Human microRNA target identification by RRSM

MicroRNAs (miRNAs) are small endogenously expressed non-coding RNAs that regulate target messenger RNAs in various biological processes. In recent years, there have been many studies concentrated on the discovery of new miRNAs and identification of their mRNA targets. Although researchers have identified many miRNAs, few miRNA targets have been identified by actual experimental methods. To expedite the identification of miRNA targets for experimental verification, in the literature approaches based on the sequence or microarray expression analysis have been established to discover the potential miRNA targets. In this study, we focus on the human miRNA target prediction and propose a generalized relative R2 method (RRSM) to find many high-confidence targets. Many targets have been confirmed from previous studies. The targets for several miRNAs discovered by the HITS-CLIP method in a recent study have also been selected by our study.     

miRNA及其靶位点多态性的研究进展

微RNA(microRNA,miRNA)是一类进化上保守、长度为21～23nt的非编码单链小RNA,参与个体发育、器官形成、细胞增殖、分化和细胞凋亡等生物学过程,并在其中发挥重要的调节作用。近年来研究发现,miRNA及其靶位点的多态将引起不同类型的疾患。文章主要从miRNA及其靶位点的多态类型,以及由多态性引起的相关疾病等方面来阐述miRNA的最新进展。     

Mutation in a novel gene SMALL AND CORDATE LEAF 1 affects leaf morphology in cucumber

Plant species exhibit substantial variation in leaf morphology.VWe isolated a recessive mutant gene termed small and cordate leaf 1(sclh)that causes alteration in both leaf size and shape of cucumber.Compared to wild type leaves,the sclh mutant had fewer numbers of epidermal pavement cells.A single nucleotide polymorphism was associated with this leaf phenotype,which occurred in a putative nucleoside bisphosphate phosphatase.RNA-seq analysis of the wild type and sclh mutant leaves suggested that SCL_1 regulation may not involve known hormonal pathways.Our work identified a candidate gene for SCL_1 that may play a role in leaf development.     

Systematic identification of microRNA functions by combining target prediction and expression profiling

Target predictions and validations are major obstacles facing microRNA (miRNA) researchers. Animal miRNA target prediction is challenging because of limited miRNA sequence complementarity to the targets. In addition, only a small number of predicted targets have been experimentally validated and the miRNA mechanism is poorly understood. Here we present a novel algorithm for animal miRNA target prediction. The algorithm combines relevant parameters for miRNA target recognition and heuristically assigns different weights to these parameters according to their relative importance. A score calculation scheme is introduced to reflect the strength of each parameter. We also performed microarray time course experiments to identify downregulated genes due to miRNA overexpression. The computational target prediction is combined with the miRNA transfection experiment to systematically identify the gene targets of human miR-124. miR-124 overexpression led to a significant downregulation of many cell cycle related genes. This may be the result of direct suppression of a few cell growth inhibitors at the early stage of miRNA overexpression, and these targeted genes were continuously suppressed over a long period of time. Our high-throughput approach can be generalized to globally identify the targets and functions of other miRNAs.     

Regulation of angiogenesis by hypoxia: the role of microRNA

Understanding the cellular pathways that regulate angiogenesis during hypoxia is a necessary aspect in the development of novel treatments for cardiovascular disorders. Although the pathways of angiogenesis have been extensively studied, there is limited information on the role of miRNAs in this process. miRNAs or their antagomirs could be used in future therapeutic approaches to regulate hypoxia-induced angiogenesis, so it is critical to understand their role in governing angiogenesis during hypoxic conditions. Although hypoxia and ischemia change the expression profile of many miRNAs, a functional role for a limited number of so-called hypoxamiRs has been demonstrated in angiogenesis. Here, we discuss the best examples that illustrate the role of hypoxamiRs in angiogenesis.     

Identification and characterization of NARROW AND ROLLED LEAF 1, a novel gene regulating leaf morphology and plant architecture in rice

Leaf morphology is an important agronomic trait in rice breeding. We isolated three allelic mutants of NARROW AND ROLLED LEAF 1 (nrl1) which showed phenotypes of reduced leaf width and semi-rolled leaves and different degrees of dwarfism. Microscopic analysis indicated that the nrl1-1 mutant had fewer longitudinal veins and smaller adaxial bulliform cells compared with the wild-type. The NRL1 gene was mapped to the chromosome 12 and encodes the cellulose synthase-like protein D4 (OsCslD4). Sequence analyses revealed single base substitutions in the three allelic mutants. Genetic complementation and over-expression of the OsCslD4 gene confirmed the identity of NRL1. The gene was expressed in all tested organs of rice at the heading stage and expression level was higher in vigorously growing organs, such as roots, sheaths and panicles than in elsewhere. In the mutant leaves, however, the expression level was lower than that in the wild-type. We conclude that OsCslD4 encoded by NRL1 plays a critical role in leaf morphogenesis and vegetative development in rice.     

