miR-34基因家族的分子进化

根据miRNA基因在进化中高度保守的特点,利用生物信息学方法在目前已测序的动物物种中搜寻参与哺乳动物早期发育调控的mir-34基因的同源序列,在33个不同的动物物种中获得了miR-34基因的54条同源序列,其中18条为新发现的序列。表明miR-34是高度保守的,广泛存在于后生动物中。目前发现的mir-34基因80%位于基因间隔区,少数位于蛋白编码基因的内含子区和3′UTR上。不同动物中,mir-34基因成熟序列的同源性为68%,前体序列为38.89%。在无脊椎动物中只有一个mir-34,而在几乎所有的脊椎动物中都有mir-34a,mir-34b,mir-34c,形成miR-34基因家族。系统进化分析表明,脊椎动物中miR-34基因家族是通过基因的串联和局部重复形成的,这个过程中伴随着个别碱基的变异。     

miR-34基因家族的分子进化

根据miRNA基因在进化中高度保守的特点，利用生物信息学方法在目前已测序的动物物种中搜寻参与哺乳动物早期发育调控的mir-34基因的同源序列，在33个不同的动物物种中获得了miR-34基因的54条同源序列，其中18条为新发现的序列。表明miR-34是高度保守的，广泛存在于后生动物中。目前发现的mir-34基因80％位于基因间隔区，少数位于蛋白编码基因的内含子区和3′UTR上。不同动物中，mir-34基因成熟序列的同源性为68%，前体序列为38.89%。在无脊椎动物中只有一个mir-34，而在几乎所有的脊椎动物中都有mir-34a，mir-34b，mir-34c, 形成miR-34基因家族。系统进化分析表明,脊椎动物中miR-34基因家族是通过基因的串联和局部重复形成的，这个过程中伴随着个别碱基的变异。     

12个物种miR-302基因簇的生物信息学分析

很多microRNA (miRNA)基因在基因组上聚集排列形成miRNA基因簇.miRNA基因簇在进化上较为保守,有其特殊的生物学意义.miR-302基因簇在胚胎干细胞中特异表达,对胚胎干细胞的自我更新和多潜能维持有重要的作用.本文采用miRBase数据库查询和BLAST同源搜索方法共搜寻并分析了12个物种的miR-302基因簇.生物信息学分析表明,这些物种miR-302基因簇均位于LARP7蛋白基因的内含子区,但转录方向与LARP7基因转录方向相反.序列相似性分析显示,同一物种miR-302簇成员间以及不同物种相应miR-302簇成员间相似性均较高.进化分析表明,基因复制可能是miR-302基因簇进化的主要驱动力.     

杜氏盐藻泛素基因cDNA的克隆及系统进化分析

根据玉米,水稻等物种泛素序列设计一对简并引物.提取杜氏盐藻细胞的总RNA,利用RT-PCR方法扩增盐藻泛素基因的cDNA片断,回收两个长度不同的片断ubi-1和ubi-2,将其克隆到pMDl8-T载体上,测序后进行序列分析,为克隆杜氏盐藻泛素基因的cDNA序列并进行进化分析.结果 ubi-1经测序后得到一个完整拷贝(228 bp)和一个不完整的泛素cDNA序列(191 bp).Ubi-2经测序后得到两个拷贝(556 bp)和一个不完整的泛素cDNA序列(191 bp).盐藻3个不同拷贝泛素cDNA序列之间存在差异,但所编码氨基酸序列相同.盐藻泛素cDNA序列与其他物种的泛素cDNA序列具有高的同源(70%～85%),所推导的氨基酸序列与其他物种仅存在1～2个氨基酸的差异.进化分析显示,所分离的盐藻泛素基因与两个模式生物果蝇和衣藻的泛素基因共处一个进化支,彼此亲缘关系最近.盐藻泛素基因与其他物种的泛素基因可能来自共同的"祖先"基因.在进化中高度保守.     

