MicroRNA enrichment among short 'ultraconserved' sequences in insects

MicroRNAs are short (approximately 22 nt) regulatory RNA molecules that play key roles in metazoan development and have been implicated in human disease. First discovered in Caenorhabditis elegans, over 2500 microRNAs have been isolated in metazoans and plants; it has been estimated that there may be more than a thousand microRNA genes in the human genome alone. Motivated by the experimental observation of strong conservation of the microRNA let-7 among nearly all metazoans, we developed a novel methodology to characterize the class of such strongly conserved sequences: we identified a non-redundant set of all sequences 20 to 29 bases in length that are shared among three insects: fly, bee and mosquito. Among the few hundred sequences greater than 20 bases in length are close to 40% of the 78 confirmed fly microRNAs, along with other non-coding RNAs and coding sequence.     

An analysis of human microRNA and disease associations

It has been reported that increasingly microRNAs are associated with diseases. However, the patterns among the microRNA-disease associations remain largely unclear. In this study, in order to dissect the patterns of microRNA-disease associations, we performed a comprehensive analysis to the human microRNA-disease association data, which is manually collected from publications. We built a human microRNA associated disease network. Interestingly, microRNAs tend to show similar or different dysfunctional evidences for the similar or different disease clusters, respectively. A negative correlation between the tissue-specificity of a microRNA and the number of diseases it associated was uncovered. Furthermore, we observed an association between microRNA conservation and disease. Finally, we uncovered that microRNAs associated with the same disease tend to emerge as predefined microRNA groups. These findings can not only provide help in understanding the associations between microRNAs and human diseases but also suggest a new way to identify novel disease-associated microRNAs.     

Expanding roles for miRNAs and siRNAs in cell regulation

The role of small RNAs as key regulators of mRNA turnover and translation has been well established. Recent advances indicate that the small RNAs termed microRNAs play important roles in cell proliferation, apoptosis and differentiation. Moreover, the microRNA mechanism is an efficient means to regulate production of a diverse range of proteins. As new microRNAs and their mRNA targets rapidly emerge, it is becoming apparent that RNA-based regulation of mRNAs may rival ubiquitination as a mechanism to control protein levels.     

Human papillomavirus genotype 31 does not express detectable microRNA levels during latent or productive virus replication

It has recently become clear that several pathogenic DNA viruses express virally encoded microRNAs in infected cells. In particular, numerous microRNAs have been identified in a range of human and animal herpesviruses, and individual microRNAs have also been identified in members of the polyoma- and adenovirus families. Although their functions remain largely unknown, it seems likely that these viral microRNAs play an important role in viral replication in vivo. Here we present an analysis of the microRNAs expressed in human cells during the latent and productive phases of the human papillomavirus genotype 31 (HPV31) replication cycle. Although over 500 cellular microRNAs were cloned and identified, not a single HPV31-specific microRNA was obtained. We therefore concluded that HPV31, and possibly human papillomaviruses in general, does not express viral microRNAs.     

MicroRNA functions in animal development and human disease

Five years into the 'small RNA revolution' it is hard not to share in the excitement about the rapidly unravelling biology of microRNAs. Since the discovery of the first microRNA gene, lin-4, in the nematode Caenorhabditis elegans, many more of these short regulatory RNA genes have been identified in flowering plants, worms, flies, fish, frogs and mammals. Currently, about 2% of the known human genes encode microRNAs. MicroRNAs are essential for development and this review will summarise our current knowledge of animal microRNA function. We will also discuss the emerging links of microRNA biology to stem cell research and human disease, in particular cancer.     

