miRNAs与植物生长发育的调控

miRNAs是microRNAs的简称,是长度约19～25 nt的单链核苷酸片段,它们广泛存在于真核生物中.miRNAs可以调节靶基因的转录和翻译.miRNAs介导调控的靶基因很多都是转录因子.近来发现和鉴定的许多植物miRNAs在植物生长发育中起着关键的调节作用.该文概述了miRNAs的特征、作用机制、参与miRNAs途径的蛋白质、miRNAs途径的突变体、miRNAs介导的植物生长发育调控以及miRNAs与siRNAs途径交互作用的最新研究进展.     

MicroRNAs研究方法与技术

MicroRNAs简称miRNAs(微小RNAs),是真核生物、原核生物以及病毒中由非编码蛋白基因转录的初级microRNAs加工成的调控因子.在转录后水平和蛋白质翻译水平,microRNAs通过降解或翻译抑制甚至激活来调控靶mRNA.实验和计算机方法已应用于microRNAs和靶基因的鉴定.大规模测序技术使得microRNAs在不同物种的多样性分析得以实现.着重介绍microRNAs、靶基因及其功能研究的实验技术和计算机方法,以及基于microRNAs的保守性,借助模式生物中已知的microRNAs,研究其在其他生物中的功能和作用.     

玉米microRNAs及其靶基因的生物信息学预测

microRNAs (miRNAs) 是一类非编码的小分子RNA, 通过碱基互补调控靶基因的表达。鉴定和发现新的miRNAs及其靶基因, 对揭示miRNAs在基因表达调控中的作用至关重要。玉米全基因组测序工作开展较晚, 已经鉴定登记的miRNAs很少, 对靶基因的调控作用尚待解明。文章根据miRNA进化上的保守性, 以已知的植物miRNAs为探针, 与相关数据库中玉米表达序列标签(EST)和基因组序列(GSS)中的非编码序列比对, 共发现11个新的miRNA前体。虽然在序列长度和二级结构方面各有变化, 但这11个前体均可折叠形成miRNA家族的标准二级结构。通过靶基因预测, 找到其中7条miRNAs的26个靶基因, 分别编码与新陈代谢、信号转导、转录调节、跨膜运输、生物和非生物胁迫及叶绿体组装等相关的蛋白。这些miRNAs及其靶基因的鉴定, 补充了miRNA数据库的不足。     

植物microRNAs在植物发育和非生物胁迫响应中的作用

microRNAs(miRNAs)是一类内源的长度约为22个核苷酸的非编码小分子RNA,其通过对靶基因mRNA进行切割或翻译抑制调节mRNA的表达,在植物中起到重要的作用.主要介绍了植物miRNAs的特征、合成和作用机制,综述了miRNAs在植物生长发育和非生物胁迫响应中的作用.     

植物microRNAs研究进展

植物microRNAs(miRNAs)是一类与RNA诱导沉默复合体相关的约由22个核苷酸组成的单链小RNA分子, 其主要功能是, 通过特异性剪切靶mRNA或阻遏靶mRNA的正常翻译在转录后水平调控基因的负表达。植物miRNAs的靶标主要是参与调控植物生长发育和防御应答的转录因子家族。文章主要综述miRNAs在植物体内的生物发生、作用机制及其调控作用研究新进展。     

基于数据挖掘分析microRNAs在冠状动脉支架内再狭窄中的调控机制

目的:通过寻找支架内再狭窄相关的循环microRNAs(miRNAs)及其作用靶基因,阐释miRNAs在经皮冠状动脉介入治疗的同时带来的支架内再狭窄(ISR)中的网络调控作用及机制。方法:由美国NCBI的GEO公共数据平台下载GSE60959中的miRNAs芯片数据,通过GeneSpringGX芯片分析软件分析得到ISR患者和对照组之间差异表达的循环miRNAs;采用miRNAs靶基因预测算法TargetScan和miRanda预测差异表达miRNAs的靶基因,通过DAVID平台和KEGG数据库分析得到靶基因所参与的信号通路;用GSE46560的mRNA芯片数据分析得到ISR患者较非ISR患者循环mRNAs差异表达谱,用来验证miRNAs调控ISR所作用的靶基因;采用Cytoscape软件构建基于miRNAs-信号通路、miRNAs-靶基因的共表达网络。结果:与对照组相比,ISR组存在131个差异表达循环miRNAs,其中上调41个。前5个上调miRNAs分别是miR-1183、miR-512-5p、miR-187-5p、miR-144-3p和miR-1225-5p。5个miRNAs的预测靶基因共6587个,信号通路富集分析显示这些基因主要参与的信号通路包括MAPK signaling pathway、ErbB signaling pathway、Wnt signaling pathway、Focal adhesion、Neurotrophin signaling pathway和Regulation of actin cytoskeleton。进一步对mRNAs芯片进行差异分析显示,与对照组相比,ISR患者差异循环mRNAs共171个,其中最可能受上述5个miRNAs调控的基因共43个。构建的共表达网络显示,miR-512-5p是作用靶基因和参与信号通路最多的miRNAs。结论:ISR患者循环miRNAs和mRNAs表达谱均存在改变,多个差异表达miRNAs通过作用于多个靶mRNAs,进而影响多个信号通路的活性,最终对ISR的发生、发展形成网络调控作用。     

