哈萨克族食管癌中Survivin基因启动子区CpG岛真核表达载体的构建

 食管癌的形成与多种基因的异常表达有关,哈萨克族食管癌的发病又有其独特的机制。克隆并研究早期相关基因的启动子区CpG岛可为进一步揭示其发病机制奠定基础。本研究构建Survivin基因启动子区CpG岛真核表达载体,探讨其甲基化在新疆哈萨克族食管癌中的作用。通过Primer 5.0设计软件设计引物,采用常规PCR法从新疆哈萨克族食管癌患者的基因组DNA中扩增出Survivin基因启动子区CpG岛,CpG岛与真核表达载体pCAT3 promoter经HindⅢ单酶切后,连接试剂盒将二者连接并转导入甲基化酶缺陷的大肠杆菌E. coli ER1793中扩增。DNA测序证明获得Survivin基因启动子区CpG岛,并成功克隆入真核表达载体pCAT3 promoter中。     

基于KL散度和BP神经网络的人类基因启动子识别

人类基因启动子预测和识别是DNA序列分析中的一项重要任务.提出了一个基于KL散度和BP神经网络的人类基因启动子识别算法.利用KL散度提取分辨力最强的六联体来区分启动子和非启动子区域,将这些六联体的出现频率作为识别启动子的组成成分特征,结合CpG岛特征,应用BP神经网络技术建立人类启动子识别系统.该系统有3个分类器,即启动子-外显子分类器,启动子-内含子分类器和启动子-3’UTR分类器,每个分类器都是一个BP神经网络,通过3个分类器的结果来综合预测启动子序列.对测试集的实验结果为:敏感性达到51.4%,特异性达到52.9%.     

CpG-rich islands and the function of DNA methylation

It is likely that most vertebrate genes are associated with 'HTF islands'--DNA sequences in which CpG is abundant and non-methylated. Highly tissue-specific genes, though, usually lack islands. The contrast between islands and the remainder of the genome may identify sequences that are to be constantly available in the nucleus. DNA methylation appears to be involved in this function, rather than with activation of tissue specific genes.     

Genome-scale DNA methylation maps of pluripotent and differentiated cells

DNA methylation is essential for normal development and has been implicated in many pathologies including cancer. Our knowledge about the genome-wide distribution of DNA methylation, how it changes during cellular differentiation and how it relates to histone methylation and other chromatin modifications in mammals remains limited. Here we report the generation and analysis of genome-scale DNA methylation profiles at nucleotide resolution in mammalian cells. Using high-throughput reduced representation bisulphite sequencing and single-molecule-based sequencing, we generated DNA methylation maps covering most CpG islands, and a representative sampling of conserved non-coding elements, transposons and other genomic features, for mouse embryonic stem cells, embryonic-stem-cell-derived and primary neural cells, and eight other primary tissues. Several key findings emerge from the data. First, DNA methylation patterns are better correlated with histone methylation patterns than with the underlying genome sequence context. Second, methylation of CpGs are dynamic epigenetic marks that undergo extensive changes during cellular differentiation, particularly in regulatory regions outside of core promoters. Third, analysis of embryonic-stem-cell-derived and primary cells reveals that 'weak' CpG islands associated with a specific set of developmentally regulated genes undergo aberrant hypermethylation during extended proliferation in vitro, in a pattern reminiscent of that reported in some primary tumours. More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine.     

A unique regulatory phase of DNA methylation in the early mammalian embryo

DNA methylation is highly dynamic during mammalian embryogenesis. It is broadly accepted that the paternal genome is actively depleted of 5-methylcytosine at fertilization, followed by passive loss that reaches a minimum at the blastocyst stage. However, this model is based on limited data, and so far no base-resolution maps exist to support and refine it. Here we generate genome-scale DNA methylation maps in mouse gametes and from the zygote through post-implantation. We find that the oocyte already exhibits global hypomethylation, particularly at specific families of long interspersed element 1 and long terminal repeat retroelements, which are disparately methylated between gametes and have lower methylation values in the zygote than in sperm. Surprisingly, the oocyte contributes a unique set of differentially methylated regions (DMRs)--including many CpG island promoters--that are maintained in the early embryo but are lost upon specification and absent from somatic cells. In contrast, sperm-contributed DMRs are largely intergenic and become hypermethylated after the blastocyst stage. Our data provide a genome-scale, base-resolution timeline of DNA methylation in the pre-specified embryo, when this epigenetic modification is most dynamic, before returning to the canonical somatic pattern.     

