RNAi, DRD1, and histone methylation actively target developmentally important Non-CG DNA methylation in Arabidopsis

Cytosine DNA methylation protects eukaryotic genomes by silencing transposons and harmful DNAs, but also regulates gene expression during normal development. Loss of CG methylation in the Arabidopsis thaliana met1 and ddm1 mutants causes varied and stochastic developmental defects that are often inherited independently of the original met1 or ddm1 mutation. Loss of non-CG methylation in plants with combined mutations in the DRM and CMT3 genes also causes a suite of developmental defects. We show here that the pleiotropic developmental defects of drm1 drm2 cmt3 triple mutant plants are fully recessive, and unlike phenotypes caused by met1 and ddm1, are not inherited independently of the drm and cmt3 mutations. Developmental phenotypes are also reversed when drm1 drm2 cmt3 plants are transformed with DRM2 or CMT3, implying that non-CG DNA methylation is efficiently re-established by sequence-specific signals. We provide evidence that these signals include RNA silencing though the 24-nucleotide short interfering RNA (siRNA) pathway as well as histone H3K9 methylation, both of which converge on the putative chromatin-remodeling protein DRD1. These signals act in at least three partially intersecting pathways that control the locus-specific patterning of non-CG methylation by the DRM2 and CMT3 methyltransferases. Our results suggest that non-CG DNA methylation that is inherited via a network of persistent targeting signals has been co-opted to regulate developmentally important genes. © 2006 Chan et al.

HSPC117 deficiency in cloned embryos causes placental abnormality and fetal death

Somatic cell nuclear transfer (SCNT) has been successfully used in many species to produce live cloned offspring, albeit with low efficiency. The low frequency of successful development has usually been ascribed to incomplete or inappropriate reprogramming of the transferred nuclear genome. Elucidating the genetic differences between normal fertilized and cloned embryos is key to understand the low efficiency of SCNT. Here, we show that expression of HSPC117, which encodes a hypothetical protein of unknown function, was absent or very low in cloned mouse blastocysts. To investigate the role of HSPC117 in embryo development, we knocked-down this gene in normal fertilized embryos using RNA interference. We assessed the post-implantation survival of HSPC117 knock-down embryos at 3 stages: E9 (prior to placenta formation); E12 (after the placenta was fully functional) and E19 (post-natal). Our results show that, although siRNA-treated in vivo fertilized/produced (IVP) embryos could develop to the blastocyst stage and implanted without any difference from control embryos, the knock-down embryos showed substantial fetal death, accompanied by placental blood clotting, at E12. Furthermore, comparison of HSPC117 expression in placentas of nuclear transfer (NT), intracytoplasmic sperm injection (ICSI) and IVP embryos confirmed that HSPC117 deficiency correlates well with failures in embryo development: all NT embryos with a fetus, as well as IVP and ICSI embryos, had normal placental HSPC117 expression while those NT embryos showing reduced or no expression of HSPC117 failed to form a fetus. In conclusion, we show that HSPC117 is an important gene for post-implantation development of embryos, and that HSPC117 deficiency leads to fetal abnormalities after implantation, especially following placental formation. We suggest that defects in HSPC117 expression may be an important contributing factor to loss of cloned NT embryos in vivo. (C) 2010 Elsevier Inc. All rights reserved.

RNA干扰在抗病毒研究中的应用

国家自然科学基金海外杰出青年基金(30428024)资助

Zebrafish peptidoglycan recognition protein SC (zfPGRP-SC) mediates multiple intracellular signaling pathways

