After the recent publication in the Journal of Biophysical Chemistry entitled “Retracted HIV Study Provides New Information about the Status of the in Vitro Inhibition of DNA Replication by Back-bone Methylation”, i...After the recent publication in the Journal of Biophysical Chemistry entitled “Retracted HIV Study Provides New Information about the Status of the in Vitro Inhibition of DNA Replication by Back-bone Methylation”, it is of importance to review the results of Buck’s group on the synthesis and conformation analyses of phosphate-methylated RNAs in order to afford information on the absence of a further investigation with regard to this de facto acceptable approach. In fact these compounds belong to the very first group of RNAs with a modified neutral backbone by phosphatemethylation. In contrast to the corresponding phosphate-methylated DNAs with a frozen B-conformation, the phosphate-methylated RNAs show an A-conformation. The latter is a prerequisite for duplex formation with (complementary) (natural) RNA. A number of experiments support this fundamental statement. After the HIV study was retracted, the overall results concerning the phosphate-methylated RNAs were published without mentioning Buck’s initial proof of concept and his contributions. Generally, the (modified) dimer RNAs and DNAs possess a number of specific biophysical properties. A novel explanation is given for conflicting structural determinations.展开更多
HPLC analysis is important for determination of total level on DNA methylation in plants. It can be used to help characterise epigenetic changes during growth, development and stress. HPLC methods have been optimised ...HPLC analysis is important for determination of total level on DNA methylation in plants. It can be used to help characterise epigenetic changes during growth, development and stress. HPLC methods have been optimised for mammalian and microbial DNA, but not for plants. This article examines several important factors in the HPLC analysis of plant DNA methylation including extraction and purification of DNA and HPLC conditions choice by using leaves of rice seedling. The experimental results showed that RNA of nucleic acid was removed by using RNase A. This study also identified critical components of HPLC analysis. With the optimized method of HPLC conditions, the better result was achieved in the chromatogram of cytosine and 5-methylcytosine in genomic DNA acid hydrolysis. The study would offer a comprehensive guide for the stringent analysis of DNA methylation in plants.展开更多
In plants, demethylation of 5-methylcytosine (5 mC) residues is controlled by DNA glycosylases, while in mammals it requires oxidation of 5 mC by TET proteins, a group of Fe(II)/2-oxoglutaratedependent dioxygenases. W...In plants, demethylation of 5-methylcytosine (5 mC) residues is controlled by DNA glycosylases, while in mammals it requires oxidation of 5 mC by TET proteins, a group of Fe(II)/2-oxoglutaratedependent dioxygenases. We analysed the effects of expressing the C-terminal catalytic domain of the human TET3 gene (TET3c) in Arabidopsis thaliana, using an rDNA region as a methylation reporter. In TET3c transformants, epialleles with hypomethylation or hypermethylation patterns can be induced, which is each stably retained in progeny lines even after removal of the TET3c transgene. In TET3c transformants, 5-hydroxymethylcytosine (5 hmC) marks are detected, indicative of the oxidative activity of the transgenic enzyme. 5-formylcytosine (5 fC) is only detectable in TET3c transformants with a DNA glycosylase mutant background suggesting further oxidation of 5 hmC residues to 5 fC by TET3c, and efficient recognition and removal of 5 fC by plant glycosylases. The results suggest that TET3c can be employed to induce heritable locus-specific changes in DNA methylation, and that accumulation of 5 hmC can be used as a marker for TET3c target regions.展开更多
目的 探讨乳腺癌患者血清核受体亚家族C组成员2(nuclear receptor subfamily 3, group C, member 2,NR3C2),DNA甲基化转移酶-3A[DNA(cytosine-5)-methyltransferase 3A,DNMT3A]水平及其临床诊断价值。方法收集复旦大学附属华东医院2017...目的 探讨乳腺癌患者血清核受体亚家族C组成员2(nuclear receptor subfamily 3, group C, member 2,NR3C2),DNA甲基化转移酶-3A[DNA(cytosine-5)-methyltransferase 3A,DNMT3A]水平及其临床诊断价值。方法收集复旦大学附属华东医院2017年5月~2020年12月期间住院的94例乳腺癌患者为乳腺癌组,另选取同期健康体检者86例作为对照组。酶联免疫吸附试验(enzyme-linked immunosorbent assay,ELISA)检测两组血清NR3C2和DNMT3A水平,Pearson法分析乳腺癌患者血清NR3C2和DNMT3A表达水平相关性,多因素Logistic回归分析乳腺癌发生的影响因素,受试者工作特征(receiver operating characteristic,ROC)曲线评估NR3C2和DNMT3A对乳腺癌的诊断价值。结果 乳腺癌组患者血清NR3C2水平为317.84±33.47 ng/L,低于对照组(374.25±47.72ng/L),DNMT3A的表达水平为451.63±75.47μg/L,高于对照组(349.85±63.72μg/L),差异有统计学意义(t=9.243,9.729,均P<0.05)。Pearson分析结果显示,乳腺癌患者血清NR3C2与DNMT3A表达水平存在明显负相关(r=-0.501,P=0.000)。Logistic回归分析结果显示,NR3C2高水平为乳腺癌发生的保护因素(OR=0.563,95%CI:0.372~0.851,P=0.006),DNMT3A高水平是乳腺癌发生的危险因素(OR=1.834,95%CI:1.249~2.693,P=0.002)。ROC曲线结果发现,血清NR3C2与DNMT3A诊断乳腺癌的曲线下面积(area under the curve,AUC)分别为0.853(0.791~0.915),0.930(0.896~0.965),当两者联合时其AUC为0.969(0.949~0.990),高于两者单独检测(Z=3.460,1.894,P=0.000,0.034)。结论 乳腺癌患者血清NR3C2表达水平降低,DNMT3A表达水平升高,两者联合检测能够提高乳腺癌的诊断价值。展开更多
文摘After the recent publication in the Journal of Biophysical Chemistry entitled “Retracted HIV Study Provides New Information about the Status of the in Vitro Inhibition of DNA Replication by Back-bone Methylation”, it is of importance to review the results of Buck’s group on the synthesis and conformation analyses of phosphate-methylated RNAs in order to afford information on the absence of a further investigation with regard to this de facto acceptable approach. In fact these compounds belong to the very first group of RNAs with a modified neutral backbone by phosphatemethylation. In contrast to the corresponding phosphate-methylated DNAs with a frozen B-conformation, the phosphate-methylated RNAs show an A-conformation. The latter is a prerequisite for duplex formation with (complementary) (natural) RNA. A number of experiments support this fundamental statement. After the HIV study was retracted, the overall results concerning the phosphate-methylated RNAs were published without mentioning Buck’s initial proof of concept and his contributions. Generally, the (modified) dimer RNAs and DNAs possess a number of specific biophysical properties. A novel explanation is given for conflicting structural determinations.