PLOD3基因3’调控区的人类特异突变改变miR-124a对PLOD3的调控

microRNAs(miRNAs)是一类在转录后水平调控基因表达的不编码蛋白质的小RNA(长度20-24个碱基).其中,miR-124a是一个在哺乳动物中枢神经系统高度表达的miRNA,在神经前体细胞向神经元分化的过程中起着举足轻重的作用.由于miRNAs特异性地识别靶基因的3'端调控区(3'UTR)的靶序列,因此,在人类起源过程中基因3'UTR的单核苷酸序列变异有可能导致miRNA调控的改变.通过靶基因预测和3'UTR区在哺乳动物代表物种间的同源序列比较,我们发现miR-124a的靶基冈中有一个基因(PLOD3)3UTR的靶位点中存在人类特异突变位点.利用体外报告基因系统,发现PLOD3基因3'UTR靶位点中所含的一个人类特异的突变导致miR-124a对PLOD3的调控效率降低.研究表明,miRNAs靶基因3'UTR的序列变异具有功能效应,它有可能足人类中枢神经系统在起源和演化中发挥关键作用的重要遗传机制之一.     

绵羊cdh1基因cDNA全编码区的克隆及序列分析

在哺乳动物成体睾丸中,精子发生的过程开始于未分化的A型精原细胞的干细胞群.目前已有报道在小鼠未分化的A型精原细胞中特异性表达钙依赖性跨膜黏着蛋白基因(cdh1),但绵羊的cdh1基因全序列未见报道.为了更好地研究绵羊精原干细胞的特性,根据已报道的其他物种的cdh1基因的cDNA保守区设计引物,从成年蒙古绵羊睾丸中提取总RNA,采用RT-PCR和分子克隆方法克隆了蒙古绵羊cdh1基因cDNA全编码区.DNA序列测定结果与牛的核苷酸序列比对,同源性为96.5％,说明该基因在进化上是高度保守的.这为制备绵羊CDHI的抗体奠定了基础,并且为绵羊精原干细胞的分子水平鉴定提供了研究备件.     

miRNA-9基因家族进化分析及其靶基因预测

microRNAs(miRNA)是真核生物中一类长度约为21～25个核苷酸的非编码小分子RNA,在转录后水平调控基因的表达。该文在miRBase中搜索后生动物的mir-9基因序列。47个物种中共搜索到120条mir-9基因序列,说明mir-9基因家族广泛存在于不同物种中。基因定位显示86%的mir-9基因存在于基因间隔区(IGR),多序列比对发现miR-9基因家族成熟序列的第2位到第8位碱基以及第14位到第18位碱基为保守碱基。进化分析表明mir-9b和mir-9c可能是此基因家族最早出现的基因形式,即祖先基因。这些祖先基因经过串联重复、大片段重复、个别碱基的缺失及突变等方式形成了脊椎动物中miR-9-1至miR-9-7数个基因。分别采用四个miRNA靶基因预测软件对mmu-miR-9的靶基因进行预测,发现miR-9与神经系统发育、心肌系统疾病和跨膜运输系统等密切相关。该研究为今后进一步研究miRNA调控的神经系统发生和神经细胞生长与分化的机制奠定了基础。     

Pax-6基因在发育中的表达与动物眼的进化

近年在脊椎动物和无脊椎动物中分离出Pax-6基因及其同源基因,这些基因都与动物的眼与神经系统的发育和形态发生有关.本文着重比较了无脊椎动物果蝇、文昌鱼、哺乳动物小鼠和人的Pax-6基因编码蛋白,Pax-6基因在发育过程中的表达,Pax-6与眼进化的关系等几个方面,并介绍Pax-6基因为靶基因的转基因果蝇的上游制作技术和原理.探讨了Pax-6基因作为眼发育的主导基因的作用和时空表达模式的保守性.     

PLOD3基因3′调控区的人类特异突变改变miR-124a对PLOD3的调控

microRNAs(miRNAs)是一类在转录后水平调控基因表达的不编码蛋白质的小RNA(长度20—24个碱基)。其中,miR-124a是一个在哺乳动物中枢神经系统高度表达的miRNA,在神经前体细胞向神经元分化的过程中起着举足轻重的作用。由于miRNAs特异性地识别靶基因的3′端调控区(3′UTR)的靶序列,因此,在人类起源过程中基因3′UTR的单核苷酸序列变异有可能导致miRNA调控的改变。通过靶基因预测和3′UTR区在哺乳动物代表物种间的同源序列比较,我们发现miR-124a的靶基因中有一个基因(PLOD3)3′UTR的靶位点中存在人类特异突变位点。利用体外报告基因系统,发现PLOD3基因3′UTR靶位点中所含的一个人类特异的突变导致miR-124a对PLOD3的调控效率降低。研究表明,miRNAs靶基因3′UTR的序列变异具有功能效应,它有可能是人类中枢神经系统在起源和演化中发挥关键作用的重要遗传机制之一。     

