Genome-wide analysis of the transcriptional and alternative splicing landscape in intestinal organoids undergoing nutrient starvation or ER stress. Mus musculus

Our study represents the first detailed analysis of the transcriptional and alternative splicing landscape of intestinal organoids undergoing stress, with biologic replicates, generated by RNA-seq technology. We report significant changes in the expression of genes involved in inflammation, proliferation and transcription, among others. Splicing events commonly regulated by both stresses affected genes regulating splicing and were associated with nonsense-mediated decay (NMD), suggesting that splicing is modulated by an auto-regulatory feedback loop during stress. Overall design: Murine intestinal organoids were stimulated in triplicate with conditions for either ER stress or nutrient starvation and RNA-seq was conducted to analyze global changes in both gene expression at the transcriptional level and alternative splicing

本研究首次对处于应激状态下的肠道类器官的转录组与可变剪接谱展开系统性详细分析，实验设置生物学重复，所有样本均通过RNA测序（RNA-seq）技术完成检测与分析。本研究报道了炎症反应、细胞增殖与转录调控等多个功能通路相关基因的表达出现显著变化。同时受两种应激调控的剪接事件，其靶基因多参与剪接调控过程，且与无义介导的mRNA降解（nonsense-mediated decay, NMD）通路显著相关，这提示应激状态下剪接过程可通过自调控反馈环路实现动态调节。实验设计概述：将小鼠肠道类器官以一式三份（生物学重复）分别施加内质网应激（ER stress）与营养饥饿两种处理条件，随后通过RNA-seq技术分析转录水平基因表达与可变剪接的全局变化特征。