植物snoRNA

植物体含有的小分子核仁RNA(small nucleolar RNA,snoRNA)是一类典型的非编码RNA,参与rRNA的加工与修饰.该文就植物snoRNA的结构、功能、生物合成与调控研究进展作介绍.     

核仁小分子RNA的结构、功能与合成

九十年代以来,许多新的核仁小分子ＲＮＡ（ｓｎｏＲＮＡ）陆续被发现。它们的大小一般在几十到几百个核苷酸,能与特定的蛋白质如核纤蛋白（ｆｉｂｒｉｌａｒｉｎ）或Ｔｈ／Ｔｏ自身免疫抗原等相结合生成ｓｎｏＲＮＰ,在细胞中稳定地存在,并且富集于核仁区。ｓｎｏＲＮ...     

snoRNA的结构与功能

核仁小分子RNA（snoRNA）是一类广泛分布于真核生物细胞核仁的小分子非编码RNA,具有保守的结构元件,并以此划分为3大类：boxC／DsnoRNA、boxH／ACAsnoRNA和MRPRNA。其中boxC／D和boxH／ACA是已知snoRNA的主要类型,以碱基配对的方式分别指导着核糖体RNA的甲基化和假尿嘧啶化修饰。研究发现,snoRNA除了在核糖体RNA的生物合成中发挥作用之外,还能够指导snRNA、tRNA和mRNA的转录后修饰。此外,还有相当数量的snoRNA功能不明,被称为孤儿sn0RNA（orphansnoRNA）。在哺乳动物的孤儿snoRNA中,印迹snoRNA（imprintedsnoRNA）是最为特殊的一群,由基因组印迹区编码,具有明显的组织表达特异性。原核生物古细菌中类snoRNA的鉴定表明这些非编码RNA家族成员的古老起源;而哺乳动物中大量的snoRNA反转座子的存在更为人们探索snoRNA在基因组中扩增和功能进化提供了新的思路。     

U83 Box C/D snoRNA构建果蝇科系统发生树

利用已报道的黑腹果蝇U83基因搜索果蝇基因数据库,鉴定了10种新的果蝇科U83同源基因,它们均位于相应物种核蛋白基因rpl3的内含子中。以冈比亚按蚊为外类群,对11种果蝇的U83核苷酸序列作进化关系分析,用邻接法重建了系统发生树,结果与传统方法构建的系统发生树相比,能反映果蝇科的大致进化关系,但还存在部分差别。为增加序列信息,把序列长度拓展至整个U83所在的内含子,同法构建系统发生树,结果与传统系统发生树几乎完全一致。该研究是用boxC/D snoRNA基因序列构建系统发生树的首次尝试,实验结果证明U83可以很好地用于构建果蝇科内各物种的种系发生树。     

拟南芥中一个新的snoRNA基因簇的鉴定及结构分析

在拟南芥中发现和鉴定了Z2 snoRNA基因簇, 该基因簇由4个相同的 Z2 snoRNA 基因组成,分别命名为Z2a, Z2b, Z2c和Z2d. 在Z2 snoRNA基因簇的基因间隔区中没有发现已知的植物snoRNA基因保守的启动元件,因此,Z2 snoRNA基因簇是由一个上游启动子控制转录的. 对Z2 snoRNA基因间隔区序列的二级结构分析也表明,在3个基因间隔区中都编码一种与酿酒酵母snoRNA前体切割加工的识别信号类似的发夹结构. Z2 snoRNA基因簇的发现,揭示出植物snoRNA基因具有多拷贝的特点,并为进一步研究植物snoRNA基因簇的转录和转录后的加工机制提供了一个良好的研究体系.     

豌豆细胞核仁中U3 snoRNA的分布和转运

rRNA前体剪切是发生在核仁中的重要生物学事件.U3 snoRNA作为rRNA的一个剪切因子被认为是rRNA前体剪切第一步,即5′ ETS剪切所必需的.鉴定U3能够为确定rRNA前体剪切位点和剪切产物转运提供间接证据.本文利用原位杂交技术研究了豌豆(Pisum sativum L.)核仁中U3 snoRNA的分布和转运.结果表明, U3 snoRNA分布在致密纤维组分(dense fibrillar component, DFC)和颗粒组分(granular component, GC)中,在纤维中心(fibrillar center, FC)没有分布.当用放线菌素D (actinomycin D, AMD)处理豌豆根端分生细胞时,rDNA转录受到抑制,标记信号减弱.随着AMD处理时间的延长,标记信号逐渐变弱并出现在DFC远轴区域和GC区域.本文结果提示,rRNA前体剪切发生在DFC和GC区域,剪切产物从围绕FC的区域向周边转运.     

