鸡mir-17-92基因簇的结构、功能及其调控

mir-17-92基因簇(mir-17-92 cluster)是脊椎动物的一个保守miRNA基因簇,在哺乳动物细胞增殖、分化、凋亡及发育等多种生物学过程中起重要的调控作用.同时,mir- 17-92基因簇又是一个癌基因,在多种肿瘤中表达.尽管对mir-17-92基因簇的研究非常广泛,但其作用机制还不完全清楚.鸡mir- 17-92基因簇的结构组成特点、功能及其作用机制尚未见研究报道.该文根据同一miRNA基因簇的miRNAs在功能上相关的特点,以鸡mir- 17-92基因簇序列为研究对象,采用生物信息学研究方法和手段,开展了鸡mir- 17-92基因簇的基因组结构、miRNAs序列组成、靶生物学过程和信号通路以及miRNAs结合位点分布特点等分析研究.结果发现,鸡mir- 17-92基因簇调控MAPK、Wnt和TGF-β等多个重要细胞信号通路;miRNA结合位点分布分析显示,该miRNA基因簇多个成员共同作用于同一个靶基因,提示该基因簇的miRNAs成员以组合和协同的方式调控靶基因.该研究为深入了解mir-17-92基因簇如何调控癌症和发育中的关键细胞过程奠定了基础.     

固始鸡1日龄和36周龄下丘脑高丰度差异性MiRNA的鉴定及功能预测分析

为鉴定鸡下丘脑发育相关特异性表达miRNA,基于固始鸡1日龄和36周龄下丘脑小RNA的Solexa测序数据,共鉴定到266种2个发育阶段共表达的miRNA,其中157种miRNA的表达水平被显著下调,22种被显著上调.聚类分析显示,鸡下丘脑高丰度差异性miRNA主要集中于let-7、mir-181、mir-30、mir-99、mir-1和mir-17等基因家族.另外,预测了10种高丰度差异性miRNA的靶基因,并进行了相应的GO分析和KEGG通路分析.结果显示,预测靶基因在发育过程、代谢过程、细胞过程和生物学过程调节等4个生物学过程以及细胞周期、粘着斑、TGF-beta信号通路和MAPK信号通路等通路中显著富集.研究结果为进一步揭示miRNA调控鸡下丘脑发育的分子机制提供了有益线索.     

植物miRNA参与调控作物农艺性状的研究进展

植物microRNA (miRNA)是一类长度约为20～24 nt的内源非编码小RNA,它们通过在转录后水平调控靶基因的表达,在植物的生长发育、逆境响应和环境适应等过程中起着关键作用. miRNA对水稻、玉米、大豆等重要经济作物的农艺性状也起着重要的调控作用,在改良农作物性状上具有重大的应用潜能.本文重点介绍了参与作物农艺性状(如株型、花期、种子发育及抗逆等)调控的关键miRNA及其调控途径,同时总结了miRNA参与作物性状改良的主要研究方法和手段,并讨论了miRNA在作物性状改良应用中的前景.     

DNA甲基化与microRNA

细胞中DNA甲基化和microRNA（miRNA）相互影响,并共同调控着下游靶基因的表达活性,在细胞生长代谢、免疫、肿瘤和心血管疾病等生理和病理过程中发挥重要作用。首先简要介绍DNA甲基化与miRNA的概况,然后分析了miRNA调控下的DNA甲基化改变,探讨了DNA甲基化影响miRNA的表达活性变化,并归纳了miRNA与DNA甲基化之间的反馈调控关系;最后对DNA甲基化和miRNA的应用前景进行了简单探讨。研究DNA甲基化与miRNA间的网络调控关系,可为表观调控机制在理论和实践中的深入研究和应用提供参考。     

miRNA在冠心病诊断和治疗中的研究进展

miRNA是一类长度为18~22 nt的非编码小RNA,可通过影响靶mRNA的翻译,对靶基因表达进行调控.最新研究表明,miRNA在冠心病的发生发展中起重要的调控作用,本文将对与冠心病密切联系的miRNA相关研究及miRNA干扰技术在冠心病治疗方面的研究进展进行综述,以探讨miRNA在冠心病等疾病诊断和治疗的应用前景.     

