宫颈癌中CALCA基因甲基化与HPV16-E7致癌蛋白表达的依存关系

 选择HPV16 阳性宫颈癌细胞和RNAi 技术,研究CALCA 基因甲基化与HPV16-E7 致癌蛋白表达的依存关系。构建慢病毒siRNA 重组表达载体,建立稳定表达HPV16-E7-siRNA 的RNAi 细胞模型。以SiHa 细胞和RNAi 细胞模型的基因组DNA 为对象,选择CALCA 基因启动子区富含CpG 岛屿的目标片段,使用亚硫酸氢盐测序法（bisulfite sequencing PCR,BSP）筛查分析,研究RNAi 抑制HPV16-E 7 表达后,CALCA 基因甲基化状态的可逆性程度。选出CALCA 基因启动子区富含CpG 位点的目标片段,其大小为365 bp,含有19 个CpG 岛屿,发现其中13 个CpG 位点的胞嘧啶在SiHa 细胞基因组DNA 中发生了甲基化（13/19）,而在表达HPV16-E7-siRNA 的RNAi 细胞模型中,所有CpG 位点的甲基化已发生逆转（0/19 位点）。本研究从细胞水平证明了宫颈癌细胞内的CALCA 基因启动子高甲基化对HPV16-E7 致癌蛋白表达有依赖性,为进一步研究E7 蛋白的作用及致癌机制奠定了重要的物质基础。     

DNA甲基化在肿瘤形成中的作用（综述）

DNA甲基化改变是肿瘤细胞中常见的现象,DNA甲基化与肿瘤的发生有密切关系。从以下几方面对此做一综述。（1）简介哺乳动物细胞的DNA甲基化;（2）DNA甲基化与肿瘤基因突变;（3）肿瘤DNA甲基化的基因外作用,其中包括：原癌基因的低甲基化和抑癌基因的高甲基化。     

大肠杆菌—枯草杆菌穿梭质料载体pSUGV4的构建

作者用DNA重组技术,构建了大肠杆菌-枯草杆菌空梭质粒载体pSUGV4,它是以大肠杆菌（Es-cherichia coli）质粒载体pUC18为骨架,与来自空梭质粒表达载体pREP9含有革兰氏阳性菌复制起点（ori^ )和卡那霉素抗性（kan^r)基因片段重组而成,上述穿梭质粒载体可用于在大肠杆菌（E.coli）和枯草杆菌（Bacillus subtilis）中进行基因克隆工作。     

产毒性大肠杆菌CFA／I基因表达与DNA超螺旋状态的关系

将CFA／I结构基因(cfaABCE)克隆到载体pJRD184上构建了质粒pJGX15A，并将其转入大肠杆菌fDpA野生株E．coli HB101和topA缺陷株E．coli DM800中．Western blot测定的结果表明，在CFA／I的正调控基因cfaD基因缺失时，两株重组菌株都能够表达CFA／I抗原．分别抽提两个重组菌株对数前期和对数中期的质粒pJGX15ADNA，并对其进行氯喹琼脂糖凝胶电泳分析，结果显示E．coli DM800细胞中质粒pJGX15A的负超螺旋水平比野生型细胞E．coli HB101中的较低．同时，菌落免疫酶斑分析的结果显示DM800受体菌中CFA／I的表达水平比HB101受体菌中的表达水平高．实验结果表明，CFA／I结构基因的表达与DNA负超螺旋水平有明显的负相关性，与负超螺旋促进基因表达的看法不同．     

高产S-腺苷蛋氨酸合成酶基因工程菌的构建

应用PCR技术,以大肠杆菌BL21（DE3）染色体DNA为模板,扩增得到S-腺苷蛋氨酸（SAM）合成酶基因。将所得基因连接至表达载体pET-22b（+）,利用T7强启动子进行转录,然后转化进E. coli BL21（DE3）表达菌株,构建出了具有高效表达SAM合成酶基因的基因工程菌。重组菌所表达的酶活为115U/g（以细胞干重计）。     

原核DNA甲基化的表观调控作用的研究进展

自从2009年第三代DNA测序技术平台商业化以来，测序、绘制原核DNA甲基化组飞速发展，10余年来已完成甲基化组测序的细菌超过4 000种，极大推动了原核表观遗传学的研究.越来越多的研究表明，DNA甲基化修饰不仅仅局限于宿主的防御功能，而且广泛参与各种细胞过程及基因的表达调控，在染色体的复制起始、细胞周期、致病性、抗生素抗性等方面起到了重要的作用.在简要回顾原核DNA甲基转移酶及其甲基化修饰的相关研究的基础上，着重对近期原核甲基化修饰的调控作用的研究进展进行综述，以期推动原核甲基化修饰表观遗传的研究.     