Computational identification of microRNA targets

Recent experiments have shown that the genomes of organisms such as worm, fly, human, and mouse encode hundreds of microRNA genes. Many of these microRNAs are thought to regulate the translational expression of other genes by binding to partially complementary sites in messenger RNAs. Phenotypic and expression analysis suggests an important role of microRNAs during development. Therefore, it is of fundamental importance to identify microRNA targets. However, no experimental or computational high-throughput method for target site identification in animals has been published yet. Our main result is a new computational method that is designed to identify microRNA target sites. This method recovers with high specificity known microRNA target sites that have previously been defined experimentally. Based on these results, we present a simple model for the mechanism of microRNA target site recognition. Our model incorporates both kinetic and thermodynamic components of target recognition. When we applied our method to a set of 74 Drosophila melanogaster microRNAs, searching 3'UTR sequences of a predefined set of fly mRNAs for target sites which were evolutionary conserved between D. melanogaster and Drosophila pseudoobscura, we found that many key developmental body patterning genes such as hairy and fushi-tarazu are likely to be translationally regulated by microRNAs.     

转基因动物在microRNA研究中的应用

MicroRNA是一类在转录后水平上调节基因表达的非编码小分子RNA,在生物体生理、病理等过程中发挥重要作用．MicroRNA功能的研究将是未来人们关注的焦点．通过转基因技术建立的多种动物模型在整体水平揭示了基因的功能．近年,以microRNA为研究对象的转基因动物模型数量不断增加,构建策略不断丰富．通过miRNA过表达、敲除及敲减等手段已揭示了miRNA在肿瘤、心血管系统疾病等多方面的作用．转基因动物正成为microRNA研究中不可或缺的工具．     

Micromanagers of malignancy: role of microRNAs in regulating metastasis

It has become evident that cancer pathogenesis involves, among other macromolecules, a class of small regulatory RNAs named microRNAs, and that microRNA expression profiles are associated with prognosis and therapeutic outcome in several human cancers. Although the oncogenic or tumor-suppressing functions of several microRNAs have been characterized, the mechanistic roles played by microRNAs specifically in mediating metastasis have been addressed only recently. In this review, we focus on our emerging understanding of the contributions of microRNAs to malignant progression, specifically their functions in mediating tumor invasion and metastasis. These findings illuminate the molecular basis of metastasis and begin to connect small-RNA discoveries to the development of novel clinical biomarkers and therapeutic targets in neoplastic diseases.     

转录因子与microRNA在基因表达调控中的功能联系及差异

转录因子和微RNA(microRNA)是最大的两类反式作用因子,它们是基因表达调控的重要调控因子.它们协调发挥调控作用,精细调控基因的表达,在细胞分化和动物生长发育过程中发挥重要的作用.随着对转录因子和microRNA研究的深入,人们发现转录因子和microRNA在基因表达调控网络中关系紧密,它们的分子作用机制有许多相似之处,两者都通过各自的顺式作用元件调控基因表达,且作用的方式类似.但转录因子和microRNA也存在不同之处,转录因子既可以激活基因表达,也可抑制基因表达,而microRNA主要是抑制基因表达.另外,转录因子调控区的复杂性一般高于microRNA的调控区域.本文综述了转录因子和microRNA的异同点,并提出了未来转录因子和microRNA的研究方向.     

Riboregulators in kidney development and function

The discovery of microRNAs has brought in another level of intricacy in gene regulation. These microRNAs are small non-coding RNAs that have dual ability to act as repressors or inducers of gene activity. MicroRNAs have been implicated in a wide spectrum of biological processes and their expressions have been found to be dysregulated in several diseases. Recently, microRNAs have emerged as a new area of interest in renal development and pathology. MicroRNA profilings have revealed a number of microRNAs that are specific to the kidney or restricted to certain regions of the organ suggesting possible exclusive roles therein. Recently, knockout studies have shown that these riboregulators are critical for normal renal growth and functional renal system. Individual microRNAs have also been identified in renal disease models including kidney cancers, diabetic nephropathy and polycystic kidney disease. Several mechanisms of modulating microRNA activity have also been introduced in recent years. Further progress in the understanding of microRNA activity, identification of microRNA signatures in different states as well as advancement of microRNA manipulation techniques will be valuable for kidney research.     