酿酒酵母一个新的基因簇转录多顺反子的snoRNA前体

核仁小分子RNA (snoRNA)是一类在真核生物核糖体生物合成过程中起重要作用的小分子RNA .通过计算机分析国际分子生物学数据库及实验的方法 ,在酿酒酵母 (Saccharomycescerevisiae)中发现和鉴定了一个新的snoRNA(Z8)及其特殊的基因组织 .Z8snoRNA基因位于酿酒酵母第 13号染色体上 ,是酵母snoRNA基因簇的第 1个基因 ,编码boxC/D类反义snoRNA .结构分析指出该snoRNA指导 2 5SrRNA中第 2 42 1位尿苷酸的 2′ O 核糖的甲基化 .用遗传学方法将该基因缺失后 ,其对应位点的甲基化被取消 ,但细胞的生长并未受到影响 .Z8snoRNA基因的上游 2 47位 ,有一UsnoRNA启动子保守元素 .RT PCR的结果证明 ,Z8与该基因簇中其他snoRNA(Z7和Z6)基因共同转录成一个多顺反子的snoRNA前体 ,然后再被加工成熟 ,这是一种新的snoRNA基因表达方式 .     

核仁小RNA源性小RNA

最新研究结果表明,一些与RNA介导基因沉默相关的小RNA由核仁小RNA(small nucleolar RNA,snoRNA)加工产生,这种小RNA被称为核仁小RNA源性小RNA(snoRNA derived small RNA,sdRNA)。sdRNA现象分布物种广;涉及的snoRNA种类全,数量多;产生的小RNA分子大小不一、数量、种类多。表明这种小RNA在生物中存在着广泛的普遍性。sdRNA的发现拓展了snoRNA的功能,揭示了snoRNA与RNA介导的基因沉默之间的紧密关系,增强了snoRNA在RNA调控网络中的重要性,并为进一步研究RNA调控网络开启了一扇门。     

Quantitative analysis of snoRNA association with pre-ribosomes and release of snR30 by Rok1 helicase

In yeast, three small nucleolar RNAs (snoRNAs) are essential for the processing of pre-ribosomal RNA—U3, U14 and snR30—whereas 72 non-essential snoRNAs direct site-specific modification of pre-rRNA. We applied a quantitative screen for alterations in the pre-ribosome association to all 75 yeast snoRNAs in strains depleted of eight putative helicases implicated in 40S subunit synthesis. For the modification-guide snoRNAs, we found no clear evidence for the involvement of these helicases in the association or dissociation of pre-ribosomes. However, the DEAD box helicase Rok1 was required specifically for the release of snR30. Point mutations in motif I, but not in motif III, of the helicase domain of Rok1 impaired the release of snR30, but this was less marked than in strains depleted of Rok1, and resulted in a dominant-negative growth phenotype. Dissociation of U3 and U14 from pre-ribosomes is also dependent on helicases, suggesting that release of the essential snoRNAs might differ mechanistically from release of the modification-guide snoRNAs.     

snoRNP的生物发生

核仁小核糖核蛋白体颗粒(small nucleolar ribonucleoproteins partical,snoRNP)是一种定位于核仁的复合物,它由一系列核仁小RNA(small nucleolar RNA,snoRNA)和核心蛋白质结合而成。这些snoRNP指导核糖体RNA(rRNA)前体的加工修饰,在核糖体的生物发生中起着重要的作用。研究显示大多数snoRNP加工和组装的早期阶段发生在核浆,在Cajal小体(Cajal body,CB)中组装成熟之后,在PHAX、p50、p55、SMN和Nopp140等蛋白质的帮助下穿越各种不同的核间隔转运至核仁,并在核仁中发挥功能。本文对snoRNP的生物发生过程作一综述。     

Dynamic guide-target interactions contribute to sequential 2'-O-methylation by a unique archaeal dual guide box C/D sRNP

Assembly and guide-target interaction of an archaeal box C/D-guide sRNP was investigated under various conditions by analyzing the lead (II)-induced cleavage of the guide RNA. Guide and target RNAs derived from Haloferax volcanii pre-tRNA(Trp) were used with recombinant Methanocaldococcus jannaschii core proteins in the reactions. Core protein L7Ae binds differentially to C/D and C'/D' motifs of the guide RNA, and interchanging the two motifs relative to the termini of the guide RNA did not affect L7Ae binding or sRNA function. L7Ae binding to the guide RNA exposes its D'-guide sequence first followed by the D guide. These exposures are reduced when aNop5p and aFib proteins are added. The exposed guide sequences did not pair with the target sequences in the presence of L7Ae alone. The D-guide sequence could pair with the target in the presence of L7Ae and aNop5p, suggesting a role of aNop5p in target recruitment and rearrangement of sRNA structure. aFib binding further stabilizes this pairing. After box C/D-guided modification, target-guide pairing at the D-guide sequence is disrupted, suggesting that each round of methylation may require some conformational change or reassembly of the RNP. Asymmetric RNPs containing only one L7Ae at either of the two box motifs can be assembled, but a functional RNP requires L7Ae at the box C/D motif. This arrangement resembles the asymmetric eukaryal snoRNP. Observations of initial D-guide-target pairing and the functional requirement for L7Ae at the box C/D motif are consistent with our previous report of the sequential 2'-O-methylations of the target RNA.     