Insect PGRPs can function as bacterial recognition molecules triggering proteolytic and/or signal transduction pathways, with the resultant production of antimicrobial peptides. To explore if zebrafish peptidoglycan recognition protein SC (zfPGRP-SC) has such effects, RNA interference (siRNA) and high-density oligonucleotide microarray analysis were used to identify differentially expressed genes regulated by zfPGRP-SC. The mRNA levels for a set of genes involved in Toll-like receptor signaling pathway, such as TLRs, SARM, MyD88, TRAF6 and nuclear factor (NF)-kappa B2 (p100/p52), were examined by quantitative RT-PCR (QT-PCR). The results from the arrays and QT-PCR showed that the expression of 133 genes was involved in signal transduction pathways, which included Toll-like receptor signaling, Wnt signaling, BMP signaling, insulin receptor signaling, TGF-beta signaling, GPCR signaling, small GTPase signaling, second-messenger-mediated signaling, MAPK signaling, JAK/STAT signaling, apoptosis and anti-apoptosis signaling and other signaling cascades. These signaling pathways may connect with each other to form a complex network to regulate not just immune responses but also other processes such as development and apoptosis. When transiently over-expressed in HEK293T cells, zfPGRP-SC inhibited NF-kappa B activity with and without lipopolysacharide (LPS) stimulation. (C) 2008 Elsevier Ltd. All rights reserved.

RNAi suppression of zebrafish peptidoglycan recognition protein 6 (zfPGRP6) mediated differentially expressed genes involved in Toll-like receptor signaling pathway and caused increased susceptibility to Flavobacterium columnare

In Drosophila, Toll signaling cascade, which resembles the mammalian Toll-like receptor (TLR)/IL-1R signaling pathways and regulates the expression of anti-microbial peptide genes, mainly relies on peptidoglycan recognition proteins (PGRPs) for the detection of bacterial pathogens. To explore the effect of zebrafish peptidoglycan recognition protein 6 (zfPGRP6) on Toll-like receptor signaling pathway, RNA interference (siRNA) and real time quantitative PCR (RQ-PCR) methods were used to identify differentially expressed genes regulated by zfPGRP6. The target genes included TLR2, TLR3, TLR5, TLR7, TLR8, IL1R, Sterile-alpha and Armadillo motif containing protein (SARM), myeloid differentiation factor 88 (MyD88) and nuclear factor (NF)-kappa B2 (p100/p52). The results of RQ-PCR showed that RNAi-mediated Suppression of zfPGRP6 significantly down-regulated the expression of TLR2, TLR5, IL1R, SARM, MyD88 and p100/p52. The expression of beta-defensin-1 was also down-regulated in those embryos silenced by zfPGRP6. In challenge experiments to determine the anti-bacterial response to Gram-negative bacteria, RNAi knock-down of zfPGRP6 markedly increased susceptibility to Flavobacterium columnare. (C) 2008 Elsevier B.V. All rights reserved.

Knock down of gfp and no tail expression in zebrafish embryo by in vivo-transcribed short hairpin RNA with T7 plasmid system

A short-hairpin RNA (shRNA) expression system, based on T7 RNA polymerase (T7RP) directed transcription machinery, has been developed and used to generate a knock down effect in zebrafish embryos by targeting green fluorescent protein (gfp) and no tail (ntl) mRNA. The vector pCMVT7R harboring T7RP driven by CMV promoter was introduced into zebrafish embryos and the germline transmitted transgenic individuals were screened out for subsequent RNAi application. The shRNA transcription vectors pT7shRNA were constructed and validated by in vivo transcription assay. When pT7shGFP vector was injected into the transgenic embryos stably expressing T7RP, gfp relative expression level showed a decrease of 68% by analysis of fluorescence real time RT-PCR. As a control, injection of chemical synthesized siRNA resulted in expression level of 40% lower than the control when the injection dose was as high as 2 mu g/mu l. More importantly, injection of pT7shNTL vector in zebrafish embryos expressing T7RP led to partial absence of endogenous ntl transcripts in 30% of the injected embryos when detected by whole mount in situ hybridization. Herein, the T7 transcription system could be used to drive the expression of shRNA in zebrafish embryos and result in gene knock down effect, suggesting a potential role for its application in RNAi studies in zebrafish embryos.

