Molecular mechanism of the inhibitory effect of methylation outside the recognition sequence of restriction endonuclease Pvu Π on its cleavage activity

In 1991, we found that methylation outside the PvuⅡ recognition sequence could partially inhibit its cleavage activity. To clarify the molecular mechanism, three plasmids with different methylation states were constructed. Then, together with the original one, four plasmids were digested with different amounts of PvuⅡ. Results show that methylation on both sites results in 90% inhibition; moving the methylated site one base further away decreases the inhibitory effect to about 30%; with the adjacent dam methylation site eliminated, the inhibitory effect disappears. The data suggest that the inhibition of cleavage activity caused by outside methylation is not "all or none", and the degree of inhibition is dependent on the position and the number of methylated bases.     

四种植物25S rRNA sarcin/ricin结构域甲基化核苷的分析

应用不同浓度的dNTP逆转录反应，分析丁苦瓜、丝瓜、蓖麻和水稻的25SrRNA sarcin/ricin区域中的甲基化核苷，发现了这4种植物25SrRNA的第3023、2966和2962位的腺嘌呤、胸腺嘧啶和腺嘌呤是2’-0-甲基化核苷；在丝瓜和苦瓜25SrRNA的第2992、2990位的胞嘧啶和鸟嘿吟是葫芦科植物所特有的两个2’-0—甲基化核苷；第2994位点的尿嘧啶是苦瓜、丝瓜、蓖麻和水稻的一个碱基甲基化核苷；而且，植物25SrRNA第3023位甲基化腺嘌呤核苷刚好位于sarcin/ricin结构域的茎环上，与核糖体失活蛋白切割位点相距仅5个核苷酸，而在哺乳动物和酵母的rRNA相同位点上没有甲基化修饰的存在，根据这一结果推测，RIPS来源植物核糖体RNA的自我保护可能与这一位点的修饰有关。     

Detection of DNA methylation changes during seed germination in rapeseed （Brassica napus）

DNA methylation is a common yet important modi- fication of DNA in eukaryotic organisms. DNA methy- lation, especially methylation of cytosine (m5C), have both epigenetic and mutagenic effects on various cellu- lar activities such as differential gene exp…     

Covalent inhibition revealed by the crystal structure of the caspase-8/p35 complex

Apoptosis is a highly regulated process that is crucial for normal development and homeostasis of multicellular organisms. The p35 protein from baculoviruses effectively prevents apoptosis by its broad-spectrum caspase inhibition. Here we report the crystal structure of p35 in complex with human caspase-8 at 3.0 A resolution, and biochemical and mutagenesis studies based on the structural information. The structure reveals that the caspase is inhibited in the active site through a covalent thioester linkage to p35, which we confirmed by gel electrophoresis, hydroxylamine treatment and mass spectrometry experiments. The p35 protein undergoes dramatic conformational changes on cleavage by the caspase. The repositioning of the amino terminus of p35 into the active site of the caspase eliminates solvent accessibility of the catalytic dyad. This may be crucial for preventing hydrolysis of the thioester intermediate, which is supported by the abrogation of inhibitory activity through mutations at the N terminus of p35. The p35 protein also makes conserved contacts with the caspase outside the active-site region, providing the molecular basis for the broad-spectrum inhibitory activity of this protein. We demonstrate a new molecular mechanism of caspase inhibition, as well as protease inhibition in general.     

Patterns of DNA cytosine methylation between haploids and corresponding diploids in rice

In higher plant, about 30% cytosines are methy-lated[1], among which about 90% methylated sites lie in CpG dinucleotide and CpNpG trinucleotide[2]. The me-thylated DNA has inducing and epigenetic effects on cell biological procedures such as gene differen…     

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.     

Maternal inhibition of hepatitis B surface antigen gene expression in transgenic mice correlates with de novo methylation

Differential modifications of the genome during gametogenesis result in a functional difference between the paternal and maternal genomes at the moment of fertilization. A possible cause of this imprinting is the methylation of DNA. The insertion of foreign DNA into transgenic mice allows the tagging of regions that are differentially methylated during gametogenesis. We describe here a transgenic mouse strain in which the expression of the hepatitis B surface antigen gene is irreversibly repressed following its passage through the female germ line. This inhibition is accompanied by the methylation of all the HpaII and HhaI sites within the foreign gene, which we have shown to be integrated into a site on chromosome 13. The irreversibility reported here contrasts with what is found with other transgenic mice sequences which are reversibly methylated after passage through the male or female germ line, though in both cases methylation appears to be important in the imprinting process.     

