microRNAs - powerful repression comes from small RNAs

microRNAs (miRNAs) encode a novel class of small, non-coding RNAs that regulate gene expression post-trancriptionally. miRNAs comprise one of the major non-coding RNA families, whose diverse biological functions and unusual capacity for gene regulation have attracted enormous interests in the RNA world. Over the past 16 years, genetic, biochemical and computational approaches have greatly shaped the growth of the field, leading to the identification of thousands of miRNA genes in nearly all metazoans. The key molecular machinery for miRNA biogenesis and silencing has been identified, yet the precise biochemical and regulatory mechanisms still remain elusive. However, recent findings have shed new light on how miRNAs are generated and how they function to repress gene expression. miRNAs provide a paradigm for endogenous small RNAs that mediate gene silencing at a genome-wide level. The gene silencing mediated by these small RNAs constitutes a major component of gene regulation during various developmental and physiological processes. The accumulating knowledge about their biogenesis and gene silencing mechanism will add a new dimension to our understanding about the complex gene regulatory networks.     

The roles of miRNAs in wing imaginal disc development in Drosophila

During development, it is essential for gene expression to occur in a very precise spatial and temporal manner. There are many levels at which regulation of gene expression can occur, and recent evidence demonstrates the importance of mRNA stability in governing the amount of mRNA that can be translated into functional protein. One of the most important discoveries in this field has been miRNAs (microRNAs) and their function in targeting specific mRNAs for repression. The wing imaginal discs of Drosophila are an excellent model system to study the roles of miRNAs during development and illustrate their importance in gene regulation. This review aims at discussing the developmental processes where control of gene expression by miRNAs is required, together with the known mechanisms of this regulation. These developmental processes include Hox gene regulation, developmental timing, growth control, specification of SOPs (sensory organ precursors) and the regulation of signalling pathways.     

Novel and mechanical stress-responsive MicroRNAs in Populus trichocarpa that are absent from Arabidopsis

MicroRNAs (miRNAs) are small, noncoding RNAs that can play crucial regulatory roles in eukaryotes by targeting mRNAs for silencing. To test whether miRNAs play roles in the regulation of wood development in tree species, we isolated small RNAs from the developing xylem of Populus trichocarpa stems and cloned 22 miRNAs. They are the founding members of 21 miRNA gene families for 48 miRNA sequences, represented by 98 loci in the Populus genome. A majority of these miRNAs were predicted to target developmental- and stress/defense-related genes and possible functions associated with the biosynthesis of cell wall metabolites. Of the 21 P. trichocarpa miRNA families, 11 have sequence conservation in Arabidopsis thaliana but exhibited species-specific developmental expression patterns, suggesting that even conserved miRNAs may have different regulatory roles in different species. Most unexpectedly, the remaining 10 miRNAs, for which 17 predicted targets were experimentally validated in vivo, are absent from the Arabidopsis genome, suggesting possible roles in tree-specific processes. In fact, the expression of a majority of the cloned miRNAs was upregulated or downregulated in woody stems in a manner consistent with tree-specific corrective growth against tension and compression stresses, two constant mechanical loads in trees. Our results show that plant miRNAs can be induced by mechanical stress and may function in one of the most critical defense systems for structural and mechanical fitness.     

Systematic investigation of Amphioxus (Branchiostoma floridae) microRNAs

MicroRNAs (miRNAs) participate in various biological processes via controlling gene activity. Amphioxus is the best available stand-in as the proximate invertebrate ancestor of the vertebrates. Here, we systematically investigated the miRNAs in amphioxus. First, we identified 245 candidate amphioxus miRNAs, in which 183 miRNAs were firstly reported. Second, we gave evidences to support a birth-and-death process of miRNA genes in some families and gave implications for the functional diversification of miRNA during evolution. Third, we identified 47 development-specific expression miRNAs. We found that only 19 miRNAs were expressed in all developmental stages, 16 miRNAs were neurula-specific and 13 miRNAs were larva-specific. In addition, these potential miRNA-targeting genes were mainly classified into development, muscle formation, cell adhesion, and gene regulation categories. Finally, we found 79 immune related genes targeted by 136 miRNAs in amphioxus. In conclusion, our results take an insight into both the function and evolution of the amphioxus miRNAs.     

miRNA调控昆虫与病毒互作的研究进展

miRNA是一类重要的非编码小分子RNA,可在转录后水平调控基因表达,参与并调控机体的生长发育、细胞分化、细胞凋亡、抗病毒、激素分泌、神经系统等重要生物过程。本文介绍了miRNA的合成途径及其生物学功能,并重点阐述miRNA在昆虫宿主与病毒互作中的调控作用:通过mRNA剪切或抑制靶标蛋白的翻译负调控靶标基因,实现基因沉默,调控约50%的蛋白质编码基因的表达,许多miRNA已被发现在人体和植物中参与调控病毒的复制侵染,因此也有可能控制害虫对病毒抗性的产生,恢复病毒对害虫的防控作用。最近有研究将害虫特异的miRNA转入植物,干扰昆虫蜕皮过程导致幼虫的死亡,作为Bt转基因作物的替代,成为抗虫基因工程的新选择。研究miRNA在昆虫对病毒抗性产生中的作用,将为昆虫抗病毒机制的研究提供新的思路,为害虫生物防治措施的应用及改进提供理论参考。     

Identifying functional miRNA-mRNA regulatory modules with correspondence latent dirichlet allocation

MOTIVATION: MicroRNAs (miRNAs) are small non-coding RNAs that cause mRNA degradation and translational inhibition. They are important regulators of development and cellular homeostasis through their control of diverse processes. Recently, great efforts have been made to elucidate their regulatory mechanism, but the functions of most miRNAs and their precise regulatory mechanisms remain elusive. With more and more matched expression profiles of miRNAs and mRNAs having been made available, it is of great interest to utilize both expression profiles to discover the functional regulatory networks of miRNAs and their target mRNAs for potential biological processes that they may participate in. RESULTS: We present a probabilistic graphical model to discover functional miRNA regulatory modules at potential biological levels by integrating heterogeneous datasets, including expression profiles of miRNAs and mRNAs, with or without the prior target binding information. We applied this model to a mouse mammary dataset. It effectively captured several biological process specific modules involving miRNAs and their target mRNAs. Furthermore, without using prior target binding information, the identified miRNAs and mRNAs in each module show a large proportion of overlap with predicted miRNA target relationships, suggesting that expression profiles are crucial for both target identification and discovery of regulatory modules.     

MicroRNAs and Their Cross-Talks in Plant Development

Plant development is a complex process influenced by exogenous and endogenous elements. A series of postembryonic developmental events is involved to form the final architecture and contend with the changing environment. MicroRNA (miRNA) is one of endogenous non-coding RNAs, which plays an important role in plant developmental regulation. In this review, we summarized 34 miRNA families that are closely associated with plant development. Among these families, nine are expressed only in specific organs, whereas 20 families are expressed in at least two different organs. It is known that some miRNAs are expressed across most processes of plant growth, while some appear only at particular developmental stages or under special environmental conditions such as drought, waterlogging and short-day time. These miRNAs execute their diverse functions by regulating developmental gene expression levels, interacting with phytohormone signaling response, participating in the biogenesis of ta-siRNAs and affecting the production of miRNAs.