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.     

An Exploration of Evolution,Maturation, Expression and Function Relationships in Mir-23～27～24 Cluster

The study aims to explore the potential relationships of evolution, maturation, expression and function between homologous/clustered miRNAs. mir-23∼27∼24 gene cluster, including the two gene clusters (mir-23a and mir-23b) and the three miRNA gene families (mir-23, mir-27 and mir-24), was typically selected as an example. These related miRNAs show similar evolutionary patterns and various expression patterns. Most of them show consistent isomiR expression pattern, and the “switching” phenomenon can be found between different abundant isomiR species. These findings suggest that these sequence or location related miRNAs show the similar miRNA processing and maturation processes, and the robust selection of the most dominant isomiR exists in specific tissues. Functional analysis show that these miRNAs show similar distributions of enriched gene categories, suggesting the close functional prelateships via direct or indirect coordinate regulation in biological processes. The study reveals the close evolutionary, expression and functional relationships between related homologous/clustered miRNAs, which will further enrich miRNA studies and understand direct or indirect interactions between miRNAs.     

Roles of microRNAs in mammalian reproduction: from the commitment of germ cells to peri‐implantation embryos

MicroRNAs (miRNAs) are active regulators of numerous biological and physiological processes including most of the events of mammalian reproduction. Understanding the biological functions of miRNAs in the context of mammalian reproduction will allow a better and comparative understanding of fertility and sterility in male and female mammals. Herein, we summarize recent progress in miRNA‐mediated regulation of mammalian reproduction and highlight the significance of miRNAs in different aspects of mammalian reproduction including the biogenesis of germ cells, the functionality of reproductive organs, and the development of early embryos. Furthermore, we focus on the gene expression regulatory feedback loops involving hormones and miRNA expression to increase our understanding of germ cell commitment and the functioning of reproductive organs. Finally, we discuss the influence of miRNAs on male and female reproductive failure, and provide perspectives for future studies on this topic.     

Functional similarity analysis of human virus-encoded miRNAs

miRNAs are a class of small RNAs that regulate gene expression via RNA silencing machinery. Some viruses also encode miRNAs, contributing to the complex virus-host interactions. A better understanding of viral miRNA functions would be useful in designing new preventive strategies for treating diseases induced by viruses. To meet the challenge for how viruses module host gene expression by their encoded miRNAs, we measured the functional similarities among human viral miRNAs by using a method we reported previously. Higher order functions regulated by viral miRNAs were also identified by KEGG pathway analysis on their targets. Our study demonstrated the biological processes involved in virus-host interactions via viral miRNAs. Phylogenetic analysis suggested that viral miRNAs have distinct evolution rates compared with their corresponding genome.     

In vitro analysis of microRNA processing using recombinant Dicer and cytoplasmic extracts of HeLa cells

MicroRNAs (miRNAs) constitute a novel class of short, non-coding RNAs that play crucial roles as silencers of gene expression during biological processes such as development, growth control, cell death, and differentiation. To ensure correct function, the expression of miRNAs must be tightly regulated, a process that is believed to take place at the promoter level. Regulation of the miRNA processing cascade has only recently been shown to play an important role as well and we envision the discovery of additional factors affecting or modulating miRNA processing and ultimately miRNA expression. The biochemical analysis of such factors requires a robust assay to monitor miRNA processing. Here, we discuss protocols and techniques that were used to investigate how the expression of brain-specific miRNA miR-138 is controlled at the level of precursor-miRNA (pre-miRNA) processing.     

MicroRNAs in tomato plants

MicroRNAs (miRNAs) are a specialized class of small silencing RNAs that regulate gene expression in eukaryotes. In plants, miRNAs negatively regulate target mRNAs containing a highly complementary sequence by either mRNA cleavage or translational repression. As a model plant to study fleshy fruit ripening, miRNA studies in tomato have made great progress recently. MiRNAs were predicted to be involved in nearly all biological processes in tomato, particularly development, differentiation, and biotic and abiotic stress responses. Surprisingly, several miRNAs were verified to be involved in tomato fruit ripening and senescence. Recent studies suggest that miRNAs are related to host-virus interactions, which raises the possibility that miRNAs can be used as diagnostic markers for response to virus infection in tomato plants. In this review, we summarize our current knowledge systematically and advance future directions for miRNA research in tomato.