APOBEC3G 多重转录本的发现和部分表达特征的研究

APOBEC3G（apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G，载脂蛋白B mRNA编辑酶催化多肽样蛋白3G，简称为A3G）是2002年Sheehy 发现的天然抗病毒限制因子，代表近年来病毒研究领域的一项重大进展,不仅拓 展了对病毒宿主相互作用的认识,也为研发抗病毒药提供了新的思路和方向。不 过，A3G的结构、功能和抗病毒机制仍有许多未解的重大问题，进一步深入和系 统的研究，可能为预防和治疗HIV/AIDS及多种病毒性疾病，提供新的线索。 本研究的最初线索，来源于前期工作中的偶然发现：我们试图在一个健康个 体PBMC 中克隆A3G 编码序列，经双向测序后发现，有5 个位点属非同义突变， 造成氨基酸序列的改变。为排除个体差异并出于研究的便利，我们采用单核样细 胞系THP-1，进行多条序列的克隆和分析。在研究中，我们使用错误率仅为 1.6x10-6 的高保真酶Pfu，共克隆到23 条A3G 基因编码序列。经双向测序和对比 分析，较为意外地发现，其中20 条序列具有2 个以上的非同义突变或截断错位， 突变率高达87%，显示A3G 基因在THP-1 细胞中存在多重正常或变异的转录本。 这一现象，是否代表天然突变的普遍性以及其频度和意义，有待于进一步在多种 细胞和人群多个个体中验证和大规模的系统研究。 为建立基本的实验体系和研究手段，我们通过RT-PCR 与Western blotting， 检测了A3G 基因在9 个细胞系内的本底表达水平，并在此筛选结果的基础上， 在低本底的细胞系中，以慢病毒系统表达A3G 基因，而在高本底细胞系中，通 过siRNA 沉默A3G 基因，建立了A3G 高低表达体系，为后续研究A3G 功能提 供了方便可行的实验平台。 我们选取野生型A3G、带有3 个位点（H186R、I309T、F310S）连锁的突 变体和5 个位点（W34R、Y222H、V224G、A246V、F289L）非连锁的突变体， 构建真核表达载体，转染HEK293T 细胞，对比观察不同转录本在细胞中的表达 动态和水平。结果发现，3 个位点的突变对A3G 蛋白细胞内定位无明显影响，5 个位点的突变明显增加了单个细胞中A3G 蛋白点灶状团块的比例。并且突变位 点明显减缓了A3G 的表达速率，降低了表达水平。而连锁、非连锁以及截断错 位的突变体在抗病毒功能和结构生物学上的意义，有待于进一步的深入分析。 综上，我们发现A3G 在THP-1 细胞中存在多重转录本，并在确定细胞系A3G 本底表达的基础上，建立了A3G 体外高低表达体系，为后续我们进一步研究 A3G 的功能奠定了基础。而部分突变体在细胞内的表达趋势和细胞内定位的观 察和分析，为进一步的深入研究提供了新的线索。

贾第虫microRNA 及其靶基因的预测与验证

MicroRNAs (miRNAs)是一类长约21-25nt 的非编码小分子RNAs，通过与靶基因的互补结合在转录水平及转录后水平来负调控基因表达。人们已在众多高等多细胞生物中如人、果蝇、线虫、拟南芥等鉴定出众多microRNAs 分子。近来报道单细胞原生生物衣藻中也存在大量microRNAs。然而到目前为止，在被很多证据证实是最原始的单细胞真核生物贾第虫中却仍未有microRNAs 的报道。那么到底贾第虫这种具有特殊进化地位的单细胞原生动物是否存在有microRNAs 呢？如果存在的话，其microRNAs 的特点是什么？与高等多细胞生物及单细胞衣藻的 microRNA 相比又有何异同点呢？贾第虫的microRNAs 是否与其致病性相关呢？已有研究表明，贾第虫基因组中存在与RNAi 相关的Argonaute（AGO）家族蛋白和Dicer 酶。有意思的是，这些与siRNA 引起RNAi 作用关键的蛋白AGO 和Dicer 同样也是miRNA 系统的关键成份，这就提示我们在贾第虫中很有可能也存在有miRNA 并发挥功能。有研究发现在贾第虫基因组中存在大量的非编码转录物，这些大量的非编码转录物中，是否都是后来所认为的为双向启动子转录有用基因时的副产物，还是也存在一些起调控作用的RNA 分子（如miRNAs 等），需要进一步的研究。本文利用生物信息学的手段，依据miRNAs 的生物学特征，结合多种计算机预测的方法，在贾第虫基因组中筛选可能的microRNAs 分子，结果共鉴定出50 个miRNAs 候选分子，这50 个可能的贾第虫miRNAs 不具有保守性，在已知的其他物种的miRNAs 中找不到同源物。用这50 个microRNAs BLASTN 贾第虫的蛋白质编码序列及其相邻5’端和3’端各200bp 的序列，来寻找这些microRNAs 所调控的靶基因。结果表明，寻找到的贾第虫miRNA 的靶基因除很大一部分未知功能的蛋白外，还包括了很多涉及不同功能的蛋白，如VSP 蛋白（various surface proteins）这样一类表面抗原蛋白，提示我们贾第虫miRNA 可能与其致病性相关。接下来我们对其中14 个预测的贾第虫microRNAs 进行了RT-PCR 检测并克隆测序，结果表明gla-mir-6, gla-mir-35 在贾第虫滋养体细胞中稳定表达。我们的研究第一次用生物信息学结合实验的方法在贾第虫寻找到了microRNAs，为下一步深入研究这些microRNAs 在贾第虫中的功能提供了可能。

