小RNAs在沉默转座因子中的作用

在很多生物基因组中都存在DNA成分的转座序列,它们能够转座到基因组的很多位点,对基因组造成很大的危害,如破坏编码基因、改变基因表达的调节网络、使染色体断裂或造成大范围基因重排等。真核生物已经进化出了多种机制来控制这些寄生核酸序列造成的损伤,以维持基因组完整性。虽然这些机制在不同生物中有些差异,但其中一种主要的机制是通过小RNAs介导的,这些小RNAs包括小干扰RNAs、piwi相互作用的小RNAs、微小RNAs、扫描RNAs和21U-RNAs等。这些小RNAs可以通过DNA水平剪切转座序列,或在转录和(或)转录后水平沉默转座成分。该文就这些小RNAs沉默转座成分的机制和功能做一论述。     

内源小RNAs在植物病原体抗性反应中的作用

内源小RNAs是动植物基因表达的重要调节分子,它们可以通过指导mRNA的降解、抑制翻译或染色体修饰等机制,在转录水平或转录后水平或两个水平沉默基因.内源小RNAs在植物生长发育和生物和非生物胁迫适应反应中具有重要作用,其中3种内源性的小RNAs参与了植物基本免疫反应和对病原体的特异性免疫反应.内源小RNAs的发现为植物抗菌和抗病研究开辟了新思路,就这几种内源性的小RNAs的产生和它们在植物抗病原体反应中的作用做一概述.     

植物小RNAs的研究进展

小RNAs(长度小于40 nt)是nc-RNAs重要的一部分,现在植物中已发现了多种小RNAs,如小干扰RNAs(siRNAs)、微小RNAs(miRNAs)、反式作用的小干扰RNAs、天然反义转录小干扰RNAs、异染色质小干扰RNAs、长小片段小干扰RNAs、天然反义转录的微小RNAs及其一些未命名的小RNAs.成熟的小RNAs聚集相关的蛋白质因子,可以抑制转录,导致转录水平的基因沉默(TGS);或介导目标mRNA的剪切,抑制翻译,导致转录后水平基因沉默(PTGS).就这些植物小RNAs产生及其作用的研究进展作一概述     

小RNAs在生殖细胞发育过程中的作用

很多动物可以产生具调节作用的小RNAs,根据产生方式和作用机制可以将它们分为三类:微小RNAs(miRNAs)、与Piwi相互作用的RNAs(piRNAs)和内源小干扰RNAs(endo-siRNAs),这些小RNAs可以在生物生殖细胞发育过程中发挥重要作用。其中miRNAs的主要作用是调节蛋白质基因的表达;piRNAs主要的作用是沉默转座因子,但piRNAs主要存在于生殖细胞中;endo-siRNAs则可能具有上述两种主要作用。该文论述了这三种小RNAs在生物生殖细胞发育过程中的作用,同时也讨论了它们在治疗生物不育及其在生物节育方面的应用前景。     

抑制基因组转座子活性的小RNAs在生育调节中的作用

小RNAs可以在转录和转录后水平沉默转座子, 最近发现的几类小RNAs(piRNAs、endo-siRNAs)均具有抑制转座子活性的作用, 其中, 果蝇piRNAs、小鼠piRNAs、小鼠endo-siRNAs及其相关蛋白主要在生殖系表达, 说明小RNAs作用途径在生殖系转座子沉默中扮演着重要角色。最新的研究揭示了小RNAs、转座子沉默、生殖生育调节之间的联系, 然而其具体作用机制尚未得到阐明。文章综述了小RNAs对基因组转座子活性的控制及其在生育调节中的作用。     