豌豆细胞核仁中U3 snoRNA的分布和转运

rRNA前体剪切是发生在核仁中重要生物学事件。U3 snoRNA作为rRNA的一个剪切因子被认为是rRNA前体剪切第一步,即5′ETS剪切所必需的,鉴定U3能够为确定rRNA前体剪切位点和剪切产物转运提供间接证据。,本文利用原位杂交技术研究了豌豆（Pisum sativum L.)核仁中U3 snoRNA的分布和转运。结果表明,U3 snoRNA分布在致密纤维组分（dense fibrillar component,DFC)和颗粒组分（granular component,GC)中,在纤维中心（fibrillar center,FC)没有分布 ,当用放线菌素D（actinomycin,D,AMD)处理豌豆根端分生细胞时,rDNA转录受到抑制,标记信号减弱,随着AMD处理时间的延长,标记信号逐渐变弱并出现在DFC远轴区域和GC区域。本文结果提示,rRNA前体剪切发生在DFC和GC区域,剪切产物从围绕FC的区域向周边转运。     

Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing

2'-O-methylation of eukaryotic ribosomal RNA (r)RNA, essential for ribosome function, is catalysed by box C/D small nucleolar (sno)RNPs. The RNA components of these complexes (snoRNAs) contain one or two guide sequences, which, through base-pairing, select the rRNA modification site. Adjacent to the guide sequences are protein-binding sites (the C/D or C'/D' motifs). Analysis of >2000 yeast box C/D snoRNAs identified additional conserved sequences in many snoRNAs that are complementary to regions adjacent to the rRNA methylation site. This 'extra base-pairing' was also found in many human box C/D snoRNAs and can stimulate methylation by up to five-fold. Sequence analysis, combined with RNA-protein crosslinking in Saccharomyces cerevisiae, identified highly divergent box C'/D' motifs that are bound by snoRNP proteins. In vivo rRNA methylation assays showed these to be active. Our data suggest roles for non-catalytic subunits (Nop56 and Nop58) in rRNA binding and support an asymmetric model for box C/D snoRNP organization. The study provides novel insights into the extent of the snoRNA-rRNA interactions required for efficient methylation and the structural organization of the snoRNPs.     

Exploration of pairing constraints identifies a 9 base-pair core within box C/D snoRNA-rRNA duplexes

2'-O-ribose methylation of eukaryotic ribosomal RNAs is guided by RNA duplexes consisting of rRNA and box C/D small nucleolar (sno)RNA sequences, the methylated sites invariably mapping five positions apart from the D box. Here we have analyzed the RNA duplex pairing constraints by investigating the features of 415 duplexes from the fungus, plant and animal kingdoms, and the evolution of those duplexes within the 124 sets they group into. The D-box upstream 1st and >or=15th positions consist of Watson-Crick base-pairs, G:U base-pairs and mismatched bases with ratios close to random assortments; these positions display single base differences in >60% of the RNA duplex sets. The D-box upstream 2nd to 11th positions have >90% Watson-Crick base-pairs; they display single base mutations with a U-shaped distribution of lower values of 0% and 1.6% at the methylated site 5th and 4th positions, and double compensatory mutations leading to new Watson-Crick base-pairs with an inverted U-shaped distribution of higher values at the 8th to 11th positions. Half of the single mutations at the 3rd to 11th positions resulted in G:U base-pairing, mainly through A-->G mutations in the rRNA strands and C-->T mutations in the snoRNA strands. Double compensatory mutations at the 3rd to 11th positions are extremely frequent, representing 36% of all mutations; they frequently arose from an A-->G mutation in the rRNA strands followed by a T-->C mutation in the snoRNA strands. Differences in the mutational pathways through which the rRNA and snoRNA strand evolved must be related to differences in the rRNA and snoRNA copy number and gene organization. Altogether these data identify the D-box upstream 3rd to 11th positions as box C/D snoRNA-rRNA duplex cores. The impact of the pairing constraints on the evolution of the 9 base-pair RNA duplex cores is discussed.     

Differential expression of human 5S snoRNA genes

Four novel small nucleolar RNAs (snoRNAs), h5sn1, h5sn2, h5sn3, and h5sn4, were successfully amplified from human total RNAs using RT-PCR. They exhibited the structural hallmarks of box H/ACA snoRNAs and formed sequence complementarity to 5S rRNA. The nucleotide sequences of the snoRNAs from different donors were highly conserved as evidenced by single-stranded conformational polymorphism and direct nucleotide sequence analysis. Although their host genes had no protein-coding potential, the expression of the snoRNAs was differentially displayed in different tissues. Noticeably, h5sn2 was highly expressed in normal brain, but its expression drastically decreased in meningioma. This opens the fascinating possibility of the relationship between the processing of snoRNAs and carcinogenesis.