综述: 适配子介导的siRNA转运

小分子干扰RNA(small interfering RNA,siRNA)因能快速抑制哺乳动物特定基因的表达而用于各种疾病的治疗,然而选择合适的载体将siRNA安全有效地转运进入靶细胞仍是制约siRNA应用于临床治疗的重要因素．越来越多的转运载体被开发出来,其中包括针对细胞表面蛋白的适配子(aptamer)．Aptamer是一种能与靶分子高特异性和高亲和结合的寡核苷酸,已经越来越多地用于疾病的诊断和治疗．Aptamer作为载体介导siRNA转运可提高治疗的靶向性并减少副作用,这将为siRNA应用于临床靶向治疗提供一种特异有效的途径．目前,已经发现几种aptamers可以介导siRNA的转运,如anti-PSMA aptamer,anti-HIV gp120 aptamer,anti-CD4 aptamer等．本文将综述aptamer介导siRNA转运的最新研究进展．     

Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants

Many plant small RNAs are sequence-specific negative regulators of target mRNAs and/or chromatin. In angiosperms, the two most abundant endogenous small RNA populations are usually 21-nucleotide microRNAs (miRNAs) and 24-nucleotide heterochromatic short interfering RNAs (siRNAs). Heterochromatic siRNAs are derived from repetitive regions and reinforce DNA methylation at targeted loci. The existence and extent of heterochromatic siRNAs in other land plant lineages has been unclear. Using small RNA-sequencing (RNA-seq) of the moss Physcomitrella patens, we identified 1090 loci that produce mostly 23- to 24-nucleotide siRNAs. These loci are mostly in intergenic regions with dense DNA methylation. Accumulation of siRNAs from these loci depends upon P. patens homologs of DICER-LIKE3 (DCL3), RNA-DEPENDENT RNA POLYMERASE2, and the largest subunit of DNA-DEPENDENT RNA POLYMERASE IV, with the largest subunit of a Pol V homolog contributing to expression at a smaller subset of the loci. A MINIMAL DICER-LIKE (mDCL) gene, which lacks the N-terminal helicase domain typical of DCL proteins, is specifically required for 23-nucleotide siRNA accumulation. We conclude that heterochromatic siRNAs, and their biogenesis pathways, are largely identical between angiosperms and P. patens, with the notable exception of the P. patens-specific use of mDCL to produce 23-nucleotide siRNAs.     

Arabidopsis RNA-Dependent RNA Polymerases and Dicer-Like Proteins in Antiviral Defense and Small Interfering RNA Biogenesis during Turnip Mosaic Virus Infection

Plants respond to virus infections by activation of RNA-based silencing, which limits infection at both the single-cell and system levels. Viruses encode RNA silencing suppressor proteins that interfere with this response. Wild-type Arabidopsis thaliana is immune to silencing suppressor (HC-Pro)-deficient Turnip mosaic virus, but immunity was lost in the absence of DICER-LIKE proteins DCL4 and DCL2. Systematic analysis of susceptibility and small RNA formation in Arabidopsis mutants lacking combinations of RNA-dependent RNA polymerase (RDR) and DCL proteins revealed that the vast majority of virus-derived small interfering RNAs (siRNAs) were dependent on DCL4 and RDR1, although full antiviral defense also required DCL2 and RDR6. Among the DCLs, DCL4 was sufficient for antiviral silencing in inoculated leaves, but DCL2 and DCL4 were both involved in silencing in systemic tissues (inflorescences). Basal levels of antiviral RNA silencing and siRNA biogenesis were detected in mutants lacking RDR1, RDR2, and RDR6, indicating an alternate route to form double-stranded RNA that does not depend on the three previously characterized RDR proteins.     

Small cytoplasmic RNAs and their location within the cytoplasm

These studies were designed to establish the location of various species of small RNAs within the subcellular cytoplasmic compartments. Four cytoplasmic RNA-containing compartments were examined: (A) cytoskeleton-bound polyribosomal ribonucleoprotein (RNP) complexes, (B) soluble-phase polyribosomal RNP complexes, (C) cytoskeleton-bound free RNP complexes, (D) soluble-phase free RNP complexes. The presence of the small cytoplasmic RNA (scRNA) population and histone H4 and actin mRNAs in each compartment was examined to determine their spatial distribution within the cytoplasm. The 7S signal recognition RNA and the 5S and 5.8S rRNAs were distributed among all four compartments, while 4S tRNAs were localized largely in fraction D. Fraction C contained a group of seven abundant scRNAs, of approximately 105-348 nucleotides in length, which were localized almost entirely within the cytoskeleton-bound free RNP compartment. Actin mRNAs were localized in fraction A, the actively translating cytoskeleton-bound compartment. Actin mRNAs were localized in fraction A, the actively translating cytoskeleton-bound compartment. Following cytochalasin B treatment, actin mRNAs were released into the soluble phase, implicating a dependence on the integrity of actin filaments in its binding. Such treatment also released several of the scRNAs from their cytoskeleton-bound location. In contrast histone H4 mRNAs were much more widely dispersed, being present in all four cytoskeletal compartments. Approximately 60% of the H4 mRNAs, however, were localized within the soluble-phase polyribosomes in fraction B. Cytochalasin B treatment released only the small portion of untranslated histone H4 mRNA associated with the cytoskeleton in fraction C, suggesting that the binding of these H4 mRNAs was dependent in some manner upon the integrity of actin filaments.     