Demethylation of CpG islands in embryonic cells

DNA in differentiated somatic cells has a fixed pattern of methylation, which is faithfully copied after replication. By contrast, the methylation patterns of many tissue-specific and some housekeeping genes are altered during normal development. This modification of DNA methylation in the embryo has also been observed in transgenic mice and in transfection experiments. Here we report the fate in mice of an in vitro-methylated adenine phosphoribosyltransferase transgene. The entire 5' CpG island region became demethylated, whereas the 3' end of the gene remained modified and was even methylated de novo at additional sites. Transfection experiments in vitro show that the demethylation is rapid, is specific for embryonic cell-types and affects a variety of different CpG island sequences. This suggests that gene sequences can be recognized in the early embryo and imprinted with the correct methylation pattern through a combination of demethylation and de novo methylation.     

The methylated component of the Neurospora crassa genome

Cytosine methylation is common, but not ubiquitous, in eukaryotes. Mammals and the fungus Neurospora crassa have about 2-3% of cytosines methylated. In mammals, methylation is almost exclusively in the under-represented CpG dinucleotides, and most CpGs are methylated whereas in Neurospora, methylation is not preferentially in CpG dinucleotides and the bulk of the genome is unmethylated. DNA methylation is essential in mammals but is dispensable in Neurospora, making this simple eukaryote a favoured organism in which to study methylation. Recent studies indicate that DNA methylation in Neurospora depends on one DNA methyltransferase, DIM-2 (ref. 6), directed by a histone H3 methyltransferase, DIM-5 (ref. 7), but little is known about its cellular and evolutionary functions. As only four methylated sequences have been reported previously in N. crassa, we used methyl-binding-domain agarose chromatography to isolate the methylated component of the genome. DNA sequence analysis shows that the methylated component of the genome consists almost exclusively of relics of transposons that were subject to repeat-induced point mutation--a genome defence system that mutates duplicated sequences.     

DNA甲基化异常与人类肿瘤

DNA甲基化是表遗传学上研究最深入的一种机制,是一种酶介导的化学修饰过程,在DNA的某些碱基上增加一个甲基.在人类的肿瘤中都可以发现不同程度的DNA异常甲基化现象.介绍DNA甲基化在基因表达中的作用及其抑制基因转录、表达的机理,尤其发生在抑癌基因CpG岛和其他相关基因的甲基化异常与肿瘤发生、演进的关系,甲基化的检测方法以及去甲基化在肿瘤治疗方面的应用前景.     

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。     

人IDE基因启动子生物信息学分析

对人IDE基因启动子进行生物信息学分析以获得人IDE基因启动子、CpG岛及转录因子结合位点特征.从UCSC基因组数据库成功获得人IDE基因5’调控区2 000 bp序列.Promoter 2.0、FPROM、NNPP预测人IDE基因分别有3个、2个、6个启动子.Relative profile score threshold选择80%、85%、90%、95%、100%时,JASPAR预测该序列存在5170、1771、454、87和5个可能的转录因子结合位点.Relative profile score threshold选择80%,搜索到6个潜在的TCF7L2转录因子结合位点.采用进化足迹法,LAGAN预测方法获得位于人和小鼠同源IDE基因启动子保守区域相同位置的转录因子结合位点为14个,包含转录因子SPI-1、cap、c-FOS、FREAC-3、c-ETS、Cdxa、HSF2等.发现一个CpG岛,位于1 303～1 705 bp 之间,大小为403 bp.人IDE基因启动子、CpG岛及转录因子结合位点的生物学信息学分析,为下一步基因表达调控实验奠定了基础.     