Predicted methylation landscape of all CpG islands on the human genome

CpG island methylation plays important role in various biological processes. To investigate methylation landscape of all CpG islands on the human genome, we develop a model for predicting the CpG island methylation status. This model outperforms other existing methods. We apply the model on the whole human genome and predict the landscape of DNA methylation of all CpG islands. Based on the methylation profile, we find that about 31% of CpG islands are methylation-prone and CpG islands located in promoter regions are seldom methylated. There is no significant difference in the CpG island methylation level between R and G bands among the chromosomes. The occupancy of RNA polymerase II is significantly higher in methylation-resistant promoter CpG islands, indicating that genes with such promoter CpG islands tend to be more active.     

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.     

Adrenomedullin inhibits the endothelin production induced by urotensin II in rat vascular smooth muscle cells

The aim of this study was to observe the effects of adrenomedullin (ADM) on endothelin (ET) production induced by urotensin Ⅱ (UⅡ) in rat vascular smooth muscle cells (VSMCs). Cultured VSMCs which were incubated with UⅡ (10^-8 mol/L) and with various concentrations of ADM were used to measure the VSMCs ³H-TdR incorpora- tion, the activity of extracellular signal-regulated kinase (ERK), the amount of ET mRNA and ET production in VSMCs. In this work we found that incubation with UⅡ(10^-8 mol/L) increased obviously the amount of ET mRNA in VSMCs and ET production in medium, however, coincubation with ADM (10^-10—10^-8 mol/L) and UⅡ(10^-8 mol/L) reduced the amount of ET mRNA by 15%, 24% and 45% (P< 0.01) respectively, compared with UⅡ alone. The content of ET in medium was 14.13, 11.38 and 11.00 pg/mL. ADM alone (10^-8 mol/L) had no effect on ET production in VSMCs. UⅡ (10^-8 mol/L) promoted the 3H-TdR incorpo- ration and activity of ERK in VSMCs. ADM inhibited VSMCs 3H-TdR incorporation and activation of ERK in a concentration-dependent manner. Compared with UⅡ group, after coincubation with ADM (10^-10—10^-8 mol/L) and UⅡ (10^-8 mol/L) the VSMCs 3H-TdR incorporation was decreased by 7% (P > 0.05), 32% (P < 0.05) and 41% (P < 0.01), respectively, and the activity of ERK was decreased by 24% (P > 0.05), 32% (P < 0.05) and 36% (P < 0.05), re- spectively, in a concentration-dependent manner. The results show that in cultured VSMCs ADM inhibits ET mRNA expression, ET production and proliferation stimulated by UⅡ, and that inhibitory effect of ADM on UⅡ bioaction could be mediated through inhibiting MAPK pathway.     

芦荟汁中胶原酶抑制成分的分离纯化与抑制效果测定

芦荟汁提取物对胶原酶活性具有抑制作用,经萃取、硅胶柱层析和半制备液相色谱分离出两种主要抑制成分,化学结构鉴定为芦荟素和异芦荟素;羟脯氨酸化学比色法测定胶原酶抑制效果,两者具有相似的抑制效果并随质量浓度的增大而近似线性升高:芦荟素1 mg/mL时百分抑制率达到42%,低质量浓度下的抑制作用高于四环素.芦荟素、异芦荟素的抑制作用可能与其对胶原酶活性位点上Zn2 的螯合有关.     