小RNA与蛋白质的相互作用

小分子调控RNA,包括siRNA（small interfering RNA）、miRNA（microRNA）和piRNA（piwiinteracting RNA）、hsRNA（heterochromatin associatedsmall RNA）等,是当前生命科学研究的前沿热点。越来越多的证据表明,这些小分子RNA存在于几乎所有较高等的真核生物细胞中,对生物体具有非常重要的调控功能。它们通过各种序列特异性的RNA基因沉默作用,包括RNA干扰（RNAi）、翻译抑制、异染色质形成等,调控诸如生长发育、应激反应、沉默转座子等各种各样的细胞进程。随着对这些小分子调控RNA的发现,一些RNascⅢ酶家族成员、Argonaute蛋白质家族成员及RNA结合蛋白质等先后被鉴定为小RNA的胞内蛋白质合作者,参与小RNA的加工成熟和在细胞内行使功能。本综述简介一些RNA沉默作用途径中重要组分的结构和功能的研究进展。     

Natural variation in MAM within and between populations of Arabidopsis lyrata determines glucosinolate phenotype

The genetic variation that underlies the glucosinolate phenotype of Arabidopsis lyrata ssp. petraea was investigated between and within populations. A candidate glucosinolate biosynthetic locus (MAM, containing methylthioalkylmalate synthase genes) was mapped in A. lyrata to a location on linkage group 6 corresponding to the homologous location for MAM in A. thaliana. In A. thaliana MAM is responsible for side chain elongation in aliphatic glucosinolates, and the MAM phenotype can be characterized by the ratios of long- to short-chain glucosinolates. A quantitative trait loci (QTL) analysis of glucosinolate ratios in an A. lyrata interpopulation cross found one QTL at MAM. Additional QTL were identified for total indolic glucosinolates and for the ratio of aliphatic to indolic glucosinolates. MAM was then used as the candidate gene for a within-population cosegregation analysis in a natural A. lyrata population from Germany. Extensive variation in microsatellite markers at MAM was found and this variation cosegregated with the same glucosinolate ratios as in the QTL study. The combined results indicate that both between- and within-population genetic variation in the MAM region determines phenotypic variation in glucosinolate side chains in A. lyrata.     

脆性组氨酸三联体基因小干扰RNA的构建及干扰效果检测

目的:构建脆性组氨酸三联体(FHIT)基因的小干扰RNA(siRNA),并检测其对293T细胞内源性FHIT基因表达的干扰效果。方法:根据FHIT基因序列,通过生物信息学网站预测可能的siRNA,从中筛选出2条合理的FHIT-siRNA,将其克隆到siRNA表达载体pSilencer2.1-U6Hygro中,转化大肠杆菌DH5α,挑取阳性克隆进行测序鉴定;将构建成功的FHIT-siRNA重组载体转染人胚肾细胞293T,Western印迹检测siRNA对293T内源性FHIT表达的干扰效果。结果:构建了2个FHIT-siRNA重组质粒,2条siRNA都有干扰作用,其中一条的作用效果可达50%以上。结论:构建的FHIT-siRNA为进一步研究FHIT的功能提供了有利的工具。     

SUMO-1小干扰RNA的构建及其干扰效果检测

目的:构建小泛素相关修饰物-1(SUMO-1)基因的小干扰RNA(siRNA),并检测其对SUMO-1基因表达的干扰效果。方法:根据SUMO-1基因序列设计一条合理的SUMO-1siRNA,并将其克隆到pSliencer2.1-U6neo载体中,转化大肠杆菌DH5α,挑取阳性菌落进行酶切和测序鉴定;将构建的SUMO-1siRNA重组质粒单独转染或与带HA标签的SUMO-1表达载体共同转染人胚肾293T细胞,收集细胞裂解物,以抗HA和SUMO-1的抗体用Western印迹检测siRNA的干扰效果。结果:构建了SUMO-1siRNA重组质粒,干扰效果可达80%以上。结论:构建的SUMO-1siRNA为进一步进行蛋白质SUMO-1化修饰的研究奠定了基础。     

