The microRNAs of Caenorhabditis elegans

The soil nematode, Caenorhabditis elegans, occupies a central place in the short history of microRNA (miRNA) research. The converse is also true: miRNAs have emerged as key regulatory components in the life cycle of the worm, as well as numerous other organisms. Since the landmark discovery in 1993 of the first miRNA gene, lin-4, several other miRNAs have been characterized in detail in C. elegans and shown to participate in diverse biological processes. Moreover, the worm has provided, by virtue of its ease of genetic manipulation and amenability to high-throughput methods, an ideal platform for elucidating many general and conserved aspects of miRNA biology, namely mechanisms of biogenesis, target recognition, gene silencing, and regulation thereof. In this review, we summarize both the contribution of miRNAs to C. elegans physiology and development, as well as the contribution of C. elegans research to our understanding of general features of miRNA biology.     

MicroRNA targets in Drosophila

Background  

The recent discoveries of microRNA (miRNA) genes and characterization of the first few target genes regulated by miRNAs in Caenorhabditis elegans and Drosophila melanogaster have set the stage for elucidation of a novel network of regulatory control. We present a computational method for whole-genome prediction of miRNA target genes. The method is validated using known examples. For each miRNA, target genes are selected on the basis of three properties: sequence complementarity using a position-weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Application to the D. melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known miRNAs.     

Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation

Background  

The microRNAs (miRNAs) are an extensive class of small noncoding RNAs (18 to 25 nucleotides) with probable roles in the regulation of gene expression. In Caenorhabditis elegans, lin-4 and let-7 miRNAs control the timing of fate specification of neuronal and hypodermal cells during larval development. lin-4, let-7 and other miRNA genes are conserved in mammals, and their potential functions in mammalian development are under active study.     

microRNA-mediated translation repression through GYF-1 and IFE-4 in C. elegans development

microRNA (miRNA)-mediated gene silencing is enacted through the recruitment of effector proteins that direct translational repression or degradation of mRNA targets, but the relative importance of their activities for animal development remains unknown. Our concerted proteomic surveys identified the uncharacterized GYF-domain encoding protein GYF-1 and its direct interaction with IFE-4, the ortholog of the mammalian translation repressor 4EHP, as key miRNA effector proteins in Caenorhabditis elegans. Recruitment of GYF-1 protein to mRNA reporters in vitro or in vivo leads to potent translation repression without affecting the poly(A) tail or impinging on mRNA stability. Loss of gyf-1 is synthetic lethal with hypomorphic alleles of embryonic miR-35–42 and larval (L4) let-7 miRNAs, which is phenocopied through engineered mutations in gyf-1 that abolish interaction with IFE-4. GYF-1/4EHP function is cascade-specific, as loss of gyf-1 had no noticeable impact on the functions of other miRNAs, including lin-4 and lsy-6. Overall, our findings reveal the first direct effector of miRNA-mediated translational repression in C. elegans and its physiological importance for the function of several, but likely not all miRNAs.     

Ribosomal protein RPS-14 modulates let-7 microRNA function in Caenorhabditis elegans

The let-7 microRNA (miRNA) regulates developmental timing at the larval-to-adult transition in Caenorhabditis elegans. Dysregulation of let-7 results in irregular hypodermal and vulval development. Disrupted let-7 function is also a feature of human lung cancer. However, little is known about the mechanism and co-factors of let-7. Here we demonstrate that ribosomal protein RPS-14 is able to modulate let-7 function in C. elegans. The RPS-14 protein co-immunoprecipitated with the nematode Argonaute homolog, ALG-1. Reduction of rps-14 gene expression by RNAi suppressed the aberrant vulva and hypodermis development phenotypes of let-7(n2853) mutant animals and the mis-regulation of a reporter bearing the lin-41 3′UTR, a well established let-7 target. Our results indicate an interactive relationship between let-7 miRNA function and ribosomal protein RPS-14 in regulation of terminal differentiation that may help in understanding the mechanism of translational control by miRNAs.     