高分辨熔解曲线法检测哈萨克族食管癌患者癌组织中FHIT、CDKN2A启动子区甲基化水平及临床意义

 建立高分辨熔解曲线法(HRM)定量检测哈萨克族食管癌患者癌组织中FHIT、CDKN2A甲基化水平,并分析甲基化水平与食管癌病理参数的相关性。选取30例食管癌癌患者癌组织及30例癌旁组织,提取DNA,进行甲基化修饰。将标准品DNA(甲基化DNA与非甲基化DNA相互的掺入)稀释成0,5%,25%,50%,75%,100%甲基化DNA,并进行重复性和灵敏性评价。应用HRM定量检测癌组织及癌旁组织甲基化水平,探讨FHIT、CDKN2A基因启动子区甲基化水平与食管癌发生发展的关系。100%,80%,50%,30%,10%,0甲基化标准品的高分辨率熔解曲线从右向左依次排列,待测基因在标准曲线上的位置即表示其甲基化程度。HRM最低检测限为1%,明显高于MSP结果最低检测限10%。在30例食管癌癌患者癌组织中,检测出存在FHIT甲基化的为36.7%。其中8例甲基化程度为0—5%,3例为5%—10%。CDKN2A甲基化的为100%,其中7例甲基化程度为0—5%,11例为5%—10%,12例为10%—25%。与正常组织比较,抑癌基因的甲基化与癌症的发生无明显相关性。进一步讨论甲基化与食管癌的病理级别以及甲基化与分化程度的关系,二者均无相关性。通过HRM技术成功建立了定量检测哈萨克族食管癌组织中FHIT、CDKN2A甲基化程度的方法,FHIT、CDKN2A基因启动子甲基化与哈萨克族食管癌的发生发展无明显相关性,但多个抑癌基因的甲基化有望成为其早期发生发展的分子指标。     

解淀粉芽孢杆菌发酵液的抑菌活性及抗氧化作用

以尖孢镰刀菌黄瓜专化型病原菌为指示菌,利用平板对峙法、牛津杯法等方法,探究解淀粉芽孢杆菌SJ100001对尖孢镰刀菌的拮抗作用、SJ100001菌株抑菌活性成分的来源、SJ100001菌株发酵液的最佳发酵条件及其理化稳定性;通过DPPH自由基清除能力和还原力的测定,探究SJ100001菌株发酵液的抗氧化活性.结果表明,...     

Depletion of phosphatidyl-glycerol head-group induces changes in oxygen evolution and protein secondary struc-tures of photosystem Ⅱ

The techniques of oxygen electrode polarogra-phy and Fourier transform infrared (FT-IR) spectroscopy were employed to explore the roles of polar head-group of phosphatidylglycerol (PG) molecules in the functional and structural aspects of photosystem Ⅱ (PS Ⅱ) through enzymatic approach. It was shown that the depletion of PG by treatment of phospholipase C (PLC) on PS Ⅱ particles caused the inhibition of oxygen evolving activity in PS Ⅱ. This effect also gave rise to changes in the protein secondary structures of PS Ⅱ, that is, an increase in a-helical conformation which is compensated by the loss of p-strand structures. It revealed that the head-group of PG molecules plays an important structural role in the maintenance of normal structure of PS Ⅱ proteins, which is required to maintain the appropriate physiological activity of the PS Ⅱ complex such as the oxygen evolving activity. It is suggested that there most probably exist hydrogen-bonding interactions between PG molecules and PS Ⅱ proteins.     

F-MSAP： A practical system to detect methylation in chicken genome

By replacing radiation with fluorescent system in the technique of methylation sensitive amplified polymorphism （MSAP） and optimizing reaction conditions, a modified technique to detect DNA methylation called F-MSAP （fluorescent labeled methylation sensitive amplified polymorphism） was developed. In the present study, cytosine methylation patterns of genomic DNA were investigated in two inbred chickens and their F1 hybrids. Three types of methylation patterns were observed in each individual, namely fully methylated, hemi-methylated or not methylated types. The average incidence of methylation was approximately 40%. The percentage that the F1 hybrid individual inherits the methylation for any given sites from either/both parent amounted to 95%, while the percentage of altered methylation patterns in F1 individual was only 5%, including 14 increased and 12 decreased methylation types, demonstrating that F-MSAP was highly efficient for large-scale detection of cytosine methylation in chicken genome. Our technique can be further extended to other animals or plants with complex genome and rich in methylation polymorphism.     

Retrovirus-induced de novo methylation of flanking host sequences correlates with gene inactivity

The pattern of DNA methylation changes during development of eukaryotes, and hypomethylation frequently correlates with gene expression (for reviews see refs 1-4). A causal relationship between hypermethylation and gene inactivity has been established for retroviral genomes which are methylated de novo when inserted into the germ line of mice (ref. 5; for review, see ref. 6). The mutual interaction of the provirus with the host genome can influence virus expression and can result in inactivation of the host gene by insertional mutagenesis. We report here that the insertion of a provirus can change the methylation pattern of the host DNA. Sequences flanking the provirus become methylated de novo within 1 kilobase (kb) of the integration site. In Mov-13 mice, which carry a lethal mutation of the alpha 1(I) collagen gene, de novo methylation of host DNA is associated with a change in chromatin conformation. This suggests that virus-induced DNA methylation can alter DNA-protein interactions and thereby interfere with correct gene activation during embryonic development.