RNAi沉默烟草GA 20-氧化酶基因研究

赤霉素是一种高效能的广谱植物生长调节剂，为五大植物激素之一，具有重要的生物学功能。目前利用赤霉素突变体研究生物合成途径和信号转导已经成为热点。 GA 20-氧化酶是GA生物合成中的一类关键酶，它位于GA合成途径的中心位置。本研究根据烟草（Nicotiana tabacum）GA 20-氧化酶基因序列，设计2对分别含有特定酶切位点的特异引物，以烟草基因组DNA为模板，扩增目的基因(约250 bp)片段。将正、反向目的片段分别插入中间载体的内含子两侧，再经BamH I和Sac I双酶切回收约700 bp的目的片段，插入到双元载体质粒p2355中，成功构建了含GA 20-氧化酶基因片段反向重复序列的植物表达载体p23700。分别将p2355质粒和p23700质粒导入根癌农杆菌（Agrobacterium tumefaciens）EHA105中并转化烟草叶片细胞，经卡那霉素选择培养，PCR及GUS组织染色鉴定，获得转基因烟草植株。以EHA105-p2355转化的烟草，获得41株转基因植株，均没有矮化表型；而以EHA105-p23700转化的烟草，获得转基因植株14株，其中具有矮化表型的烟草10株，表明反向重复序列转录产物能形成发夹RNA(hpRNA)，产生小分子干扰RNA（small interferring RNA，简称siRNA），干扰目的基因的表达。 赤霉素含量测定表明矮化植株中赤霉素合成途径的最终产物GA3总含量明显低于野生型烟草植株。荧光定量PCR结果表明，矮化转基因烟草的GA 20-氧化酶基因表达量受到明显抑制，表达量明显低于野生型对照。同时对上游内根-贝壳杉合成酶（Ent-kaurene synthase，KS）基因，下游的GA-3β羟化酶基因进行了RT-PCR分析，结果显示上游基因的表达没有规律性变化，而下游基因表达量亦降低。上述结果表明，GA 20-氧化酶基因的表达被有效地干扰了，表达受到抑制，从而影响植株体内GA3的合成，影响植株的生长发育，导致植株矮化。并推测，GA 20-氧化酶基因受到抑制，可能影响下游基因的表达。并且通过干旱胁迫测试，发现矮化植株相对于野生型植株及不含干扰片段的转基因植株，对干旱的耐受力有了很大的提高，具有更强的耐受力。 研究结果为进一步进行相关研究奠定基础。 Gibberellin(GA) is an efficient plant growth regulator. As one of five major plant hormones, it plays an important biological function. Using GA mutant for investigating biosynthetic pathways and signal transduction has become high lights. GA 20-oxidase is a crucial enzyme involved in gibberellin biosynthesis. According to tobacco (Nicotiana tabacum) GA 20-oxidase enzyme gene sequence and based on binary vector p2355, we constructed a plant expression vector p23700, which habors an inverted repeat DNA fragment of GA 20-oxidase gene drivered by Cauliflower mosaic virus promtor (CaMV 35Sp). Binary plasmid p2355 had no inverted repeat DNA fragment of GA 20-oxidase gene. The vector p2355 and p23700 were introduced into Agrobacterium tumefaciens EHA105 and tobacco leaf transformation was conducted. After selected by kanamycin and characterized by PCR and GUS hischemical reaction, transsgenic plants were obtained. Fourtheen transgenic plants, which were transformed by EHA105-p23700, were obtained. Among them, 10 were dwarf mutants. However, 41 transgenic plants with the same normal phenotype as wild type,which were transformed by EHA105-p2355, were obtained. Analysis of Gibberellin contents showed that it was lower in dwarf mutants than in normal phenotype plants. Moreover, comparing to normal phenotype plants including wild type and transgenic plants with no interference fragment, the drought tolerance of dwarf plants have greatly increased. And their proline content increased obviously after drought test. Fluorescence quantitative real time PCR (RT-PCR) showed that GA 20-oxidase gene expression was significantly inhibited in dwarf transgenic tobacco. Meanwhile, the expression of the upstream gene ent-kaurene synthase (KS) gene and downstream gene GA-3β hydroxylase gene was also detected by RT-PCR. The results presented that KS gene expression had no regular change while GA-3β hydroxylase gene expression reduced. It implied that inhibiting GA 20-oxidase gene probably reduce the expression of downstream genes. The results showed that the transcriptional products of the foreign inverted repeat fragment can form hairpin RNA (hpRNA) to induce RNAi. It presented that GA 20-oxidase gene expression was effectively interfered, resulting in reducing GA3 synthesis and inhibiting plant growth and development, then dwarf plants were produced. However, the dwarf plants had higher tolerance of drought.