我国科学家揭示全新DNA复制起始位点调控机制

<正>DNA复制是一个确保遗传信息精确传递的生命过程。细胞在DNA合成前期G1期时,复制起始识别复合物识别染色质上的复制位点,进一步招募DNA解旋酶MCM(Minichromosome maintenance)等,形成复制前体复合物,完成复制起始位点的认证。而当细胞进入复制期S期时,被认证的复制起始位点被选择性地激活使用。真核生物DNA复制起始位点的选择受DNA序列和表观遗传因素共同调控。目前,表观遗传因素对染色质上DNA复制起始位点的选择机制仍然不清楚。     

P15基因甲基化和血液病相关性的研究进展（综述）

P15基因是肿瘤抑制基因的侯选基因,受细胞生长抑制蛋白TGF－β的诱导,编码周期素依赖激酶4／6（CDK4／6）抑制因子,对细胞周期起负调控作用,P15基因操纵区5′－GpG岛的甲基化被认为是基因缺失之外的又一失活机制。P15基因5′－Gp G岛的异常甲基化导致该基因转录的抑制,5′－杂氮脱氧胞嘧啶（5′－Aza-2cdR）通过共价俘获DNA甲基转移酶抑制DNA的甲基化,使因甲基化失活的生长调控基因重新激活并表达。5′－Aza-2cdR可通过P15基因去甲基化再表达抑制细胞的生长,为临床恶性白血液病去甲基化治疗提供实验依据。     

大肠杆菌ppsA,pckA基因的克隆与串联表达

磷酸烯醇丙酮酸合成酶（ppsA)和磷酸烯醇丙酮酸羧激酶（pckA）是糖代谢中心途径中生成磷酸烯醇丙酮酸（PEP）的2个关键酶，在大肠杆菌中分别由ppsA和pckA基因编码，首先用PCR方法从大肠杆菌K12菌株基因组DNA扩增得到了ppsA和pckA基因，并将ppsA,pckA以单独或串联的方式克隆到大肠杆菌表达质粒pλPR上，构建成的质粒pλPR-ppsA,pλPR-pckA,pλPR-ppsA-PckA导入E.coli P2392菌株中表达，结果表明，ppsA,pckA基因的单独表达使宿主细胞的ppsA和pckA酶活力分别提高到5．2和2．5倍，串联表达使宿主细胞PAt和PckA酶活力分别提高到3．1和2．3倍，还使得以PEP为底物合成的3－脱氧α－阿拉伯 酮糖－7－磷酸（DAHP）产量提高到2．1倍，2个基因串联表达比单个基因表达更有利于提高DAHP的产量。     

咪唑基离子液体与小分子相互作用的理论研究

采用密度泛函理论考察了1-乙基-3-甲基咪唑四氟合硼酸盐（[EMIM][BF4]）和2-甲基噻吩（2-MT）、正己烷（HEX）、异丁基硫醇（IBT）的相互作用。采用GGA/PW91和DNP基组优化了结构,并用NBO和AIM分析了[EMIM][BF4]和2-甲基噻吩（2-MT）、正己烷（HEX）、异丁基硫醇（IBT）的氢键相互作用。[EMIM][BF4]离子对最稳定的气相结构表明,[BF4]-阴离子的F原子和咪唑环上C2-H2的氢键作用在形成离子对中起重要作用。[BF4]-阴离子和[EMIM]＋阳离子支链发生氢键作用。[BF4]-阴离子趋向于C2-H2形成氢键,这说明,2-甲基噻吩（2-MT）、正己烷（HEX）、异丁基硫醇（IBT）吸附在[EMIM][BF4]上没有改变离子液体离子对的主要作用。[EMIM][BF4]和2-甲基噻吩发生π···C-H和氢键作用,而[EMIM][BF4]和正己烷（HEX）、异丁基硫醇（IBT）主要发生氢键作用。相互作用能表明,2-甲基噻吩优先吸附在离子液体上。     

