利用人U6 snRNA启动子构建RNA干扰质粒载体

RNA干扰技术已经成为基因功能研究等领域的有力工具,构建带有筛选标记的siRNA载体可以在细胞中持续抑制靶基因的表达.为了利用RNAi技术开展生物学研究,在克隆载体pUC19的基础上改造构建了人类细胞小干扰RNA（small interference RNA,siRNA）表达质粒pUC19NU.该质粒具有新霉素抗性标记和真核细胞复制起点,利用连入的人U6 snRNA启动子起始siRNA的转录.以EGFP 和p53为靶基因的干扰实验证明,所构建的siRNA表达质粒可以显著抑制细胞外源性增强绿色荧光蛋白（enhanced green fluorescent protein,EGFP）及细胞内源性p53蛋白的表达,而且抑制效果具有特异性.     

Endogenous U2·U5·U6 snRNA complexes in S. pombe are intron lariat spliceosomes

Excision of introns from pre-mRNAs is mediated by the spliceosome, a multi-megadalton complex consisting of U1, U2, U4/U6, and U5 snRNPs plus scores of associated proteins. Spliceosome assembly and disassembly are highly dynamic processes involving multiple stable intermediates. In this study, we utilized a split TAP-tag approach for large-scale purification of an abundant endogenous U2·U5·U6 complex from Schizosaccharomyces pombe. RNAseq revealed this complex to largely contain excised introns, indicating that it is primarily ILS (intron lariat spliceosome) complexes. These endogenous ILS complexes are remarkably resistant to both high-salt and nuclease digestion. Mass spectrometry analysis identified 68, 45, and 43 proteins in low-salt-, high-salt-, and micrococcal nuclease-treated preps, respectively. The protein content of a S. pombe ILS complex strongly resembles that previously reported for human spliced product (P) and Saccharomyces cerevisiae ILS complexes assembled on single pre-mRNAs in vitro. However, the ATP-dependent RNA helicase Brr2 was either substoichiometric in low-salt preps or completely absent from high-salt and MNase preps. Because Brr2 facilitates spliceosome disassembly, its relative absence may explain why the ILS complex accumulates logarithmically growing cultures and the inability of S. pombe extracts to support in vitro splicing.     

Human U2B″ protein binding to snRNA stemloops

The human U2B″ protein is one of the unique proteins that comprise the U2 snRNP, but it is also a representative of the U1A/U2B″ protein family. In the U2 snRNP, it is bound to Stem-Loop IV (SLIV) of the U2 snRNA. We find that in vitro it binds not only to human SLIV, but also to Stem-Loop II (SLII) from human U1 snRNA and to Drosophila U2 snRNA SLIV. The thermodynamics of these binding interactions show a striking similarity, leading to the conclusion that U2B″ has a relaxed specificity for its RNA targets. The binding properties of U2B″ are distinct from those of human U1A and of Drosophila SNF, despite its high homology to those proteins, and so provide important new information on how this protein family has modulated its target preferences.     

水稻U2snRNA基因的分离及结构分析

对水稻(Oryza sativa L.)基因文库中分离到的U2snRNA基因FDRGU2.3进行序列分析,其编码区与小麦(Triticum aestivum L、)、玉米(Zea mays L.)、豌豆(Pisum sativum L.)及拟南芥(Arabidopsis thaliana(L.)Heyhy.)等植物U2基因的同源性均大于80％,且5＇端70个碱基高度保守。在基因编码区上游-70及-30区分别包含有植物UsnRNA基因特有的上游顺序元件(USE)及类TATA元件。同其它植物一样,水稻U2.3snRNA的二级结构也有保守的4个茎环区。其中环Ⅱ的结构与单子叶植物中的小麦和玉米相同,但与双子叶植物的豌豆和拟南芥存在明显差异。环Ⅳ的结构在单子叶和双子叶植物中亦有不同的变化。这些差异可能意味着单子叶和双子叶植物的剪接机构有所区别。     