文摘HPLC analysis is important for determination of total level on DNA methylation in plants. It can be used to help characterise epigenetic changes during growth, development and stress. HPLC methods have been optimised for mammalian and microbial DNA, but not for plants. This article examines several important factors in the HPLC analysis of plant DNA methylation including extraction and purification of DNA and HPLC conditions choice by using leaves of rice seedling. The experimental results showed that RNA of nucleic acid was removed by using RNase A. This study also identified critical components of HPLC analysis. With the optimized method of HPLC conditions, the better result was achieved in the chromatogram of cytosine and 5-methylcytosine in genomic DNA acid hydrolysis. The study would offer a comprehensive guide for the stringent analysis of DNA methylation in plants.
文摘In plants, demethylation of 5-methylcytosine (5 mC) residues is controlled by DNA glycosylases, while in mammals it requires oxidation of 5 mC by TET proteins, a group of Fe(II)/2-oxoglutaratedependent dioxygenases. We analysed the effects of expressing the C-terminal catalytic domain of the human TET3 gene (TET3c) in Arabidopsis thaliana, using an rDNA region as a methylation reporter. In TET3c transformants, epialleles with hypomethylation or hypermethylation patterns can be induced, which is each stably retained in progeny lines even after removal of the TET3c transgene. In TET3c transformants, 5-hydroxymethylcytosine (5 hmC) marks are detected, indicative of the oxidative activity of the transgenic enzyme. 5-formylcytosine (5 fC) is only detectable in TET3c transformants with a DNA glycosylase mutant background suggesting further oxidation of 5 hmC residues to 5 fC by TET3c, and efficient recognition and removal of 5 fC by plant glycosylases. The results suggest that TET3c can be employed to induce heritable locus-specific changes in DNA methylation, and that accumulation of 5 hmC can be used as a marker for TET3c target regions.
文摘目的 探讨乳腺癌患者血清核受体亚家族C组成员2(nuclear receptor subfamily 3, group C, member 2,NR3C2),DNA甲基化转移酶-3A[DNA(cytosine-5)-methyltransferase 3A,DNMT3A]水平及其临床诊断价值。方法收集复旦大学附属华东医院2017年5月~2020年12月期间住院的94例乳腺癌患者为乳腺癌组,另选取同期健康体检者86例作为对照组。酶联免疫吸附试验(enzyme-linked immunosorbent assay,ELISA)检测两组血清NR3C2和DNMT3A水平,Pearson法分析乳腺癌患者血清NR3C2和DNMT3A表达水平相关性,多因素Logistic回归分析乳腺癌发生的影响因素,受试者工作特征(receiver operating characteristic,ROC)曲线评估NR3C2和DNMT3A对乳腺癌的诊断价值。结果 乳腺癌组患者血清NR3C2水平为317.84±33.47 ng/L,低于对照组(374.25±47.72ng/L),DNMT3A的表达水平为451.63±75.47μg/L,高于对照组(349.85±63.72μg/L),差异有统计学意义(t=9.243,9.729,均P<0.05)。Pearson分析结果显示,乳腺癌患者血清NR3C2与DNMT3A表达水平存在明显负相关(r=-0.501,P=0.000)。Logistic回归分析结果显示,NR3C2高水平为乳腺癌发生的保护因素(OR=0.563,95%CI:0.372~0.851,P=0.006),DNMT3A高水平是乳腺癌发生的危险因素(OR=1.834,95%CI:1.249~2.693,P=0.002)。ROC曲线结果发现,血清NR3C2与DNMT3A诊断乳腺癌的曲线下面积(area under the curve,AUC)分别为0.853(0.791~0.915),0.930(0.896~0.965),当两者联合时其AUC为0.969(0.949~0.990),高于两者单独检测(Z=3.460,1.894,P=0.000,0.034)。结论 乳腺癌患者血清NR3C2表达水平降低,DNMT3A表达水平升高,两者联合检测能够提高乳腺癌的诊断价值。
