Microprotein-Encoding RNA Regulation in Cells Treated with Pro-inflammatory and Pro-Fibrotic Stimuli (RNA-Seq Caco2). Microprotein-Encoding RNA Regulation in Cells Treated with Pro-inflammatory and Pro-Fibrotic Stimuli (RNA-Seq Caco2)

Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins. Here, we examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells (PBMCs), and then used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates. This approach reveals a number of new microproteins worthy of additional functional characterization, and provides a dataset that can be queried in different ways to find additional gut microproteins of interest. Overall design: RNA-sequencing of of Caco-2 cells with or without treatment of lipid/non-lipid micelles, and differentiated or undifferentiated

近期通过蛋白质基因组学（proteogenomics）与转录组核糖体谱分析（ribosome profiling）对人类蛋白质组开展的研究，已发现数千个此前未被注释的编码微蛋白的小型开放阅读框（small open reading frames，smORFs）。多数已完成功能表征的微蛋白均因进化保守性而被选中开展后续研究。然而，小鼠体内一种非保守性免疫调节微蛋白的研究案例表明，严格依赖序列保守性会遗漏部分极具研究价值的微蛋白。本研究旨在探讨通过基因调控手段识别在肠道炎症或纤维化中发挥潜在功能的人类微蛋白的可行性。为此，我们采集了肠道细胞系与外周血单个核细胞（peripheral blood mononuclear cells，PBMCs）的核糖体谱分析数据，并通过编码微蛋白的转录本的基因表达特征，筛选出受调控程度显著的微蛋白，其中包含数种仅与灵长类存在序列保守性的微蛋白。该方法成功筛选出一批亟待开展功能鉴定的新型微蛋白，同时构建了可通过多种方式检索的数据集，用于挖掘更多具有研究价值的肠道微蛋白。整体实验设计：对经脂质/非脂质胶束处理或未处理、以及分化或未分化的Caco-2细胞进行RNA测序。