miRNA对水稻生长发育的调控

MicroRNA(miRNA)是一类小的非编码RNA,它们主要在转录后水平对靶mRNA进行切割或抑制mRNA的翻译来调控基因的表达. miRNA通过对靶基因的调控参与植物的生长发育、胁迫应答和代谢过程.在水稻中,已经发现并初步验证了许多与生长发育相关的miRNA,它们对水稻不同器官和形态发育发挥着重要作用.本文综述了水稻miRNA的发生和调控机制、靶基因的预测,重点介绍了miRNA对水稻生长发育和形态建成的研究进展,并对研究过程中存在的问题进行了讨论.为更好地了解miRNA及其靶基因在提高水稻产量和品质方面的作用,进一步解析miRNA在水稻中的调控机制提供参考.     

人类基因组miRNA转录调控区保守性DNA序列生物信息学分析

MicroRNA(miPNA)的表达调控方式一直是一个有争议的问题,为了研究miRNA潜在的转录调控特点,本文通过Sanger网站miRNA数据库获得人类miRNA的信息,并建立miRNA相关信息数据库,用MEME和Wordspy两个软件对其上游2 000 bp序列进行保守性分析,得到保守性的DNA序YU(motif),用TESS软件分析保守性DNA序列,预测其转录因子结合情况.通过比较位于基因间、反义链和内含子中的三类不同miRNA转录调控区的保守性和自主转录能力的差异,结果发现位于基因间、反义链上的miRNA上游调控区的保守性比位于内含子的miRNA高,在miRNA的转录调控区存在RNA聚合酶Ⅱ类型的转录因子结合位点,miRNA还表现出自身独特的转录调控方式.通过分析,我们还得到了miRNA表达调控中一些重要的转录因子以及独特的调控序列.本研究结果为miRNA转录调控机制的进一步研究提供了理论依据.     

microRNAs相关新型调控技术与疾病治疗

MicroRNA（miRNA）是一类在进化中高度保守的非编码小分子单链RNA(19～25 nt）,在转录后水平调控中发挥重要作用. 越来越多的证据表明,miRNA广泛参与了机体生长发育、细胞增殖与凋亡等多种重要的生理过程,并在病毒感染、恶性肿瘤、心血管与内分泌疾病等多种病理状态下呈异常表达,影响许多疾病的发生、发展及预后. 对miRNA的表达水平进行可控性干预可能成为一种有效的治疗手段. 本文综述了目前用于干预miRNA水平的调控技术,以及疾病治疗相关给药系统的研究进展,提示miRNA相关新型调控技术具有较为广阔的临床应用前景.     

miRNA调控药用植物生长发育和次生代谢

microRNA(miRNA)作为一类内源性的短链非编码RNA,广泛存在于真核细胞中,主要通过对转录本剪切和抑制翻译等方式,参与转录后基因的表达调控。近年来研究表明,多种药用植物中鉴定出大量的miRNA。这些miRNA对药用植物的生长发育和次生代谢产物合成具有调控功能。次生代谢产物是药用植物的主要有效成分,研究miRNA对药用植物次生代谢过程的调控作用具有十分重要的意义。本文综述了miRNA在植物中的产生途径、作用方式和体内功能,在此基础上重点介绍了miRNA对药用植物生长发育和次生代谢产物生物合成的调控作用,并对药用植物miRNA的研究进行了展望,以期为提高药用植物产量,高效获得药用植物有效成分以及临床应用开拓新的思路。     

乳腺癌增强子-miRNA调控网络识别与分析

乳腺癌发病率位列女性恶性肿瘤之首.先前研究表明增强子可通过调控miRNA影响肿瘤的发生发展.然而,增强子与miRNA在乳腺癌中形成何种调控网络目前尚不清楚.为了探究乳腺癌中增强子与miRNA形成的调控网络,通过分析 112个乳腺浸润癌样本和104个正常组织样本,共识别了 220对增强子-miRNA调控关系,其中包括22...     

