Rflomics upon filtering and normalization by the Trimmed Mean of M-value (TMM) method. While the genotype effect was weak under mock conditions (with a total of 182 DEGs in shoots and 195 DEGs in roots), the tunicamycin effect on each genotype was characterized by several hundred of DEGs in both shoots and roots. Among these genes, 872 and 563 genes were statistically up- and down-regulated in the shoot tissues of the double mutant when compared to those of WT, respectively. In roots of Tm-challenged seedlings, 425 and 439 genes were significantly up- and down-regulated in mutants with respect to WT. We believe that our dataset could be reused for investigating any biological questions linked to ER homeostasis and its role in plant physiology.
未折叠蛋白反应（UPR）是一种从内质网到细胞核的逆向信号通路，在不同生物界中保守存在。在植物中，它有助于植物的发育、繁殖、免疫以及对非生物胁迫的耐受性。这个RNA测序（RNA-seq）数据集来自14日龄的幼苗，这些幼苗受到衣霉素（Tm）的挑战，衣霉素是一种抑制内质网中与天冬酰胺连接的糖基化的抗生素，会导致内质网应激并最终激活UPR。在我们的实验设置中，使用野生型（WT）和UPR两个主要作用因子缺陷的双突变体作为遗传背景，从而能够区分差异表达基因（DEG）中哪些依赖于IRE1s，哪些不依赖于IRE1s。此外，分别收获地上部分和根部，以确定对衣霉素的器官特异性转录组反应。文库构建和测序由北京基因组研究所使用DNBseq™技术进行。读取的序列与拟南芥基因组进行比对和定量。通过M值修剪均值（TMM）方法进行过滤和标准化后，使用Rflomics鉴定差异表达基因。在模拟条件下，基因型效应较弱（地上部分共有182个DEG，根部有195个DEG），而衣霉素对每种基因型的影响在地上部分和根部均表现为数百个DEG。在这些基因中，与野生型相比，双突变体地上部分组织中有872个和563个基因分别在统计学上上调和下调。在受到衣霉素挑战的幼苗根部，与野生型相比，突变体中有425个和439个基因显著上调和下调。我们相信，我们的数据集可用于研究任何与内质网稳态及其在植物生理学中的作用相关的生物学问题。