Small RNA-mediated gene silencing pathways in C. elegans

Small RNA pathways, including the RNA interference (RNAi) pathway and the microRNA (miRNA) pathway, regulate gene expression, defend against transposable elements and viruses, and, in some organisms, guide genome rearrangements. The nematode Caenorhabditis elegans (C. elegans) has been at the forefront of small RNA research; not only were the first miRNAs and their function as regulators of gene expression discovered in C. elegans, but also double-stranded RNA-induced gene silencing by RNAi was discovered in this model organism. Since then, genetic and RNAi-mediated screens, candidate gene approaches, and biochemical studies have uncovered numerous factors in the small RNA pathways and painted a rich palette of interacting pathways. Here we review the different small RNAs that have been discovered in C. elegans and discuss our understanding of their biogenesis pathways and mechanisms of action.     

Myotube-derived exosomal miRNAs downregulate Sirtuin1 in myoblasts during muscle cell differentiation

It has recently been established that exosomes can mediate intercellular cross-talk under normal and pathological conditions through the transfer of specific miRNAs. As muscle cells secrete exosomes, we addressed the question of whether skeletal muscle (SkM) exosomes contained specific miRNAs, and whether they could act as “endocrine signals” during myogenesis. We compared the miRNA repertoires found in exosomes released from C2C12 myoblasts and myotubes and found that 171 and 182 miRNAs were exported into exosomes from myoblasts and myotubes, respectively. Interestingly, some miRNAs were expressed at higher levels in exosomes than in their donor cells and vice versa, indicating a selectivity in the incorporation of miRNAs into exosomes. Moreover miRNAs from C2C12 exosomes were regulated during myogenesis. The predicted target genes of regulated exosomal miRNAs are mainly involved in the control of important signaling pathways for muscle cell differentiation (e.g., Wnt signaling pathway). We demonstrated that exosomes from myotubes can transfer small RNAs (C. elegans miRNAs and siRNA) into myoblasts. Moreover, we present evidence that exosome miRNAs secreted by myotubes are functionally able to silence Sirt1 in myoblasts. As Sirt1 regulates muscle gene expression and differentiation, our results show that myotube–exosome miRNAs could contribute to the commitment of myoblasts in the process of differentiation. Until now, myokines in muscle cell secretome provided a conceptual basis for communication between muscles. Here, we show that miRNA exosomal transfer would be a powerful means by which gene expression is orchestrated to regulate SkM metabolic homeostasis.     

携带与非携带松材线虫的松墨天牛miRNA表达谱比较分析

【目的】松墨天牛是松树的重要蛀干害虫,也是林业重大外来入侵种松材线虫的媒介昆虫。虽然松墨天牛和松材线虫互作的化学生态和分子进化机制受到人们的广泛关注,但miRNA等表观遗传因子在天牛—线虫互作中的作用未见报道。【方法】使用illumina HiSeq 2000平台进行miRNA高通量测序,得到4个携带线虫的天牛miRNA库和4个未携带线虫的天牛miRNA库。此外,对鉴定出的miRNA进行了差异表达分析,并对这些miRNA的靶基因进行了GO注释和KEGG通路富集分析。【结果】在携带线虫的天牛表皮、脂肪体、中肠和气管样本中分别鉴定出780、802、617和762个miRNA;在未携带松材线虫的天牛的不同组织样本中分别鉴定出784、723、713和837个miRNA。在携带松材线虫的松墨天牛中,某些已知miRNA表达量会显著升高,如miR-14、miR279和miR-312等。差异表达miRNA的功能大多指向代谢、免疫等方面。【结论】miRNA在松墨天牛和松材线虫互作中起着重要的调控作用。     

microRNA在玉米生长发育及非生物胁迫响应中的调控功能

microRNA（miRNA）是一类广泛存在于真核生物中长度为20~24 nt的内源非编码小RNA，它们通过对靶基因mRNA进行切割或翻译抑制，在转录后水平调控靶基因的表达。近期研究表明，miRNA参与植物生长发育与逆境胁迫响应的多个重要生物学过程，对作物的农艺性状也起到重要的调控作用。玉米作为重要的粮食、饲料和工业原料，提高其产量和品质对于保障世界粮食安全至关重要，然而与模式植物拟南芥和水稻相比，玉米中miRNA的研究仍然相对较少，理解miRNA在玉米中的功能和调控机理有助于通过分子育种对关键农艺性状进行遗传改良。本文综述了玉米中miRNA的发现与鉴定，系统总结了参与玉米miRNA代谢途径的关键蛋白DCL、AGO和HEN1的研究进展，重点阐述了在玉米生长发育和非生物胁迫响应过程中已开展功能研究miRNA的调控作用，并对玉米miRNA研究当前存在的问题和未来的发展趋势进行了讨论。