Survivin表达对HepG2细胞高LET射线辐射敏感性的影响

<正>Survivin是1997年发现的凋亡抑制蛋白家族(IAPs)的成员,它特异性的表达于大多数的恶性肿瘤细胞中,而在正常组织中检测不到,具有组织特异性。以前的研究表

抑制survivin表达增强人肝癌HepG2细胞对高线性能量转移射线的辐射敏感性；Inhibiting Survivin Expression Increases The Radiosensitivity of Human Hepatoma HepG2 Cells to High-LET Radiation

探讨了肿瘤细胞中survivin的表达对高线性能量转移(LET)射线辐射敏感性的影响.根据Gen Bank提供的survivin序列,合成特异性survivin-siRNA寡核苷酸,转染人肝癌HepG2细胞,抑制survivin的表达.发现siRNA转染后诱导了HepG2细胞G2/M期阻滞,增加了自发性和辐射诱导的细胞凋亡.在高线性能量转移(LET)碳离子辐照后,siRNA转染细胞的克隆存活率明显下降.这些结果表明survivin表达是HepG2细胞产生对高LET射线辐射抗性的关键因素.

Inhibiting Survivin Expression Increases The Radiosensitivity of Human Hepatoma HepG2 Cells to High-LET Radiation

The influence of survivin expression on the radiosensitivity of tumor cells to high linear energy transfer (LET) radiation is investigated. Survivin-specific short-interfering RNA (siRNA) oligonucleotides were synthesized based on the survivin sequence provided by GenBank. Human hepatoma HepG2 cells were transfected with survivin-specific siRNA to inhibit its expressions. It was found that the transfection with surviving-specific siRNA increased the levels of G2/M arrest and the apoptotic rates induced by radiation in HepG2 cells. After exposure to high-LET carbon ions, a reduced clonogenic survival effect was observed in the cells treated with siRNA. These results show that survivin plays a key role in mediating the radioresistance of cells to high-LET radiation.