干扰小RNA序列非依赖性地影响胰腺癌细胞的基因表达

干扰小RNA(small interference RNA, siRNA)是基因敲减的常用工具,广泛用于基因沉默技术和基因功能研究,在临床疾病治疗等方面也有潜在的应用。一般认为,达到一定长度（比如大于27 bp）的双链RNA可以诱导干扰素反应,降低相关基因的表达。目前,siRNA对基因表达的非特异性作用尚不完全清楚。为研究siRNA干扰的非特异基因表达,本研究以胰腺癌细胞HPAC 和BxPC3 为模型,采用高通量测序技术对6种不同干扰小RNA处理及未作处理的HPAC和BxPC3细胞进行转录组测序分析,筛选出干扰小RNA处理后表达量共同下调的基因进行研究。通过生物信息学方法对表达下调基因的功能进行研究,并利用实时荧光定量PCR(qRT-PCR)技术对部分下调基因进行验证。结果表明,短片段双链小RNA能够显著改变细胞的基因表达,而这些基因表达谱的变化是有规律的,特定功能的基因优先发生变化。在表达下调的基因中,某些特定类型的基因变化非常显著,包括氨基酸代谢相关基因、Hedgehog信号途径基因和多巴胺受体D5基因等。这些结果表明,在使用siRNA时需要考虑其序列非依赖性地基因表达调控作用。     

Global Analyses of Small Interfering RNAs Derived from Bamboo mosaic virus and Its Associated Satellite RNAs in Different Plants

Background

Satellite RNAs (satRNAs), virus parasites, are exclusively associated with plant virus infection and have attracted much interest over the last 3 decades. Upon virus infection, virus-specific small interfering RNAs (vsiRNAs) are produced by dicer-like (DCL) endoribonucleases for anti-viral defense. The composition of vsiRNAs has been studied extensively; however, studies of satRNA-derived siRNAs (satsiRNAs) or siRNA profiles after satRNA co-infection are limited. Here, we report on the small RNA profiles associated with infection with Bamboo mosaic virus (BaMV) and its two satellite RNAs (satBaMVs) in Nicotiana benthamiana and Arabidopsis thaliana.

Methodology/Principal Findings

Leaves of N. benthamiana or A. thaliana inoculated with water, BaMV alone or co-inoculated with interfering or noninterfering satBaMV were collected for RNA extraction, then large-scale Solexa sequencing. Up to about 20% of total siRNAs as BaMV-specific siRNAs were accumulated in highly susceptible N. benthamiana leaves inoculated with BaMV alone or co-inoculated with noninterfering satBaMV; however, only about 0.1% of vsiRNAs were produced in plants co-infected with interfering satBaMV. The abundant region of siRNA distribution along BaMV and satBaMV genomes differed by host but not by co-infection with satBaMV. Most of the BaMV and satBaMV siRNAs were 21 or 22 nt, of both (+) and (−) polarities; however, a higher proportion of 22-nt BaMV and satBaMV siRNAs were generated in N. benthamiana than in A. thaliana. Furthermore, the proportion of non-viral 24-nt siRNAs was greatly increased in N. benthamiana after virus infection.

Conclusions/Significance

The overall composition of vsiRNAs and satsiRNAs in the infected plants reflect the combined action of virus, satRNA and different DCLs in host plants. Our findings suggest that the structure and/or sequence demands of various DCLs in different hosts may result in differential susceptibility to the same virus. DCL2 producing 24-nt siRNAs under biotic stresses may play a vital role in the antiviral mechanism in N. benthamiana.     

Environmental marginality and geographic range limits: a case study with Arabidopsis lyrata ssp. lyrata

Understanding the factors that govern the distribution of species is a central goal of evolutionary ecology. It is commonly assumed that geographic range limits reflect ecological niche limits and that species experience increasingly marginal conditions towards the edge of their ranges. Using spatial data and ecological niche models we tested these hypotheses in Arabidopsis lyrata. Specifically, we asked whether range limits coincide with predicted niche limits in this system and whether the suitability of sites declines towards the edge of the species’ range in North America. We further explored patterns of environmental change towards the edge of the range and asked whether genome‐wide patterns of genetic diversity decline with increasing peripherality and environmental marginality. Our results suggest that latitudinal range limits coincide with niche limits. Populations experienced increasingly marginal environments towards these limits – though patterns of environmental change were more complex than most theoretical models for range limits assume. Genomic diversity declined towards the edge of the species’ range and with increasing distance from the estimated centre of the species’ niche in environmental space, but not with the suitability of sites based on niche model predictions. Thus while latitudinal range limits in this system are broadly associated with niche limits, the link between environmental conditions and genetic diversity (and thus the adaptive potential of populations) is less clear.