茄子microRNAs与其靶基因的生物信息学预测

microRNAs(miRNAs)是一类在真核生物中发现的长度为21 nt左右、非编码、内源性的单链小分子RNA,通过与靶基因的互补发挥转录后水平的负调控作用。目前,已在许多物种中报道了miRNAs的存在,然而还未见关于茄子miRNAs的报道。根据miRNAs在植物中的高度保守性及其前体的二级结构特征,文章通过同源预测的方法,将已知植物的miRNAs与茄子EST数据库比对,经过一系列的筛选,最终预测到12个家族的16条茄子miRNAs,其中包括3个miRNA家族的正义/反义miRNAs,而miR390和miR399家族的正义/反义miRNAs属于第一次发现。文章还通过在线软件psRNATarget预测到15条茄子miRNAs的71个靶基因,这些靶基因主要编码与茄子生长发育、新陈代谢以及胁迫响应等过程相关的蛋白。     

内皮相关性miRNAs与内皮功能及心血管疾病研究进展

血管内皮细胞(vascular endothelial cells,VEC)功能改变对心血管疾病的发生与发展起着重要的作用。新近研究显示,一些microRNAs(miRNAs)特异性表达于VEC,并参与调控内皮功能相关性心血管疾病的病理过程,这些miRNAs被定义为内皮型miRNAs。对这类miRNAs的进一步研究包括其在内皮组织中的鉴定、靶基因分析以及对某些重大心血管疾病(如高血压、心肌梗塞)的病理生理学意义都有助于相关疾病的诊治以及潜在新型分子药物应用。     

microRNA层面上癌症的公共机制

microRNAs(miRNA)是一类内源性的非编码小RNA。已有研究表明miRNAs的靶基因中有不少癌症的相关基因。为了全面研究miRNA与癌症的关系,作者将19种癌症的相关基因集合分别富集到494个miRNAs靶基因集合上,得到各类癌症所富集的miRNAs。结果发现19种癌症仅集中地富集在144个miRNAs上,由此验证了癌症在miRNAs上的公共机制。在此基础上,作者对癌症富集较多的8个miRNAs做了进一步研究,结果发现这8个miRNAs均为高度保守的miRNAs,且它们的靶基因集合一致富集在基因本体论(gene ontology,GO)的基本生物学过程上,并与转录因子活性以及蛋白激酶活性相关。另一方面,在基于miRNA构建的癌症网络中,前列腺癌与乳腺癌,结肠癌与乳腺癌之间共享较多的miRNAs,表明了这些癌症在miRNA层面上存在密切的关系。     

哺乳动物乳汁miRNA的研究进展

作为真核生物体内重要的调控分子,miRNA可存在于包括血清、血浆、唾液、尿液在内的多种动物体液之中。最近的研究表明哺乳动物的乳汁中也分泌miRNA,表明miRNA有可能通过哺乳传递给新生个体,从而调控新生个体发育过程中的某些关键生理、生化途径,协助其正常发育。这一发现很可能揭开了哺乳动物世代间miRNA进行功能基因表达调控的研究序幕。文章对哺乳动物乳汁中miRNA的发现过程,这些miRNA在乳汁中的存在形态及其分离技术,以及其中数个重要miRNA的已知功能作简要概述,并探讨了相关的后续研究任务及其面临的挑战。     

Identification of miRNAs and Their Target Genes Using Deep Sequencing and Degradome Analysis in Trifoliate Orange [<Emphasis Type="Italic">Poncirus trifoliate</Emphasis> (L.) Raf]

To identify novel as well as conserved miRNAs in citrus, deep sequencing of small RNA library combined with microarray was performed in precocious trifoliate orange (an early flowering mutant of trifoliate orange, Poncirus trifoliata L. Raf.), resulting in the obtainment of a total of 114 conserved miRNAs belonging to 38 families and 155 novel miRNAs. The miRNA star sequences of 39 conserved miRNAs and 27 novel miRNAs were also discovered among newly identified miRNAs, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 172 and 149 genes were identified as targets of conserved miRNAs and novel miRNAs, respectively. GO and KEGG annotation revealed that high ranked miRNA-target genes were those implicated in biological and metabolic processes. To characterize those miRNAs expressed at the juvenile and adult development stages of citrus, further analysis on the expression profiles of these miRNAs through hybridizing the commercial microarray and real-time PCR was performed. The results revealed that some miRNAs were down-regulated at adult stage compared with juvenile stage. Detailed comparison of the expression patterns of some miRNAs and corresponding target genes revealed the negative correlation between them, while few of them are positively correlated.     