MicroRNA control of myelopoiesis and the differentiation block in acute myeloid leukaemia

In the relatively short period of time since their discovery, microRNAs have been shown to control many important cellular functions such as cell differentiation, growth, proliferation and apoptosis. In addition, microRNAs have been demonstrated as key drivers of many malignancies and can function as either tumour suppressors or oncogenes. The haematopoietic system is not outside the realm of microRNA control with microRNAs controlling aspects of stem cell and progenitor self-renewal and differentiation, with many, if not all, haematological disorders associated with aberrant microRNA expression and function. In this review, we focus on the current understanding of microRNA control of haematopoiesis and detail the evidence for the contribution and clinical relevance of aberrant microRNA function to the characteristic block of differentiation in acute myeloid leukaemia.     

植物发育与microRNA

microRNA为动、植物的一类内源、非编码小分子RNA,其长度约为23nt,对动、植物的发育具有非常重要的调节作用.microRNA作为调节类的核酸分子,通过识别和负调控靶基因来行使其生物学功能,多数microRNA的表达具有时空特异性,它们对植物的发育有多向性调节,在发育的多个层面具有重要的功能,有些microRNA的调节作用还要受到外因的诱导.该文对近年来国内外有关microRNA在植物发育过程中的功能及其研究进展进行综述.     

MicroRNAs: Crucial multi-tasking components in the complex circuitry of tumor metastasis

Distant metastases are the underlying cause of patient mortality in an overwhelming majority of human carcinomas. Certain microRNAs have recently been found capable of regulating the process of tumor metastasis. In this review, we highlight recent advances within this rapidly emerging field, endeavor to connect known microRNA pathways with recent conceptual advances in the larger field of metastasis research, and speculate regarding the future utility of microRNAs in the diagnosis and treatment of human cancers. Assessed collectively, current evidence suggests that the pleiotropic activities of microRNAs endow them with the capacity to function as crucial, yet previously unappreciated, nodes within already-identified metastasis regulatory circuitry. This has important implications for our understanding of the pathogenesis of high-grade malignancies.     

MicroRNA在肿瘤发生发展和诊断中作用的研究进展

microRNA是一类由内源基因编码的长度约为18-25个核苷酸的非编码单链RNA分子,可以与靶基因mRNA的3'非编码区结合,通过降解靶m RNA或(和)抑制靶m RNA转录后翻译调节靶蛋白的生成,从而发挥其生物学作用。目前,在人体基因组内发现的microRNA已经超过2500多个,可能调节着人类1/3的基因,在维持正常干细胞功能、调控细胞增殖分化及恶性肿瘤发生过程中均起重要作用。既往的研究表明microRNA与基因之间相互调控的失衡导致肿瘤的发生。从分子水平上研究microRNA与肿瘤发生的关系,检测microRNA与肿瘤相关基因表达情况的改变,分析肿瘤组织和血清中microRNA表达量与肿瘤分型的关系,将有利于肿瘤的病因学研究,早期发现和肿瘤治疗及预后判断。本文主要就microRNA在肿瘤发生发展和诊断中作用的研究进展进行了综述。     

Altered microRNA expression in human heart disease.

MicroRNAs are recently discovered regulators of gene expression and are becoming increasingly recognized as important regulators of heart function. Genome-wide profiling of microRNAs in human heart failure has not been reported previously. We measured expression of 428 microRNAs in 67 human left ventricular samples belonging to control (n = 10), ischemic cardiomyopathy (ICM, n = 19), dilated cardiomyopathy (DCM, n = 25), or aortic stenosis (AS, n = 13) diagnostic groups. miRNA expression between disease and control groups was compared by ANOVA with Dunnett's post hoc test. We controlled for multiple testing by estimating the false discovery rate. Out of 428 microRNAs measured, 87 were confidently detected; 43 were differentially expressed in at least one disease group. In supervised clustering, microRNA expression profiles correctly grouped samples by their clinical diagnosis, indicating that microRNA expression profiles are distinct between diagnostic groups. This was further supported by class prediction approaches, in which the class (control, ICM, DCM, AS) predicted by a microRNA-based classifier matched the clinical diagnosis 69% of the time (P < 0.001). These data show that expression of many microRNAs is altered in heart disease and that different types of heart disease are associated with distinct changes in microRNA expression. These data will guide further studies of the contribution of microRNAs to heart disease pathogenesis.