Xist nucleates local protein gradients to propagate silencing across the X chromosome

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昆虫RNA沉默抗病毒机制研究进展

RNA沉默是昆虫用来抵御病毒入侵的一种普遍而又进化保守的防御机制, 而昆虫病毒也会相应地编码沉默抑制子来破坏宿主的防御功能。本文主要结合果蝇的相关研究成果对昆虫RNA沉默抗病毒机制、 RNA沉默抑制子的作用特征及宿主与病毒的共进化关系做一综述。研究表明, 由小干扰RNA (small interfering RNAs, siRNA)介导的RNA干扰在果蝇抗病毒防御机制中发挥重要作用。果蝇中Dicer-2（Dcr-2）, argonaute-2（AGO2）和双链RNA结合蛋白R2D2是siRNA干扰途径中的3个关键组分, 这3个基因的缺失或突变会显著提高果蝇对RNA病毒的感受性。此外, 果蝇中还鉴定了其他与RNA干扰密切相关的基因, 如vasa intronic gene, aubergine, armitage, rm62 和piwi, 它们在抗病毒感染中同样发挥重要作用。果蝇病毒中已鉴定出3种RNA沉默病毒抑制子（viral suppressors of RNAi, VSRs）, 分别为果蝇FHV病毒沉默抑制子FHV-B2、 果蝇C病毒沉默抑制子DCV-1A及果蝇CrPV病毒沉默抑制子CrPV-1A。FHV-B2和DCV-1A通过与dsRNA或siRNA结合抑制RNA沉默, 而CrPV-1A通过与AGO2结合阻止RISC的形成抑制RNA沉默。在漫长的进化过程中, 病毒和宿主相互博弈, 协同进化。昆虫抗病毒沉默途径中的关键组分通过保持持续和快速进化来对抗高度变异的VSRs。     

RNA silencing movement in plants

Multicellular organisms, like higher plants, need to coordinate their growth and development and to cope with environmental cues. To achieve this, various signal molecules are transported between neighboring cells and distant organs to control the fate of the recipient cells and organs. RNA silencing produces cell non-autonomous signal molecules that can move over short or long distances leading to the sequence specific silencing of a target gene in a well defined area of cells or throughout the entire plant,respectively. The nature of these signal molecules, the route of silencing spread, and the genes involved in their production, movement and reception are discussed in this review. Additionally, a short section on features of silencing spread in animal models is presented at the end of this review.     

长非编码RNA编码微肽的研究进展

长非编码RNA(long non-coding RNA,lncRNA)是长度超过200 nt的非编码RNA,具有一个或多个短开放阅读框,可编码功能性微肽。这些功能性微肽在各种生物过程中扮演着重要角色,例如Ca2+转运、线粒体代谢、肌细胞融合和细胞衰老等过程。同时,这些生物过程又在机体稳态调控、疾病和癌症的发生与发展、胚胎发育等重要生理过程中起关键作用。因此,研究由lncRNA编码的微肽在生物体的潜在的调控机制,将有助于进一步解析生物体潜在调控过程,并为后续疾病的靶向治疗及动物生长性能的提高提供新的理论依据。本文综述了现阶段lncRNA编码微肽领域的最新研究进展,并对当前微肽在肌肉生理、炎症与免疫、人类常见癌症、胚胎发育等领域的研究进展进行描述与总结,最后简单阐述了lncRNA编码微肽现阶段面临的问题和存在的挑战,以期为后续微肽的深入研究提供科学参考及新思路。     

RNA沉默与植物病毒

植物中RNA沉默（RNAsilencing)亦称为转录后基因沉默（PTGS）或共抑制,是植物抵抗外来核酸（转座子、转基因或病毒）入侵,并保护自身基因组完整性的一种防御机制。RNA沉默是近十年来发现的植物界中普遍存在的现象,已成为植物分子生物学领域的一个新的研究方向。对RNA沉默特点和机制的研究表明,植物病毒与（转基因）植物内发生的RNA沉默有着密切的联系,作者从病毒对RNA沉默的诱导、抑制、防御等方面,简述了RNA沉默与病毒的关系。并对病毒载体所诱导的RNA沉默在植物发育和基因组功能分析等方面的应用价值进行了讨论。     

Xist-mediated chromatin changes that establish silencing of an entire X chromosome in mammals

X chromosome inactivation (XCI) ensures an equal gene dosage between the sexes in placental mammals. Xist, a modular multi-domain X-encoded long non-coding RNA coats the X chromosome in cis during XCI. Xist recruits chromatin remodelers and repressor complexes ensuring silencing of the inactive X (Xi). Here, we review the recent work focused on the role of Xist functional repeats and interacting RNA-binding factors in the establishment of the silent state. Xist orchestrates recruitment of remodelers and repressors that first facilitate removal of the active chromatin landscape and subsequently direct the transition into a repressive heterochromatic environment. Some of these factors affect silencing on a chromosome-wide scale, while others display gene-specific silencing defects. The temporal order of recruitment shows each silencing step is party dependent on one another. After the Xi is established, many of the factors are dispensable, and a different repertoire of proteins ensure the silenced Xi is maintained and propagated.     

