Analysis of mir-223 knockout cultured neutrophils versus wild-type cultured neutrophils, by ribosome profiling and mRNA-Seq

MicroRNAs (miRNAs) are endogenous ~22-nucleotide RNAs that mediate important gene-regulatory events by pairing to the mRNAs of protein-coding genes to direct their repression. Repression of these regulatory targets leads to decreased translational efficiency and/or decreased mRNA levels, but the relative contributions of these two outcomes have been largely unknown, particularly for endogenous targets expressed at low-to-moderate levels. Here, we use ribosome profiling to measure the overall effects on protein production and compare these to simultaneously measured effects on mRNA levels. For both ectopic and endogenous miRNA regulatory interactions, lowered mRNA levels account for most (≥84%) of the decreased protein production. These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output.

微小RNA（MicroRNAs，miRNAs）是一类内源性的约22核苷酸长度的RNA，通过与蛋白编码基因的信使RNA（mRNA）结合配对，介导关键的基因调控事件以指导靶基因的表达抑制。对这些调控靶点的抑制会导致翻译效率降低和/或mRNA水平下降，但这两种效应的相对贡献此前尚不明确，尤其是对于低至中等表达水平的内源性调控靶点。本研究采用核糖体谱分析（ribosome profiling）技术，检测miRNA对蛋白质合成的整体影响，并与同步检测得到的mRNA水平变化进行对比分析。无论是异位表达还是内源性的miRNA调控互作，mRNA水平降低均可解释蛋白质合成下降的绝大多数（≥84%）效应。本研究结果表明，mRNA水平的变化可精准反映miRNAs对基因表达的调控作用，同时提示靶标mRNA的去稳定化是蛋白质合成减少的主要原因。