小菜蛾U6 snRNA基因的克隆及作为miRNA定量表达分析内参基因的评价

【目的】克隆小菜蛾Plutella xylostella (L.)小分子非编码RNA U6的cDNA序列,并评价其是否适合作为定量检测小菜蛾microRNA (miRNA)表达量的内参基因。【方法】本研究采用RT-PCR 克隆获得了小菜蛾4龄幼虫核小RNA(small nuclear RNA, snRNA) U6的cDNA序列,并用定量PCR法检测了U6及8种miRNAs在小菜蛾不同发育阶段及不同杀虫药剂处理后的表达稳定性。【结果】小菜蛾U6的cDNA序列全长 94 bp,与其他昆虫U6的核苷酸序列一致性达98.9%。用geNorm和RefFinder软件分析荧光定量PCR结果表明,U6在小菜蛾卵、1-4龄幼虫、蛹和成虫7个不同发育阶段表达稳定;用马拉硫磷、毒死蜱、辛硫磷、灭多威、呋喃虫酰肼、高效氯氰菊酯、氯虫苯甲酰胺、溴虫腈和Bt 9种不同作用机理的杀虫药剂处理3龄末幼虫48 h,对U6的表达水平无显著影响。【结论】小菜蛾U6表达水平不受不同发育阶段和不同杀虫药剂处理的影响,符合作为内参基因的基本特点,可作为定量PCR法评价小菜蛾miRNA或其他非编码小分子RNA表达水平的内参基因。研究结果为小菜蛾miRNA表达水平的准确定量奠定了基础。     

Amphibian oocytes and sphere organelles: are the U snRNA genes amplified?

The sphere organelles (spheres) ofXenopus and other amphibian oocytes are known to contain small nuclear ribonucleoprotein particles (snRNPs) and have been suggested to play a role in snRNP complex assembly. Coupled with the similarities that exist between spheres and nucleoli and the quantitative and kinetic aspects of snRNA synthesis in theXenopus oocyte, we have investigated whether or not the U snRNA encoding genes are amplified inXenopus oogenesis, the spheres being possible sites for the location of such extrachromosomal gene copies. By applying a number of quantitative nucleic acid hybridization procedures to both total and fractionated oocyte and somatic DNA, employing both homologous and heterologous U snRNA gene probes and suitable amplification and non-amplification control probes, we show that the U snRNA genes do not undergo any major amplification inXenopus oogenesis. Therefore, the analogy between the sphere organelles and nucleoli appears to be limited. The role of the spheres and their relationship to other snRNP containing structures, specifically B snurposomes, and the sphere organizer loci remains obscure.by A. Spradling     

snRNA、siRNA和scRNA

RNA具有很多重要的生物学功能，本文对真核细胞内的3种小分子RNA：小分子核RNA、小干涉RNA和小胞浆RNA的功能予以简介。     

Use of a novel Förster resonance energy transfer method to identify locations of site-bound metal ions in the U2-U6 snRNA complex

U2 and U6 snRNAs pair to form a phylogenetically conserved complex at the catalytic core of the spliceosome. Interactions with divalent metal ions, particularly Mg(II), at specific sites are essential for its folding and catalytic activity. We used a novel Förster resonance energy transfer (FRET) method between site-bound luminescent lanthanide ions and a covalently attached fluorescent dye, combined with supporting stoichiometric and mutational studies, to determine locations of site-bound Tb(III) within the human U2–U6 complex. At pH 7.2, we detected three metal-ion-binding sites in: (1) the consensus ACACAGA sequence, which forms the internal loop between helices I and III; (2) the four-way junction, which contains the conserved AGC triad; and (3) the internal loop of the U6 intra-molecular stem loop (ISL). Binding at each of these sites is supported by previous phosphorothioate substitution studies and, in the case of the ISL site, by NMR. Binding of Tb(III) at the four-way junction and the ISL sites was found to be pH-dependent, with no ion binding observed below pH 6 and 7, respectively. This pH dependence of metal ion binding suggests that the local environment may play a role in the binding of metal ions, which may impact on splicing activity.     

Limited complementarity between U1 snRNA and a retroviral 5′ splice site permits its attenuation via RNA secondary structure

Multiple types of regulation are used by cells and viruses to control alternative splicing. In murine leukemia virus, accessibility of the 5′ splice site (ss) is regulated by an upstream region, which can fold into a complex RNA stem–loop structure. The underlying sequence of the structure itself is negligible, since most of it could be functionally replaced by a simple heterologous RNA stem–loop preserving the wild-type splicing pattern. Increasing the RNA duplex formation between U1 snRNA and the 5′ss by a compensatory mutation in position +6 led to enhanced splicing. Interestingly, this mutation affects splicing only in the context of the secondary structure, arguing for a dynamic interplay between structure and primary 5′ss sequence. The reduced 5′ss accessibility could also be counteracted by recruiting a splicing enhancer domain via a modified MS2 phage coat protein to a single binding site at the tip of the simple RNA stem–loop. The mechanism of 5′ss attenuation was revealed using hyperstable U1 snRNA mutants, showing that restricted U1 snRNP access is the cause of retroviral alternative splicing.     

