High-Throughput Profiling of Caenorhabditis elegans Starvation-Responsive microRNAs

MicroRNAs (miRNAs) are non-coding RNAs of ~22 nucleotides in length that regulate gene expression by interfering with the stability and translation of mRNAs. Their expression is regulated during development, under a wide variety of stress conditions and in several pathological processes. In nature, animals often face feast or famine conditions. We observed that subjecting early L4 larvae from Caenorhabditis elegans to a 12-hr starvation period produced worms that are thinner and shorter than well-fed animals, with a decreased lipid accumulation, diminished progeny, reduced gonad size, and an increased lifespan. Our objective was to identify which of the 302 known miRNAs of C. elegans changed their expression under starvation conditions as compared to well-fed worms by means of deep sequencing in early L4 larvae. Our results indicate that 13 miRNAs (miR-34-3p, the family of miR-35-3p to miR-41-3p, miR-39-5p, miR-41-5p, miR-240-5p, miR-246-3p and miR-4813-5p) were upregulated, while 2 miRNAs (let-7-3p and miR-85-5p) were downregulated in 12-hr starved vs. well-fed early L4 larvae. Some of the predicted targets of the miRNAs that changed their expression in starvation conditions are involved in metabolic or developmental process. In particular, miRNAs of the miR-35 family were upregulated 6–20 fold upon starvation. Additionally, we showed that the expression of gld-1, important in oogenesis, a validated target of miR-35-3p, was downregulated when the expression of miR-35-3p was upregulated. The expression of another reported target, the cell cycle regulator lin-23, was unchanged during starvation. This study represents a starting point for a more comprehensive understanding of the role of miRNAs during starvation in C. elegans.

微小RNA（MicroRNAs，简称miRNAs）是一类长度约为22个核苷酸的非编码RNA（non-coding RNAs），通过干扰信使RNA（messenger RNA，简称mRNA）的稳定性与翻译过程调控基因表达。它们的表达在发育进程、多种应激条件及多种病理过程中受到调控。在自然环境中，动物常面临饱食或饥饿的境遇。我们观察到，将秀丽隐杆线虫（Caenorhabditis elegans）的早期第四期幼虫进行12小时饥饿处理后，所得线虫相较于正常饱食个体更为细短，且脂质积累减少、子代数量减少、性腺尺寸缩小，寿命则有所延长。本研究旨在通过对早期第四期幼虫开展深度测序（deep sequencing），对比饥饿组与饱食组线虫，鉴定秀丽隐杆线虫已知的302种微小RNA中，哪些在饥饿条件下表达发生变化。结果显示，与12小时饱食的早期第四期幼虫相比，12小时饥饿组中有13种微小RNA（miR-34-3p、miR-35-3p至miR-41-3p家族、miR-39-5p、miR-41-5p、miR-240-5p、miR-246-3p及miR-4813-5p）表达上调，另有2种微小RNA（let-7-3p与miR-85-5p）表达下调。上述在饥饿条件下表达发生改变的微小RNA，其部分预测靶基因参与代谢或发育进程。其中，miR-35家族的微小RNA在饥饿条件下表达上调6~20倍。此外，我们证实，作为miR-35-3p已验证靶基因且在卵子发生（oogenesis）中发挥重要作用的gld-1，其表达随miR-35-3p的上调而下调；而另一已报道的靶基因、细胞周期调控因子（cell cycle regulator）lin-23的表达在饥饿过程中未发生改变。本研究为更全面理解微小RNA在秀丽隐杆线虫饥饿响应中的作用奠定了基础。