MicroRNA profiling in the bursae of Marek's disease virus-infected resistant and susceptible chicken lines

Marek's disease (MD) is a lymphoproliferative disease of domestic chickens caused by a cell-associated oncogenic alpha-herpesvirus, Marek's disease virus (MDV). Clinical signs of MD include bursal/thymic atrophy, neurologic disorders, and T cell lymphomas. MiRNAs play key roles in regulation of gene expression by targeting translational suppression or mRNA degradation. MDV encodes miRNAs that are associated with viral pathogenicity and oncogenesis. In this study, we performed miRNA sequencing in the bursal tissues, non-tumorous but viral-induced atrophied lymphoid organ, from control and infected MD-resistant and susceptible chickens at 21 days post infection. In addition to some known miRNAs, a minimum of 300 novel miRNAs were identified in each group that mapped to the chicken genome with no sequence homology to existing miRNAs in chicken miRbase. Comparative analysis identified 54 deferentially expressed miRNAs between the chicken lines that might shed light on underlying mechanism of bursal atrophy and resistance or susceptibility to MD.     

Integrated analysis of microRNA expression and mRNA transcriptome in lungs of avian influenza virus infected broilers

ABSTRACT: BACKGROUND: Avian influenza virus (AIV) outbreaks are worldwide threats to both poultry and humans. Our previous study suggested microRNAs (miRNAs) play significant roles in the regulation of host response to AIV infection in layer chickens. The objective of this study was to test the hypothesis if genetic background play essential role in the miRNA regulation of AIV infection in chickens and if miRNAs that were differentially expressed in layer with AIV infection would be modulated the same way in broiler chickens. Furthermore, by integrating with parallel mRNA expression profiling, potential molecular mechanisms of host response to AIV infection can be further exploited. RESULTS: Total RNA isolated from the lungs of non-infected and low pathogenic H5N3 infected broilers at four days post-infection were used for both miRNA deep sequencing and mRNA microarray analyses. A total of 2.6M and 3.3M filtered high quality reads were obtained from infected and non-infected chickens by Solexa GA-I Sequencer, respectively. A total of 271 miRNAs in miRBase 16.0 were identified and one potential novel miRNA was discovered. There were 121 miRNAs differentially expressed at the 5% false discovery rate by Fisher's exact test. More miRNAs were highly expressed in infected lungs (108) than in non-infected lungs (13), which was opposite to the findings in layer chickens. This result suggested that a different regulatory mechanism of host response to AIV infection mediated by miRNAs might exist in broiler chickens. Analysis using the chicken 44K Agilent microarray indicated that 508 mRNAs (347 down-regulated) were differentially expressed following AIV infection. CONCLUSION: A comprehensive analysis combining both miRNA and targeted mRNA gene expression suggests that gga-miR-34a, 122-1, 122-2, 146a, 155, 206, 1719, 1594, 1599 and 451, and MX1, IL-8, IRF-7, TNFRS19 are strong candidate miRNAs or genes involved in regulating the host response to AIV infection in the lungs of broiler chickens. Further miRNA or gene specific knock-down assay is warranted to elucidate underlying mechanism of AIV infection regulation in the chicken.     

Solexa sequencing analysis of chicken pre-adipocyte microRNAs

MicroRNAs (miRNAs) are small non-coding RNAs that play important roles in a variety of biological processes. Studies of miRNAs in mammals suggest that many are involved in lipid metabolism and adipocyte differentiation, but little is known about miRNA expression profiles during chicken adipogenesis. In this study, the Solexa sequencing approach was used to sequence a small RNA library prepared from Arbor Acres broiler pre-adipocytes, and more than 10? short sequence reads were obtained. From these, 159 known chicken miRNAs and 63 novel miRNAs were identified using a bioinformatics approach. Fifty-nine of these miRNA genes were further organized into 27 compact miRNA genomic clusters, and 34 new chicken mirtrons were also discovered, among which there were 27 mirtron candidates. These findings should serve as a foundation for future research on the functional roles of miRNAs in chicken adipocyte differentiation.     

