miR-140 mutation and skeletal dysplasia [RNA-seq]

MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression. Heterozygous loss-of-function point mutations of miRNA genes are associated with several human congenital disorders, but neomorphic (gain-of-new-function) mutations in miRNAs due to nucleotide substitutions have not been reported. Here we describe a neomorphic seed region mutation in the chondrocyte-specific, super-enhancer-associated MIR140 gene encoding microRNA-140 (miR-140) in a novel autosomal dominant human skeletal dysplasia. Mice with the corresponding single nucleotide substitution show skeletal abnormalities similar to those of the patients but distinct from those of miR-140-null mice. This mutant miRNA gene yields abundant mutant miR-140-5p expression without miRNA-processing defects. In chondrocytes, the mutation causes widespread derepression of wild-type miR-140-5p targets and repression of mutant miR-140-5p targets, indicating that the mutation produces both loss-of-function and gain-of-function effects. Furthermore, the mutant miR-140-5p seed competes with the conserved RNA-binding protein Ybx1 for overlapping binding sites. This finding may explain the potent target repression and robust in vivo effect by this mutant miRNA even in the absence of evolutionary selection of miRNA–target RNA interactions, which contributes to the strong regulatory effects of conserved miRNAs. Our study presents the first case of a pathogenic gain-of-function miRNA mutation and provides molecular insight into neomorphic actions of emerging and/or mutant miRNAs. RNA sequencing (RNA-seq) in chondrocytes with miR-140 G mutation or deletion

微小RNA（microRNAs，miRNAs）是基因表达的转录后调控因子。miRNA基因的杂合型功能丧失型点突变与多种人类先天性疾病相关，但由核苷酸替换导致的miRNA新功能型突变（neomorphic，即功能获得型，gain-of-new-function）尚未见报道。本研究报道了一例发生于软骨细胞（chondrocyte）特异性、超级增强子（super-enhancer）关联的MIR140基因（编码微小RNA-140，miR-140）的新功能型种子区突变，该突变见于一例新型常染色体显性遗传性人类骨骼发育异常患者。携带对应单核苷酸替换的小鼠表现出与患者相似的骨骼异常，但与miR-140敲除小鼠的表型存在显著差异。该突变miRNA基因可产生大量突变型miR-140-5p表达，且无miRNA加工缺陷。在软骨细胞中，该突变可广泛解除野生型miR-140-5p靶基因的抑制状态，同时抑制突变型miR-140-5p的靶基因，表明该突变同时兼具功能丧失与功能获得双重效应。此外，突变型miR-140-5p的种子区可与保守RNA结合蛋白Ybx1竞争重叠的结合位点。这一发现可解释该突变miRNA即使在缺乏miRNA-靶RNA相互作用的进化选择压力的情况下，仍能实现强效的靶基因抑制与显著的体内效应——而这类进化选择正是保守miRNAs发挥强调控作用的核心基础。本研究首次报道了致病性功能获得型miRNA突变，并为新型或突变型miRNA的新功能型作用机制提供了分子层面的见解。针对携带miR-140 G突变或敲除的软骨细胞开展RNA测序（RNA-seq）