非编码RNA与哺乳动物基因组印记的起源

基因组印记是由亲本来源不同而导致等位基因表达差异的一种遗传现象,主要发生在胎盘哺乳动物（真哺乳类）和显花植物中.大部分印记基因都分布在印记基因簇内,其中包含大量的非编码RNA基因.印记基因的表达受印记控制区（ICRs）的顺式调控.基因组印记产生的原因及过程是现代遗传学研究的一个热点问题,分析印记同源区从非印记物种到印记物种的过渡,为解决这一问题提供了重要启示.最近,原始哺乳动物（有袋类和单孔类）模式物种全基因组测序的完成,极大地促进了印记同源区的比较分析研究.本文对这些研究进行了回顾和分析,发现非编码RNA与哺乳动物基因组印记获得关系密切.主要依据为：（1）伴随着基因组印记的获得,印记区有大量的非编码RNA新基因出现;（2）与基因组印记相关的一些保守非编码RNA的表达发生了显著变化.此外,对15种脊椎动物中印记snoRNA基因系统分析的结果表明：印记snoRNA起源于真哺乳类与有袋类动物分化之后,并且在真哺乳类辐射进化之前发生了迅速的扩张,主要的基因家族在这一时期已经形成.这些结果进一步证明了非编码RNA与基因组印记获得的密切联系.非编码RNA可能主要通过调控印记表达和诱导染色体表观遗传修饰两种机制,参与哺乳动物基因组印记的获得.     

The oncoprotein EVI1 and the DNA methyltransferase Dnmt3 co-operate in binding and de novo methylation of target DNA

EVI1 has pleiotropic functions during murine embryogenesis and its targeted disruption leads to prenatal death by severely affecting the development of virtually all embryonic organs. However, its functions in adult tissues are still unclear. When inappropriately expressed, EVI1 becomes one of the most aggressive oncogenes associated with human hematopoietic and solid cancers. The mechanisms by which EVI1 transforms normal cells are unknown, but we showed recently that EVI1 indirectly upregulates self-renewal and cell-cycling genes by inappropriate methylation of CpG dinucleotides in the regulatory regions of microRNA-124-3 (miR-124-3), leading to the repression of this small gene that controls normal differentiation and cell cycling of somatic cells. We used the regulatory regions of miR-124-3 as a read-out system to investigate how EVI1 induces de novo methylation of DNA. Here we show that EVI1 physically interacts with DNA methyltransferases 3a and 3b (Dnmt3a/b), which are the only de novo DNA methyltransferases identified to date in mouse and man, and that it forms an enzymatically active protein complex that induces de novo DNA methylation in vitro. This protein complex targets and binds to a precise region of miR-124-3 that is necessary for repression of a reporter gene by EVI1. Based on our findings, we propose that in cooperation with Dnmt3a/b EVI1 regulates the methylation of DNA as a sequence-specific mediator of de novo DNA methylation and that inappropriate EVI1 expression contributes to carcinogenesis through improper DNA methylation.     

miR-124和miR-520b下调Eps8表达并抑制HeLa细胞增殖

Eps8是一个多功能的信号分子,参与肌动蛋白重排、受体内吞和肿瘤的发生发展. 为了寻找靶向Eps8的microRNAs (miRNAs)并研究其在宫颈癌中的调控作用,本文采用软件预测获得4个可能调控Eps8表达的miRNAs. 利用双荧光素酶报告系统和Western印迹研究发现,miR-124 和miR-520b结合到人EPS8 mRNA的3′非翻译区(untranslated region, UTR)并有效抑制Eps8蛋白的表达. 进一步细胞存活检测、MTT法和克隆形成实验分析显示,miR-124和miR-520b过表达显著抑制HeLa细胞的生长和增殖.而且,miRNA调节的Eps8下调能提高HeLa细胞对化疗药物顺铂的敏感性. 同时证明,miR-124和miR-520b激活肿瘤抑制基因p53与下游基因p21报告基因转录活性,也相应地上调了p53与p21的蛋白表达. 这些结果提示,miR-124和miR-520b下调癌基因EPS8表达,从而抑制HeLa细胞增殖,负调控宫颈癌细胞生长.     