The vsr gene product of E. coli K-12 is a strand- and sequence-specific DNA mismatch endonuclease

In Escherichia coli K-12, the Dcm methyltransferase catalyses methylation of the inner cytosine residue in the sequence CCA/TGG. Hydrolytic deamination of 5-methylcytosine bases in DNA leads to thymine residues, and hence to T/G mismatches, pre-mutagenic DNA lesions consisting of two natural DNA constituents and thus devoid of an obvious marker of the damaged DNA strand. These mismatches are corrected by the VSP repair pathway, which is characterized by very short patches of DNA repair synthesis. It depends on genes vsr and polA and is strongly stimulated by mutL and mutS. The vsr gene product (Vsr; Mr 18,000) was purified and characterized as a DNA mismatch endonuclease, a unique and hitherto unknown type of enzyme. Vsr endonuclease nicks double-stranded DNA within the sequence CTA/TGN or NTA/TGG next to the underlined thymidine residue, which is mismatched to 2'-deoxyguanosine. The incision is mismatch-dependent and strand-specific. These results illustrate how Vsr endonuclease initiates VSP mismatch repair.     

A histone H3 methyltransferase controls DNA methylation in Neurospora crassa.

DNA methylation is involved in epigenetic processes such as X-chromosome inactivation, imprinting and silencing of transposons. We have demonstrated previously that dim-2 encodes a DNA methyltransferase that is responsible for all known cytosine methylation in Neurospora crassa. Here we report that another Neurospora gene, dim-5, is required for DNA methylation, as well as for normal growth and full fertility. We mapped dim-5 and identified it by transformation with a candidate gene. The mutant has a nonsense mutation in a SET domain of a gene related to histone methyltransferases that are involved in heterochromatin formation in other organisms. Transformation of a wild-type strain with a segment of dim-5 reactivated a silenced hph gene, apparently by 'quelling' of dim-5. We demonstrate that recombinant DIM-5 protein specifically methylates histone H3 and that replacement of lysine 9 in histone H3 with either a leucine or an arginine phenocopies the dim-5 mutation. We conclude that DNA methylation depends on histone methylation.     

Gadd45a promotes epigenetic gene activation by repair-mediated DNA demethylation

DNA methylation is an epigenetic modification that is essential for gene silencing and genome stability in many organisms. Although methyltransferases that promote DNA methylation are well characterized, the molecular mechanism underlying active DNA demethylation is poorly understood and controversial. Here we show that Gadd45a (growth arrest and DNA-damage-inducible protein 45 alpha), a nuclear protein involved in maintenance of genomic stability, DNA repair and suppression of cell growth, has a key role in active DNA demethylation. Gadd45a overexpression activates methylation-silenced reporter plasmids and promotes global DNA demethylation. Gadd45a knockdown silences gene expression and leads to DNA hypermethylation. During active demethylation of oct4 in Xenopus laevis oocytes, Gadd45a is specifically recruited to the site of demethylation. Active demethylation occurs by DNA repair and Gadd45a interacts with and requires the DNA repair endonuclease XPG. We conclude that Gadd45a relieves epigenetic gene silencing by promoting DNA repair, which erases methylation marks.     

Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism

DNA methylation of CpG dinucleotides is an important epigenetic modification of mammalian genomes and is essential for the regulation of chromatin structure, of gene expression and of genome stability. Differences in DNA methylation patterns underlie a wide range of biological processes, such as genomic imprinting, inactivation of the X chromosome, embryogenesis, and carcinogenesis. Inheritance of the epigenetic methylation pattern is mediated by the enzyme DNA methyltransferase 1 (Dnmt1), which methylates newly synthesized CpG sequences during DNA replication, depending on the methylation status of the template strands. The protein UHRF1 (also known as Np95 and ICBP90) recognizes hemi-methylation sites via a SET and RING-associated (SRA) domain and directs Dnmt1 to these sites. Here we report the crystal structures of the SRA domain in free and hemi-methylated DNA-bound states. The SRA domain folds into a globular structure with a basic concave surface formed by highly conserved residues. Binding of DNA to the concave surface causes a loop and an amino-terminal tail of the SRA domain to fold into DNA interfaces at the major and minor grooves of the methylation site. In contrast to fully methylated CpG sites recognized by the methyl-CpG-binding domain, the methylcytosine base at the hemi-methylated site is flipped out of the DNA helix in the SRA-DNA complex and fits tightly into a protein pocket on the concave surface. The complex structure suggests that the successive flip out of the pre-existing methylated cytosine and the target cytosine to be methylated is associated with the coordinated transfer of the hemi-methylated CpG site from UHRF1 to Dnmt1.     