Growth Hormone-Regulated mRNAs and miRNAs in Chicken Hepatocytes

Growth hormone (GH) is a key regulatory factor in animal growth, development and metabolism. Based on the expression level of the GH receptor, the chicken liver is a major target organ of GH, but the biological effects of GH on the chicken liver are not fully understood. In this work we identified mRNAs and miRNAs that are regulated by GH in primary hepatocytes from female chickens through RNA-seq, and analyzed the functional relevance of these mRNAs and miRNAs through GO enrichment analysis and miRNA target prediction. A total of 164 mRNAs were found to be differentially expressed between GH-treated and control chicken hepatocytes, of which 112 were up-regulated and 52 were down-regulated by GH. A total of 225 chicken miRNAs were identified by the RNA-Seq analysis. Among these miRNAs 16 were up-regulated and 1 miRNA was down-regulated by GH. The GH-regulated mRNAs were mainly involved in growth and metabolism. Most of the GH-upregulated or GH-downregulated miRNAs were predicted to target the GH-downregulated or GH-upregulated mRNAs, respectively, involved in lipid metabolism. This study reveals that GH regulates the expression of many mRNAs involved in metabolism in female chicken hepatocytes, which suggests that GH plays an important role in regulating liver metabolism in female chickens. The results of this study also support the hypothesis that GH regulates lipid metabolism in chicken liver in part by regulating the expression of miRNAs that target the mRNAs involved in lipid metabolism.     

Identification of novel chicken microRNAs and analysis of their genomic organization

MicroRNAs (miRNAs) represent a family of small noncoding RNAs with important regulatory roles in diverse biological processes ranging from cell differentiation to organism development. In chickens, the full set of miRNAs and the expression patterns of miRNAs during development are still poorly understood when compared to the other vertebrates. In this study, we identified 29 novel miRNAs and 140 potential miRNA loci in the chicken genome by combining the experimental and computational analyses. Detailed expression patterns of 49 miRNAs were first characterized by Northern blotting and indicated the cooperativity of the miRNA expression with their function in embryogenesis and organogenesis. Twenty-seven miRNA clusters were systematically evaluated in the chicken genome and diverse expression patterns for closely linked miRNAs were observed. Our results significantly expand the set of known miRNAs in the chicken and provide the basis for understanding the structural and functional evolution of miRNA genes in vertebrates.     

Expression patterns and miRNA regulation of DNA methyltransferases in chicken primordial germ cells

DNA methylation is widespread in most species, from bacteria to mammals, and is crucial for genomic imprinting, gene expression, and embryogenesis. DNA methylation occurs via two major classes of enzymatic reactions: maintenance-type methylation catalyzed by DNA (cytosine-5-)-methyltransferase (DNMT) 1, and de novo methylation catalyzed by DNMT 3 alpha (DNMT3A) and -beta (DNMT3B). The expression pattern and regulation of DNMT genes in primordial germ cells (PGCs) and germ line cells has not been sufficiently established in birds. Therefore, we employed bioinformatics, RT-PCR, real-time PCR, and in situ hybridization analyses to examine the structural conservation and conserved expression patterns of chicken DNMT family genes. We further examined the regulation of a candidate de novo DNA methyltransferase gene, cDNMT3B by cotransfection of cDNMT3B 3'UTR- and cDNMT3B 3'UTR-specific miRNAs through a dual fluorescence reporter assay. All cDNMT family members were differentially detected during early embryonic development. Of interest, cDNMT3B expression was highly detected in early embryos and in PGCs. During germ line development and sexual maturation, cDNMT3B expression was reestablished in a female germ cell-specific manner. In the dual fluorescence reporter assay, cDNMT3B expression was significantly downregulated by four miRNAs: gga-miR-15c (25.82%), gga-miR-29b (30.01%), gga-miR-383 (30.0%), and gga-miR-222 (31.28%). Our data highlight the structural conservation and conserved expression patterns of chicken DNMTs. The miRNAs investigated in this study may induce downregulation of gene expression in chicken PGCs and germ cells.