小RNA分子与精子发生调控

近来研究发现小RNA(small RNAs)可作为转录后及翻译水平上基因表达调节的重要调节因子,利用小RNA来阐明调节精子发生的分子机制取得了显著进展。这些小RNA主要分为3类,即小干扰RNA(siRNA)、微小RNA(miRNA)以及与piwi蛋白相互作用的RNA(piRNA)。在减数分裂和精子发生过程中,小RNA具有多种生物学功能,如利用siRNA体外转染或体内注射来敲低特定基因从而研究该基因在精子发生过程中的作用;miRNA可能参与精子发生中有丝、减数及后减数分裂阶段的基因表达调节;piRNA主要参与调节雄性生殖细胞减数及后减数分裂的过程,在精子发生中起抑制反转录转座子(retrotransposons)的作用。文章对小RNAs合成、作用机制、功能及展望等最新进展进行了综述。     

小分子RNA抵御转座元件对基因组的侵袭

真核生物在漫长的进化繁衍过程中,一直处在抵御转座元件对基因组侵害的"斗争"中。在过去的十多年中,越来越多的证据指明,小分子RNA扮演了这样一个抵御转座子侵袭的角色。尽管这种抵御侵害的策略对于不同物种各具特点,但它们都呈现出惊人相似的共同特征。基本上,所有的机制都包含三个组成部分:首先,转座元件促使产生小分子RNA,在某些物种中主要是Piwi-interacting RNAs,而在其他物种中主要是small interfering RNAs;第二,作用于活跃转座子的小分子RNA通过RNA依赖性RNA聚合酶或切割机制进行扩增;第三,这些小分子RNA与含有Argonaute蛋白或Piwi蛋白的效应复合物相结合,从而作用于目标转座子的转录本,实现转录后沉默,或作用于目标转座子DNA,抑制染色质修饰和DNA甲基化。这些属性特征构成了一个限制由转座元件活动所造成的严重后果的系统,从而防止转座子侵袭所带来的突变积累,基因表达谱的改变,以及生殖腺发育不良和不育。     

天然反义转录物及其调控基因的表达机制

天然反义转录(NATs)是一组编码蛋白质或非编码蛋白质的RNAs, 与其他(有义)转录物具有互补序列, 可以调节有义链的表达。这种调节可以发生在转录水平或转录后水平, 调节方式有转录干扰、RNA封闭、双链依赖机制或染色质重建(修饰)等。正义链和反义链分别加工成小RNAs调节基因表达, 也是NATs调节基因表达的重要方式, 如piRNAs的“乒乓机制”。实验或计算机研究已经证明了NATs在生物中广泛存在, 是一种重要的基因表达调节方式。文章论述了NATs的重要作用和机理, 重点论述了NATs的调节机制和相关的小RNAs。     

miRNAs调控lincRNAs的生物信息学预测与功能分析

基因间长链非编码RNAs(Long intergenic non-coding RNAs, lincRNAs)是位于蛋白编码基因之间的长度超过200 nt的非编码RNAs, 在动物中参与细胞周期调控、免疫监视、胚胎干细胞分化等多种生物学过程, 但是lincRNAs在大多数植物中的功能尚不清楚。MicroRNAs(miRNAs)是真核生物中一类在转录水平和转录后水平介导基因沉默的21 nt左右的内源性单链小非编码RNAs分子, 通过序列互补的方式调控靶标基因的表达。目前miRNAs的靶标研究主要集中于编码蛋白的基因, 而对于靶标为非编码RNAs的研究较少, 尤其在植物中的研究更为少见。为了系统挖掘植物中lincRNAs的功能, 文章整合miRNAs数据、cDNAs数据和降解组数据, 利用生物信息学方法找到拟南芥(Arabidopsis thaliana)337个成熟miRNAs在2708个lincRNAs上的可能结合位点, 构建了miRNAs-mRNAs-lincRNAs调控网络, 并根据竞争性内源(ceRNA)假说预测lincRNAs的功能, 为进一步阐明植物中miRNAs对lincRNAs的调控机制以及lincRNAs的功能奠定了基础。     