The Effect of MicroRNA-124 Overexpression on Anti-Tumor Drug Sensitivity

MicroRNAs play critical roles in regulating various physiological processes, including growth and development. Previous studies have shown that microRNA-124 (miR-124) participates not only in regulation of early neurogenesis but also in suppression of tumorigenesis. In the present study, we found that overexpression of miR-124 was associated with reduced DNA repair capacity in cultured cancer cells and increased sensitivity of cells to DNA-damaging anti-tumor drugs, specifically those that cause the formation of DNA strand-breaks (SBs). We then examined which DNA repair–related genes, particularly the genes of SB repair, were regulated by miR-124. Two SB repair–related genes, encoding ATM interactor (ATMIN) and poly (ADP-ribose) polymerase 1 (PARP1), were strongly affected by miR-124 overexpression, by binding of miR-124 to the 3¢-untranslated region of their mRNAs. As a result, the capacity of cells to repair DNA SBs, such as those resulting from homologous recombination, was significantly reduced upon miR-124 overexpression. A particularly important therapeutic implication of this finding is that overexpression of miR-124 enhanced cell sensitivity to multiple DNA-damaging agents via ATMIN- and PARP1-mediated mechanisms. The translational relevance of this role of miR-124 in anti-tumor drug sensitivity is suggested by the finding that increased miR-124 expression correlates with better breast cancer prognosis, specifically in patients receiving chemotherapy. These findings suggest that miR-124 could potentially be used as a therapeutic agent to improve the efficacy of chemotherapy with DNA-damaging agents.     

miR-124 function during Ciona intestinalis neuronal development includes extensive interaction with the Notch signaling pathway

The nervous system-enriched microRNA miR-124 is necessary for proper nervous system development, although the mechanism remains poorly understood. Here, through a comprehensive analysis of miR-124 and its gene targets, we demonstrate that, in the chordate ascidian Ciona intestinalis, miR-124 plays an extensive role in promoting nervous system development. We discovered that feedback interaction between miR-124 and Notch signaling regulates the epidermal-peripheral nervous system (PNS) fate choice in tail midline cells. Notch signaling silences miR-124 in epidermal midline cells, whereas in PNS midline cells miR-124 silences Notch, Neuralized and all three Ciona Hairy/Enhancer-of-Split genes. Furthermore, ectopic expression of miR-124 is sufficient to convert epidermal midline cells into PNS neurons, consistent with a role in modulating Notch signaling. More broadly, genome-wide target extraction with validation using an in vivo tissue-specific sensor assay indicates that miR-124 shapes neuronal progenitor fields by downregulating non-neural genes, notably the muscle specifier Macho-1 and 50 Brachyury-regulated notochord genes, as well as several anti-neural factors including SCP1 and PTBP1. 3'UTR conservation analysis reveals that miR-124 targeting of SCP1 is likely to have arisen as a shared, derived trait in the vertebrate/tunicate ancestor and targeting of PTBP1 is conserved among bilaterians except for ecdysozoans, while extensive Notch pathway targeting appears to be Ciona specific. Altogether, our results provide a comprehensive insight into the specific mechanisms by which miR-124 promotes neuronal development.     

MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome

Many microRNAs regulate gene expression via atypical mechanisms, which are difficult to discern using native cross-linking methods. To ascertain the scope of non-canonical miRNA targeting, methods are needed that identify all targets of a given miRNA. We designed a new class of miR-CLIP probe, whereby psoralen is conjugated to the 3p arm of a pre-microRNA to capture targetomes of miR-124 and miR-132 in HEK293T cells. Processing of pre-miR-124 yields miR-124 and a 5′-extended isoform, iso-miR-124. Using miR-CLIP, we identified overlapping targetomes from both isoforms. From a set of 16 targets, 13 were differently inhibited at mRNA/protein levels by the isoforms. Moreover, delivery of pre-miR-124 into cells repressed these targets more strongly than individual treatments with miR-124 and iso-miR-124, suggesting that isomirs from one pre-miRNA may function synergistically. By mining the miR-CLIP targetome, we identified nine G-bulged target-sites that are regulated at the protein level by miR-124 but not isomiR-124. Using structural data, we propose a model involving AGO2 helix-7 that suggests why only miR-124 can engage these sites. In summary, access to the miR-124 targetome via miR-CLIP revealed for the first time how heterogeneous processing of miRNAs combined with non-canonical targeting mechanisms expand the regulatory range of a miRNA.