RNA silencing movement in plants

Higher eukaryotes have developed a mechanism of sequence-specific RNA degradation which is known as RNA silencing. In plants and some animals, similar to the nematode Caenorhabditis elegans, RNA silencing is a non-cell-autonomous event. Hence, silencing initiation in one or a few cells leads progressively to the sequence-specific suppression of homologous sequences in neighbouring cells in an RNA-mediated fashion. Spreading of silencing in plants occurs through plasmodesmata and results from a cell-to-cell movement of a short-range silencing signal, most probably 21-nt siRNAs (short interfering RNAs) that are produced by one of the plant Dicer enzymes. In addition, silencing spreads systemically through the phloem system of the plants, which also translocates metabolites from source to sink tissues. Unlike the short-range silencing signal, there is little known about the mediators of systemic silencing. Recent studies have revealed various and sometimes surprising genetic elements of the short-range silencing spread pathway, elucidating several aspects of the processes involved. In this review we attempt to clarify commonalities and differences between the individual silencing pathways of RNA silencing spread in plants.     

RNA沉默在植物生物逆境反应中的作用

RNA沉默是真核生物共有的基因表达调节机制和防御机制。在植物RNA沉默中, 一些小RNAs, 如微小 RNAs和小干扰RNAs, 在植物防御病毒、细菌或食草动物的反应中具有重要作用。为了抑制宿主的RNA沉默系统, 植物病毒或细菌进化出了在RNA沉默不同阶段起作用的病毒沉默抑制子或细菌沉默抑制子, 来克服寄主的RNA沉默反应。文章就植物RNA沉默、病毒沉默抑制子、细菌沉默抑制子及其相关防御反应的一些新进展做一概述。     

Dynamics of gene silencing by RNA interference

The large number of candidate genes identified by modern high-throughput technologies require efficient methods for generating knockout phenotypes or gene silencing in order to study gene function. RNA interference (RNAi) is an efficient method that can be used for this purpose. Effective gene silencing by RNAi depends on a number of important parameters, including the dynamics of gene expression and the RNA dose. Using mouse hepatoma cells, we detail some of the principal characteristics of RNAi as a tool for gene silencing, such as the RNA dose level, RNA complex exposure time, and the time of transfection relative to gene induction, in the context of silencing a green fluorescent protein reporter gene. Our experiments demonstrate that different levels of silencing can be attained by modulating the dose level of RNA and the time of transfection and illustrate the importance of a dynamic analysis in designing robust silencing protocols. By quantifying the kinetics of RNAi-based gene silencing, we present a model that may be used to help determine key parameters in more complex silencing experiments and explore alternative gene silencing protocols.     

植物RNA沉默的分子机制研究进展

RNA沉默（RNA silencing）是真核生物中的一种抵抗外源遗传因子（病毒、转座子或转基因）及调控基凶表达的防御机制。参与植物RNA沉默的酶及蛋白质主要包括6种RNA依赖的RNA聚合酶、4种Dicer-like（DCL）核酸内切酶和10种Argonautes蛋白。植物中4条RNA沉默途径分别由微小RNA（miRNAs）和3种小干扰RNA（siRNAs）介导,包括反式作用siRNAs（ta－siRNAs）、天然反义siRNAs（natsiRNAs）和异染色质siRNAs（hc-siRNAs）。在植物RNA沉默的系统性传播中,由DCL4或DCL2将dsRNAs裁剪为次级SiRNAS,以放大RNA沉默信号和增强沉默效应。     

Suppressors of RNA silencing encoded by plant viruses and their role in viral infections

RNA silencing as a robust host defense mechanism against plant viruses is generally countered by virus-encoded silencing suppressors. This strategy is now increasingly recognized to be used by animal viruses as well. We present here an overview of the common features shared by some of the better studied plant viral silencing suppressors. We then briefly describe the characteristics of the few reported animal viral suppressors, notably their extraordinary ability of cross-kingdom suppression. We next discuss the basis for biased protection of viral RNA and subviral parasites by silencing suppressors, the link between movement and silencing suppression, the influence of temperature on the outcome of viral infection and the effect of viral silencing suppressors on the microRNA pathway.     

RNA:诱导基因沉默

在生物体中,双链RNA(double-strand RNA,dsRNA)裂解后的小RNA可以诱导细胞质和基因组水平外源基因沉默。所谓基因沉默(gene silencing)是指生物体中特定基因由于种种原因不表达。小RNA能诱导互补信使RNA在转录后降解。RNA沉默是基因组水平的免疫现象,代表了进化过程中原始的基因组对抗外源基因序列表达的保护机制,在动植物进化中起着重要作用,RNA沉默具有抵抗病毒入侵、抑制转座子活动等作用,并调控蛋白编码基因的表达,具有十分诱人的应用前景。     

RNA沉默在分析植物基因功能方面的研究

RNA沉默是真核生物的一种高度保守的和序列特异的RNA降解系统,它不但是基础生物学领域的研究热点,同时在调节基因表达或研究基因功能方面也是非常有前景的。植物中的转录后基因沉默（PTGS）是RNA沉默的一种形式,通过PTGS能对目标RNA进行特异性降解。对双链RNA（dsRNA）在RNA沉默启动中所起中心作用的认知,形成了几种RNA沉默载体的构建方法,这些方法与基因组资源相结合,通过转基因或非转基因的方法能够快速和高效研究植物的基因功能。     

RNA silencing in fungi: mechanisms and applications

Two RNA silencing-related phenomena, quelling and meiotic silencing by unpaired DNA (MSUD) have been identified in the fungus Neurospora crassa. Similar to the case with the siRNA and miRNA pathways in Drosophila, different sets of protein components including RNA-dependent RNA polymerase, argonaute and dicer, are used in the quelling and MSUD pathways. Orthologs of the RNA silencing components are found in most, but not all, fungal genomes currently available in the public databases, indicating that the majority of fungi possess the silencing machinery. Advantage and disadvantage of RNA silencing as a tool to explore gene function in fungi are discussed.