The 5′ Stem-Loop From Human U4 snRNA Adopts a Novel Conformation Stabilized by G-C and G-U Base Pairs

Abstract

¹H NMR and molecular modeling studies of the 5′ stem-loop from human U4 snRNA were undertaken to determine the conformation of this stem-loop that is essential for spliceosome formation and pre-mRNA splicing. Sixteen of the 35 nucleotides of this stem-loop are in the loop region and inspection of the loop sequence revealed no decomposition into elements of secondary structure commonly found in other RNA stem-loops. An analysis of possible base pairing interactions for this stem-loop using the methods of Zuker revealed the lowest energy secondary structure for the 16 nucleotide loop consisted of four base pairs at the base of a non-canonical tetraloop (UUUA). This shorter stem-loop was joined to the nine base pair stem by two A residues on the 5′ side and a single bulged A on the 3′ side. Both stems also had bulged A residues. ¹H NMR experiments performed on solutions of the 35mer stem-loop, the stem region, and the loop region confirmed the 35mer adopted this secondary structure in solution. A 3D molecular model of this structure consistent with the NMR data was generated to assist in visualization of this novel structure.     

Brr2解旋U4/U6 SnRNAs的调控机制

前体mRNA(precursor messager RNA,pre-mRNA)剪接是去除内含子和将外显子彼此连接形成成熟mRNA的过程。剪接过程在一个呈动态变化的大核糖核蛋白(ribonucleoprotein, RNP)复合体,即剪接体催化作用下完成。DExD/H-box RNA解旋酶在剪接体组装、激活及解聚过程中都发挥着重要作用。Brr2(bad response to refrigeration 2)这种DExD/H-box RNA解旋酶是构成U5稳定的亚单位。Brr2含有两个串联解旋酶盒结构,在剪接体激活中负责U4/U6的解旋,还参与剪接体催化及解聚过程,因此Brr2在剪接过程中必需具备严格的调控机制。在剪接过程中,Prp8的C端包含两个连续的RNase H域和Jab1/MPN域,能够正负调控Brr2活性。Snu114在调节Brr2活性中具有非常重要的作用。此外,Brr2通过C端解旋酶盒(C-terminal cassette, CC)与N末端域(N-terminal region)进行分子内的自我活性调节。本文综述了近年来在Brr2的分子间和分子内活性调节机制的研究进展,这些不同的调节机制协同作用才确保真核生物pre-mRNA可变剪接的保真性。     

In vivo kinetics of U4/U6·U5 tri-snRNP formation in Cajal bodies

The U4/U6·U5 tri-small nuclear ribonucleoprotein particle (tri-snRNP) is an essential pre-mRNA splicing factor, which is assembled in a stepwise manner before each round of splicing. It was previously shown that the tri-snRNP is formed in Cajal bodies (CBs), but little is known about the dynamics of this process. Here we created a mathematical model of tri-snRNP assembly in CBs and used it to fit kinetics of individual snRNPs monitored by fluorescence recovery after photobleaching. A global fitting of all kinetic data determined key reaction constants of tri-snRNP assembly. Our model predicts that the rates of di-snRNP and tri-snRNP assemblies are similar and that ∼230 tri-snRNPs are assembled in one CB per minute. Our analysis further indicates that tri-snRNP assembly is approximately 10-fold faster in CBs than in the surrounding nucleoplasm, which is fully consistent with the importance of CBs for snRNP formation in rapidly developing biological systems. Finally, the model predicted binding between SART3 and a CB component. We tested this prediction by Förster resonance energy transfer and revealed an interaction between SART3 and coilin in CBs.     

Activity identification of ribozyme and U1 snRNA chimeric ribozyme against TGFβ1 in cell-free system and in hepatic stellate cells

Transforming growth factorβ1 (TGFβ1) is known to be intimately involved in many cellular processes. To explore the mechanism of TGFβ1 in these processes, the non-chimeric hammerhead ribozyme and U1 snRNA chimeric ribozyme against TGFβ1 were designed to down-regulate TGFβ1 expression. The activity of non-chimeric ribozyme and U1 snRNA chimeric ribozyme against TGFβ1 in vitro and in activated hepatic stellate cells (HSCs) was detected. Cleavage reactions of both ribozymes in vitro demonstrated that non-chimeric ribozyme possessed better cleavage activity in vitro than U1 snRNA chimeric ribozyme. The further study showed U1 snRNA chimeric ribozyme inhibited TGFβ1 expression more efficiently than non-chimeric ribozyme in transfected HSC cells. So it indicates that the U1 snRNA chimeric ribozyme provides an alternative approach for the research on the precise mechanism of TGFβ1 in many cellular processes and a potential therapeutic candidate for TGFβ1-related diseases.     

Activity identification of ribozyme and U1 snRNA chimeric ribozyme against TGFβ1 in cell-free system and in hepatic Stellate cells

The transforming growth factor (TGF) β1 are members of the essential, multifunctional family of cytokines. Of them, TGFβ1 is the most extensively studied and the best characterized. To current knowledge, TGFβ1 is known to be intimately involved in many…