Genome-wide post-transcriptional dysregulation by microRNAs in human asthma as revealed by Frac-seq
Genome-wide post-transcriptional dysregulation by microRNAs in human asthma as revealed by Frac-seq
复制标题
Frac-seq 揭示人类哮喘中 microRNA 引起的全基因组转录后失调
DOI：
10.1101/234500
复制
发表时间：
2017
期刊：
影响因子：
--
通讯作者：
Martinez-Nunez R
中科院分区：
文献类型：
--
作者：
Martinez-Nunez R
MicroRNA是一种小的非编码RNA，它在转录后抑制基因表达，几乎参与所有的生物学过程。虽然一般研究单个microRNA的作用，但对多个microRNA的全基因组作用的研究较少。我们采用亚细胞分级分离和RNA测序（Frac-seq）技术，在健康对照和重度哮喘患者的人原发性支气管上皮细胞中，评估了microRNA在全基因组范围内的成对表达，以及总（细胞质）和翻译（多聚核糖体结合）mRNA水平。严重哮喘是一种慢性气道炎症性疾病，其特征是对治疗反应不良。我们发现了在哮喘中差异表达的基因（即基因的同种型）和mRNA同种型，以及与支气管上皮相关的新的炎症和结构病理生理学机制，这些机制仅通过多核糖体结合的mRNA（例如，IL 1A和LTB基因或ITGA 6和ITGA 2选择性剪接同种型）来揭示。基因表达（即基因的同种型）和mRNA表达分析揭示了不同的分子候选物和生物学途径，差异表达的多聚核糖体结合和总mRNA也显示出很少的重叠。我们揭示了一个由六种失调的microRNA组成的中心，占所有microRNA靶向的90%，显示出对多聚核糖体结合的mRNA的偏好。在来自健康供体的支气管上皮细胞中转染该枢纽模仿哮喘特征。我们的工作证明了人类哮喘中广泛的转录后基因失调，其中microRNA发挥了核心作用，说明了在研究人类疾病时评估转录后基因表达的可行性和重要性。
MicroRNAs are small noncoding RNAs that inhibit gene expression posttranscriptionally, implicated in virtually all biological processes. Although the effect of individual microRNAs is generally studied, the genome-wide role of multiple microRNAs is less investigated. We assessed paired genome-wide expression of microRNAs with total (cytoplasmic) and translational (polyribosome-bound) mRNA levels employing subcellular fractionation and RNA sequencing (Frac-seq) in human primary bronchoepithelium from healthy controls and severe asthmatics. Severe asthma is a chronic inflammatory disease of the airways characterized by poor response to therapy. We found genes (ie, isoforms of a gene) and mRNA isoforms differentially expressed in asthma, with novel inflammatory and structural pathophysiological mechanisms related to bronchoepithelium disclosed solely by polyribosome-bound mRNAs (eg, IL1A and LTB genes or ITGA6 and ITGA2 alternatively spliced isoforms). Gene expression (ie, isoforms of a gene) and mRNA expression analysis revealed different molecular candidates and biological pathways, with differentially expressed polyribosome-bound and total mRNAs also showing little overlap. We reveal a hub of six dysregulated microRNAs accounting for∼ 90% of all microRNA targeting, displaying preference for polyribosome-bound mRNAs. Transfection of this hub in bronchial epithelial cells from healthy donors mimicked asthma characteristics. Our work demonstrates extensive posttranscriptional gene dysregulation in human asthma, in which microRNAs play a central role, illustrating the feasibility and importance of assessing posttranscriptional gene expression when investigating human disease.