小核仁RNAs及其衍生RNAs的研究进展

小核仁RNAs(small nucleolarRNAs,snoRNAs)是一类发现较早且位于核仁内的小非编码RNAs,在核糖体RNAs(ribosomalRNAs,rRNAs)、信使RNAs(messengerRNAs,mRNAs)、小核RNAs(small nuclearRNAs,snRNAs)的成熟及修饰中均发挥重要作用。snoRNAs的功能及其作用途径一直以来均是学术界的研究热点。目前,snoRNAs对rRNAs的化学修饰作用已得到广泛认可。另外,有研究表明snoRNAs与一些遗传疾病以及肿瘤性疾病的发生发展存在密切关联。近年来研究发现,部分snoRNAs经切割可生成更小的、有功能的RNAs,即小核仁RNAs衍生RNAs(snoRNAs derivedRNAs,sdRNAs),这些sdRNAs中部分具有微小RNAs(microRNAs,miRNAs)的特征,可发挥类似miRNA的作用,这一发现极大地拓展了snoRNAs的作用机制方式。结合国内外研究现状,在总结snoRNAs的结构和基本功能的基础上对sdRNAs与miRNAs之间的相关性进行了综述,以期为后续的相关研究提供参考。     

Small RNAs with 5′-Polyphosphate Termini Associate with a Piwi-Related Protein and Regulate Gene Expression in the Single-Celled Eukaryote Entamoeba histolytica

Small interfering RNAs regulate gene expression in diverse biological processes, including heterochromatin formation and DNA elimination, developmental regulation, and cell differentiation. In the single-celled eukaryote Entamoeba histolytica, we have identified a population of small RNAs of 27 nt size that (i) have 5′-polyphosphate termini, (ii) map antisense to genes, and (iii) associate with an E. histolytica Piwi-related protein. Whole genome microarray expression analysis revealed that essentially all genes to which antisense small RNAs map were not expressed under trophozoite conditions, the parasite stage from which the small RNAs were cloned. However, a number of these genes were expressed in other E. histolytica strains with an inverse correlation between small RNA and gene expression level, suggesting that these small RNAs mediate silencing of the cognate gene. Overall, our results demonstrate that E. histolytica has an abundant 27 nt small RNA population, with features similar to secondary siRNAs from C. elegans, and which appear to regulate gene expression. These data indicate that a silencing pathway mediated by 5′-polyphosphate siRNAs extends to single-celled eukaryotic organisms.     

The influences of PRG-1 on the expression of small RNAs and mRNAs

Background

In metazoans, Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that mutation of prg-1 causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects.

Results

In this study, we wanted to systematically demonstrate the function of PRG-1 in the regulation of small RNAs and their targets. By analyzing small RNAs and mRNAs with and without a mutation in prg-1 during C. elegans development, we demonstrated that (1) mutation of prg-1 leads to a decrease in the expression of 21U-RNAs, and causes 35 ~ 40% of miRNAs to be down-regulated; (2) in C. elegans, approximately 3% (6% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60 ~ 70% of these substantially altered protein-coding genes are up-regulated; (3) the target genes of the down-regulated miRNAs and the candidate target genes of the down-regulated 21U-RNAs are enriched in the up-regulated protein-coding genes; and (4) PRG-1 regulates protein-coding genes by down-regulating small RNAs (miRNAs and 21U-RNAs) that target genes that participate in the development of C. elegans.

Conclusions

In prg-1-mutated C. elegans, the expression of miRNAs and 21U-RNAs was reduced, and the protein-coding targets, which were associated with the development of C. elegans, were up-regulated. This may be the mechanism underlying PRG-1 function.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-321) contains supplementary material, which is available to authorized users.     