survivin表达对重离子诱导人肝癌HepG2细胞生物学效应的影响

放射治疗是肿瘤三大治疗手段之一（手术治疗、放疗、化疗），如何提高肿瘤细胞的放射敏感性一直是科研人员关注的研究方向。电离辐射导致细胞死亡的主要方式是细胞凋亡，然而肿瘤细胞内往往细胞凋亡信号通路异常，降低了治疗效果。其中细胞内高水平表达的细胞凋亡抑制蛋白（Inhibitor of Apoptosis Protein，IAP）抑制了caspase分子的活性，而caspase分子正是细胞凋亡的执行分子。因此科学家们通过各种手段尤其是RNA干涉的方法以抑制肿瘤细胞内细胞凋亡抑制蛋白的表达及蛋白活性来达到提高肿瘤治疗效果的目的。 Survivin是凋亡抑制蛋白家族的一员，该蛋白在大多数恶性肿瘤中高表达，而在正常组织中检测不到，因此具有组织特异性。Survivin参与肿瘤细胞分化并抑制肿瘤细胞凋亡，它的高表达被证明与很多恶性肿瘤对放射治疗中产生的辐射抗性相关。本文主要研究了不同LET射线辐照下人肝癌HepG2细胞 survivin的表达及其表达对重离子诱导的生物学效应的影响。首先，我们使用不同LET的碳离子束和X射线辐照HepG2细胞，采用标准克隆形成法确定其辐射敏感性，利用流式细胞技术（FCM）检测辐射后细胞周期分布，RT-PCR和western blotting检测survivin的表达。结果显示，人肝HepG2癌细胞经不同LET射线照射，survivin表达是不同的。与低LET的X射线相比，高LET碳离子诱导的细胞损伤和周期阻滞更明显，从而诱导了更强烈的survivin表达。 接着，根据Genbank提供的survivin序列，合成特异性survivin-siRNA寡核苷酸，转染HepG2细胞，抑制survivin的表达。我们发现siRNA转染后诱导了细胞G2/M期阻滞，增加了自发性和辐射诱导的细胞凋亡。在碳离子辐照后，siRNA细胞克隆存活率明显下降。这些结果显示survivin表达是细胞产生高LET辐射抗性的关键因素。最后，我们初步探讨了在细胞凋亡过程中，survivin基因的作用机制。发现抑制survivin表达，对离子束辐射诱导的Bcl-2和Bax表达没有明显的影响。Survivin表达直接抑制了caspase-3和-9的活性，从而抑制了细胞凋亡。以上的实验结果表明：不同LET射线辐照细胞后survivin出现差异表达，与X射线相比，高LET重离子诱导的HepG2细胞中survivin表达更明显，以survivin为靶基因的siRNA技术应用于HepG2细胞，可以极大提高该细胞对重离子辐射的敏感性。本论文研究为临床应用重离子束治疗癌症提供了非常有用的基础数据，同时也为重离子束放射治疗联合基因治疗提供了新的思路

Targeted RNA interference of cyclin A(2) mediated by functionalized single-walled carbon nanotubes induces proliferation arrest and apoptosis in chronic myelogenous leukemia K562 cells

Cyclin A(2) plays critical role in DNA replication, transcription, and cell cycle regulation. Its overexpression has been detected and related to many types of cancers including leukemia, suggesting that suppression of cyclin A(2) would be an attractive strategy to prevent tumor progression. Herein, we apply functionalized single wall carbon nanotubes (f-SWNTs) to carry small interfering RNA (siRNA) into K562 cells and determine whether inhibition of cyclin A(2) would be a potential therapeutic target for chronic myelogenous leukemia.

Multi-armed poly(L-glutamic acid)-graft-oligoethylenimine copolymers as efficient nonviral gene delivery vectors

Background The application of polyethylenimine (PEI) in gene delivery has been severely limited by significant cytotoxicity that results from a nondegradable methylene backbone and high cationic charge density. It is therefore necessary to develop novel biodegradable PEI derivates for low-toxic, highly efficient gene delivery.Methods A series of novel cationic copolymers with various charge density were designed and synthesized by grafting different kinds of oligoethylenimine (OEI) onto a determinate multi-armed poly(L-glutamic acid) backbone. The molecular structures of multi-armed poly(L-glutamic acid)-graft-OEI (MP-g-OEI) copolymers were characterized using nuclear magnetic resonance, viscosimetry and gel permeation chromatography. Moreover, the MP-g-OEI/DNA complexes were measured by a gel retardation assay, dynamic light scattering and atomic force microscopy to determine DNA binding ability, particle size, zeta potential, complex formation and shape, respectively. MP-g-OEI copolymers were also evaluated in Chinese hamster ovary and human embryonic kidney-293 cells for their cytotoxicity and transfection efficiency.