Diagnosis of Hepatocellular Carcinoma by Using Methylation Specific-PCR

To find a more sensitive and earlier diagnostic marker for hepatocellular carcinoma, methylation-profils of CpG islands in the promoter of eleven genes in hepatocellular carcinoma（HCC） carcinoma and pericarcinoma tissues from ten patients were examined by using methylation-specific PCR （MSP） method. MSP was used to detect the methylation of p16, p53, Secreted frizzled-related protein 1 （SFRP 1） and SFRP2 promoters. Meanwhile, plasma alpha-fetoprotein （AFP） levels in 53 patients were also determined. The results showed that HCC was closely correlated to methylation in promoter of tumor-suppressing gene p16, p53, SFRP1 and SFRP2. The results suggest that methylation of SFRP2 promoter is possible a better marker for diagnosis of HCC than plasma Alpha-fetoprotein （AFP） levels. The false negative of SFRP1 and SFRP2 are perfectly complementary. If SFRP1 and SFRP2 were both considered as a complementary positive marker at the same time, the accurate rate for diagnosis of HCC is 100%.     

The DNA sequence and analysis of human chromosome 14

Chromosome 14 is one of five acrocentric chromosomes in the human genome. These chromosomes are characterized by a heterochromatic short arm that contains essentially ribosomal RNA genes, and a euchromatic long arm in which most, if not all, of the protein-coding genes are located. The finished sequence of human chromosome 14 comprises 87,410,661 base pairs, representing 100% of its euchromatic portion, in a single continuous segment covering the entire long arm with no gaps. Two loci of crucial importance for the immune system, as well as more than 60 disease genes, have been localized so far on chromosome 14. We identified 1,050 genes and gene fragments, and 393 pseudogenes. On the basis of comparisons with other vertebrate genomes, we estimate that more than 96% of the chromosome 14 genes have been annotated. From an analysis of the CpG island occurrences, we estimate that 70% of these annotated genes are complete at their 5' end.     

猪hnRNPK基因启动子的克隆及序列分析

首次克隆了猪hnRNPK基因启动子序列,并进一步对该序列进行了分析.结果显示:该基因启动子约1 kb,与已报道的人的相应序列相似度为78.9%,具有相同的"TCTCGCGAGA"核心启动子序列和转录起始位点.利用在线软件分析发现,猪hnRNPK基因启动子不含TATA盒,而含有CAAT盒的GC富集区,存在两处CpG岛,具有SP1、UCE.2、GCF、EARLY-SEQ1、TTR_inverted_repeat、NGFI-C、EARLY-SEQ1等多种转录因子潜在结合位点,并且具有8种基序结构.     

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

The architecture of human chromosomes in interphase nuclei is still largely unknown. Microscopy studies have indicated that specific regions of chromosomes are located in close proximity to the nuclear lamina (NL). This has led to the idea that certain genomic elements may be attached to the NL, which may contribute to the spatial organization of chromosomes inside the nucleus. However, sequences in the human genome that interact with the NL in vivo have not been identified. Here we construct a high-resolution map of the interaction sites of the entire genome with NL components in human fibroblasts. This map shows that genome-lamina interactions occur through more than 1,300 sharply defined large domains 0.1-10 megabases in size. These lamina-associated domains (LADs) are typified by low gene-expression levels, indicating that LADs represent a repressive chromatin environment. The borders of LADs are demarcated by the insulator protein CTCF, by promoters that are oriented away from LADs, or by CpG islands, suggesting possible mechanisms of LAD confinement. Taken together, these results demonstrate that the human genome is divided into large, discrete domains that are units of chromosome organization within the nucleus.     

糖尿病大鼠肾、胰基因组DNA甲基化状态的变化

从正常大鼠，糖尿病大鼠，中药糖微康治疗的糖尿病大鼠，西药开搏通治疗的糖尿病大鼠的肾，胰等组织中提取出其基因组DNA，应用对DNA甲基化作用敏感的限制性核酸内切酶HpaⅡ和MspⅠ（为一组同裂酶（进行了限制性酶切图谱分析，结果表明，DNA化作用的主要位点在CpG二核苷酸处，且“糖微康”在关闭患糖尿病后肾组织中被异常活化的基因的同时，还能活化糖尿病动物胰组织中处于静息状态的基因，由此可见糖尿病的发病和治疗都与DNA甲基化作用密切相关。