利用种子序列检测山羊皮肤中microRNA靶基因分子方法的建立

文章旨在建立一种种子序列介导的可控遗传操作—microRNA靶基因指纹图谱(MicroRNA targets fingerprint,MTFP),用于在基因表达检测中筛选与特定microRNA相关的靶基因。在设定上游种子序列的互补序列和下游锚定序列的基础上添加特殊接头,通过反转录和特殊二步PCR将microRNA的靶基因扩增;扩增后的microRNA靶基因在聚丙烯酰胺凝胶电泳中检测其片段大小和表达丰度,用于筛选在不同生理状态或试验条件下特异表达的基因;特定的靶基因序列通过DNA回收和测序方法得到。以miR-203为例,在不同生理状态的山羊皮肤样品中获得了5条大小分别为718 bp(JN709494)、349 bp(JN709495)、243 bp(JN709496)、156 bp(JN709497)和97 bp(JN709498)的靶基因序列。MTFP经济适用、可操作性强,可用于探索microRNA调节的靶基因,或用来评估靶基因的表达谱特征。     

Regulation of microRNA activity in stress

Stressors substantially affect the physiology of cells. Depending on the severity and duration of stress exposure, cells either strive to maintain homeostasis or adapt by adjusting their gene expression patterns. One of the mechanisms to change gene expression is regulating the microRNA (miRNA) levels and activities of microRNA–protein complexes. A fine tuning of the interaction of miRNAs with their mRNA targets determines the specificity of protein synthesis and the quantitative composition of the protein pool in stress. The review considers the mechanisms that regulate miRNA biogenesis, miRNA-mediated mRNA repression, and activity of miRNA–protein complexes in animal cells exposed to various stress factors.     

MicroRNA基因及其靶位点的单核苷酸多态性与疾病易感性

微小RNAs(MicroRNAs)是一类内源性19～25个核苷酸大小的非编码RNA分子,能够通过碱基匹配原则识别并结合于靶基因3'非翻译区的靶位点,从而抑制靶基因的翻译和/或促进靶基因降解。近年许多研究表明,单核苷酸多态性(single nucleotide polymorphisms,SNPs)可影响m icroRNA对靶基因的调控过程。SNPs可发生在m icroRNA基因(指在pri-,pre-and mature-miRNA序列中),也可发生在靶基因的3'非翻译区的靶位点。这些SNPs通过影响microRNA对靶基因的调控过程,参与许多疾病如肿瘤、神经系统疾病、肌肥大、心血管疾病以及2型糖尿病的发生发展过程。本文拟对MicroRNAs及其靶mRNA的结合位点SNPs与疾病的相关研究做一综述。     

SEMI-ROLLED LEAF 10 stabilizes catalase isozyme B to regulate leaf morphology and thermotolerance in rice (Oryza sativa L.)

Plant architecture and stress tolerance play important roles in rice breeding. Specific leaf morphologies and ideal plant architecture can effectively improve both abiotic stress resistance and rice grain yield. However, the mechanism by which plants simultaneously regulate leaf morphogenesis and stress resistance remains elusive. Here, we report that SRL10, which encodes a double-stranded RNA-binding protein, regulates leaf morphology and thermotolerance in rice through alteration of microRNA biogenesis. The srl10 mutant had a semi-rolled leaf phenotype and elevated sensitivity to high temperature. SRL10 directly interacted with catalase isozyme B (CATB), and the two proteins mutually increased one other's stability to enhance hydrogen peroxide (H₂O₂) scavenging, thereby contributing to thermotolerance. The natural Hap3 (AGC) type of SRL10 allele was found to be present in the majority of aus rice accessions, and was identified as a thermotolerant allele under high temperature stress in both the field and the growth chamber. Moreover, the seed-setting rate was 3.19 times higher and grain yield per plant was 1.68 times higher in near-isogenic line (NIL) carrying Hap3 allele compared to plants carrying Hap1 allele under heat stress. Collectively, these results reveal a new locus of interest and define a novel SRL10–CATB based regulatory mechanism for developing cultivars with high temperature tolerance and stable yield. Furthermore, our findings provide a theoretical basis for simultaneous breeding for plant architecture and stress resistance.     

Improving performance of mammalian microRNA target prediction

Background  

MicroRNAs (miRNAs) are single-stranded non-coding RNAs known to regulate a wide range of cellular processes by silencing the gene expression at the protein and/or mRNA levels. Computational prediction of miRNA targets is essential for elucidating the detailed functions of miRNA. However, the prediction specificity and sensitivity of the existing algorithms are still poor to generate meaningful, workable hypotheses for subsequent experimental testing. Constructing a richer and more reliable training data set and developing an algorithm that properly exploits this data set would be the key to improve the performance current prediction algorithms.     

Regulation of cholinergic development by target contact

Avian ciliary ganglion neurons in cell culture have been used as a model neuronal system to examine the developmental role of direct contact with an appropriate target tissue. Live myotubes, which are immediately innervated, and their membrane remnants, on which neurons form terminal structures, were both found to stimulate or accelerate the acquisition or retention of important parameters of neuronal function. Contact with the target membrane supports survival, aids retention of active nicotinic receptors to acetylcholine, and accelerates the acquisition of adult transmitter synthetic capacity. These results emphasize the multifaceted nature of neurodevelopment, with soluble protein factors, membrane-bound elements, and other functional events all acting in concert in the embryonic nervous system.