Whole miRNome-wide Differential Co-expression of MicroRNAs

Co-regulation of genes has been extensively analyzed, however, rather limited knowledge is available on co-regulations within the miRNome. We investigated differential co-expression of microRNAs (miRNAs) based on miRNome profiles of whole blood from 540 individuals. These include patients suffering from different cancer and non-cancer diseases, and unaffected controls. Using hierarchi-cal clustering, we found 9 significant clusters of co-expressed miRNAs containing 2-36 individual miRNAs. Through analyzing multiple sequencing alignments in the clusters, we found that co-expression of miRNAs is associated with both sequence similarity and genomic co-localization. We calculated correlations for all 371,953 pairs of miRNAs for all 540 individuals and identified 184 pairs of miRNAs with high correlation values. Out of these 184 pairs of miRNAs, 16 pairs (8.7%) were differentially co-expressed in unaffected controls, cancer patients and patients with non-cancer diseases. By computing correlated and anti-correlated miRNA pairs, we constructed a network with 184 putative co-regulations as edges and 100 miRNAs as nodes. Thereby, we detected specific clusters of miRNAs with high and low correlation values. Our approach represents the most comprehensive co-regulation analysis based on whole miRNome-wide expression profiling. Our findings further decrypt the interactions of miRNAs in normal and human pathological processes.     

Solexa sequencing identification of conserved and novel microRNAs in backfat of Large White and Chinese Meishan pigs

The domestic pig (Sus scrofa), an important species in animal production industry, is a right model for studying adipogenesis and fat deposition. In order to expand the repertoire of porcine miRNAs and further explore potential regulatory miRNAs which have influence on adipogenesis, high-throughput Solexa sequencing approach was adopted to identify miRNAs in backfat of Large White (lean type pig) and Meishan pigs (Chinese indigenous fatty pig). We identified 215 unique miRNAs comprising 75 known pre-miRNAs, of which 49 miRNA*s were first identified in our study, 73 miRNAs were overlapped in both libraries, and 140 were novelly predicted miRNAs, and 215 unique miRNAs were collectively corresponding to 235 independent genomic loci. Furthermore, we analyzed the sequence variations, seed edits and phylogenetic development of the miRNAs. 17 miRNAs were widely conserved from vertebrates to invertebrates, suggesting that these miRNAs may serve as potential evolutional biomarkers. 9 conserved miRNAs with significantly differential expressions were determined. The expression of miR-215, miR-135, miR-224 and miR-146b was higher in Large White pigs, opposite to the patterns shown by miR-1a, miR-133a, miR-122, miR-204 and miR-183. Almost all novel miRNAs could be considered pig-specific except ssc-miR-1343, miR-2320, miR-2326, miR-2411 and miR-2483 which had homologs in Bos taurus, among which ssc-miR-1343, miR-2320, miR-2411 and miR-2483 were validated in backfat tissue by stem-loop qPCR. Our results displayed a high level of concordance between the qPCR and Solexa sequencing method in 9 of 10 miRNAs comparisons except for miR-1a. Moreover, we found 2 miRNAs, miR-135 and miR-183, may exert impacts on porcine backfat development through WNT signaling pathway. In conclusion, our research develops porcine miRNAs and should be beneficial to study the adipogenesis and fat deposition of different pig breeds based on miRNAs.     

The microRNA expression profiles of mouse mesenchymal stem cell during chondrogenic differentiation

MicroRNAs are potential key regulators in mesenchymal stem cells chondrogenic differentiation. However, there were few reports about the accurate effects of miRNAs on chondrogenic differentiation. To investigate the mechanisms of miRNAs-mediated regulation during the process, we performed miRNAs microarray in MSCs at four different stages of TGF-β3-induced chondrogenic differentiation. We observed that eight miRNAs were significantly up-regulated and five miRNAs were downregulated. Interestingly, we found two miRNAs clusters, miR-143/145 and miR-132/212, kept on down-regulation in the process. Using bioinformatics approaches, we analyzed the target genes of these differentially expressed miRNAs and found a series of them correlated with the process of chondrogenesis. Furthermore, the qPCR results showed that the up-regulated (or down-regulated) expression of miRNAs were inversely associated with the expression of predicted target genes. Our results first revealed the expression profiles of miRNAs in chondrogenic differentiation of MSCs and provided a new insight on complicated regulation mechanisms of chondrogenesis.