小RNAs与其靶标的相互调控

小RNAs 是生命活动非常重要且广泛存在的调节因子,可以调控基因表达和基因组稳定性. 然而最近的研究发现,小RNAs与它们的靶标间的调控是相互的调控(reciprocal regulation),因为它们的靶标反过来也可以调控小RNAs. 也就是说,它们的靶标可以通过自身与小RNA的互补程度或自身丰度水平,引发小RNAs无需模板地在其3′ 端添加核苷酸,导致小RNAs降解. 另外,病毒也可以通过这种方式调控宿主基因的表达. 这种现象的发现挑战了以前对小RNAs作用过程的理解,这不仅可以解释以前一些关于小RNAs所不能解释的问题,而且对于转基因技术、反义核酸技术和RNA干扰技术都有重要的启示作用. 本文综述了这种靶标引发小RNA修饰并降解现象的研究进展和应用前景.     

Epigenetic gene regulation by noncoding RNAs

Functional noncoding RNAs have distinct roles in epigenetic gene regulation. Large RNAs have been shown to control gene expression from a single locus (Tsix RNA), from chromosomal regions (Air RNA), and from entire chromosomes (roX and Xist RNAs). These RNAs regulate genes in cis; although the Drosophila roX RNAs can also function in trans. The chromatin modifications mediated by these RNAs can increase or decrease gene expression. These results suggest that the primary role of RNA molecules in epigenetic gene regulation is to restrict chromatin modifications to particular regions of the genome. However, given that RNA has been shown to be at the catalytic core of other ribonucleoprotein complexes, it is also possible that RNA also plays a role in modulating changes in chromatin structure.     

Reproducible features of small RNAs in C. elegans reveal NU RNAs and provide insights into 22G RNAs and 26G RNAs

Small RNAs regulate gene expression and most genes in the worm Caenorhabditis elegans are subject to their regulation. Here, we analyze small RNA data sets and use reproducible features of RNAs present in multiple data sets to discover a new class of small RNAs and to reveal insights into two known classes of small RNAs—22G RNAs and 26G RNAs. We found that reproducibly detected 22-nt RNAs, although are predominantly RNAs with a G at the 5′ end, also include RNAs with A, C, or U at the 5′ end. These RNAs are synthesized downstream from characteristic sequence motifs on mRNA and have U-tailed derivatives. Analysis of 26G RNAs revealed that they are processed from a blunt end of double-stranded RNAs and that production of one 26G RNA generates a hotspot immediately downstream for production of another. To our surprise, analysis of RNAs shorter than 18 nt revealed a new class of RNAs, which we call NU RNAs (pronounced “new RNAs”) because they have a NU bias at the 5′ end, where N is any nucleotide. NU RNAs are antisense to genes and originate downstream from U bases on mRNA. Although many genes have complementary NU RNAs, their genome-wide distribution is distinct from that of previously known classes of small RNAs. Our results suggest that current approaches underestimate reproducibly detected RNAs that are shorter than 18 nt, and theoretical considerations suggest that such shorter RNAs could be used for sequence-specific gene regulation in organisms like C. elegans that have small genomes.     

microRNAs - powerful repression comes from small RNAs

microRNAs (miRNAs) encode a novel class of small, non-coding RNAs that regulate gene expression post-trancriptionally. miRNAs comprise one of the major non-coding RNA families, whose diverse biological functions and unusual capacity for gene regulation have attracted enormous interests in the RNA world. Over the past 16 years, genetic, biochemical and computational approaches have greatly shaped the growth of the field, leading to the identification of thousands of miRNA genes in nearly all metazoans. The key molecular machinery for miRNA biogenesis and silencing has been identified, yet the precise biochemical and regulatory mechanisms still remain elusive. However, recent findings have shed new light on how miRNAs are generated and how they function to repress gene expression. miRNAs provide a paradigm for endogenous small RNAs that mediate gene silencing at a genome-wide level. The gene silencing mediated by these small RNAs constitutes a major component of gene regulation during various developmental and physiological processes. The accumulating knowledge about their biogenesis and gene silencing mechanism will add a new dimension to our understanding about the complex gene regulatory networks.