A whole genome approach to in vivo DNA-protein interactions in E. coli.

The increasingly rapid pace at which genomic DNA sequences are being determined has created a need for more efficient techniques to determine which parts of these sequences are bound in vivo by the proteins controlling processes such as gene expression, DNA replication and chromosomal mechanics. Here we describe a whole-genome approach to identify and characterize such DNA sequences. The method uses endogenous or artificially introduced methylases to methylate all genomic targets except those protected in vivo by protein or non-protein factors interfering with methylase action. These protected targets remain unmethylated in purified genomic DNA and are identified using methylation-sensitive restriction endonucleases. When the method was applied to the Escherichia coli genome, 0.1% of the endogenous adenine methyl-transferase (Dam methylase) targets were found to be unmethylated. Five foreign methylases were examined by transfection. Database-matched DNA sequences flanking the in vivo-protected Dam sites all fell in the non-coding regions of seven E. coli operons (mtl, cdd, flh, gut, car, psp and fep). In the first four operons these DNA sequences closely matched the consensus sequence that binds to the cyclic AMP-receptor protein. The in vivo protection at the Dam site upstream of the car operon was correlated with a downregulation of car expression, as expected of a feedback repressor-binding model.     

DNA甲基化研究进展

DNA甲基化已成为阐明正常和病理基因表达现象的重要机制,因而已成为当前分子生物学的研究热点之一。对DNA甲基化的转录抑制机制、在肿瘤发生中的作用、与细胞衰老和凋亡的关系、抑制剂以及分析方法等方面的研究新进展进行了综述。     

A common regulatory region shared by divergently transcribed genes of the Escherichia coli SOS system

The Escherichia coli single-stranded DNA binding protein (SSB) is implicated in DNA replication, recombination and repair. On the chromosome, the ssb gene is located adjacent to the excision repair gene uvrA, but the two genes are transcribed in opposite directions. uvrA has been shown to be part of the E. coli SOS system by introducing Mud(Ap, lac) insertions distal to the regulatory region of the gene in the chromosome. Recent investigations suggest that SSB is also involved in the SOS response. However, because the SSB protein is essential to the cell, the inducibility of the ssb gene cannot be investigated by the insertion method. Therefore, we used plasmids harbouring the regulatory region of ssb fused to the galK structural gene, while leaving an intact ssb gene in the chromosome. We show here that expression of the ssb gene is dependent on two promoters of which one is damage inducible. Evidence is presented that the divergently transcribed ssb and uvrA genes are controlled by a common LexA binding site.     

Expression of a bacterial modification methylase gene in yeast

Methylation of specific cytosines in the DNA is generally believed to play some role in the regulation of gene expression in eukaryotes. However, some eukaryotes, such as Drosophila and yeast (S. Hattman, personal communication) seem not to contain 5-methylcytosine in their DNA. It would be interesting to test, how gene expression in such organisms would respond to the methylation of specific cytosines in the genome. As a first step towards this goal, we have introduced the gene encoding the Bacillus sphaericus R modification methylase, which methylates the internal cytosine within the recognition sequence 5'-GGCC, into yeast cells. Southern-type hybridization to DNAs isolated from the transformed yeast clones revealed that the yeast plasmid carrying the prokaryotic methylase gene, as well as the two chromosomal genes tested (his3 and leu2) were methylated, whereas the bulk of the yeast DNA remained largely unmethylated. This indicates that the Bacillus sphaericus modification methylase was expressed in yeast but it modified only certain parts of the yeast DNA.