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DNA methylation in poultry:a review
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作者 Xing Ju Zhijun Wang +2 位作者 Danfeng Cai Semiu Folaniyi Bello Qinghua Nie 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2024年第2期509-518,共10页
As an important epigenetic modification,DNA methylation is involved in many biological processes such as animal cell differentiation,embryonic development,genomic imprinting and sex chromosome inactivation.As DNA meth... As an important epigenetic modification,DNA methylation is involved in many biological processes such as animal cell differentiation,embryonic development,genomic imprinting and sex chromosome inactivation.As DNA methylation sequencing becomes more sophisticated,it becomes possible to use it to solve more zoological problems.This paper reviews the characteristics of DNA methylation,with emphasis on the research and application of DNA methylation in poultry. 展开更多
关键词 CpG islands differentially methylated genes differentially methylated regions dna methylation POULTRY
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mRNA expression and DNA methylation in three key genes involved in caste differentiation in female honeybees(Apis mellifera) 被引量:3
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作者 Xin-Liang SHAO Shao-Yu HE +3 位作者 Xin-Ying ZHUANG Ying FAN Ya-Hui LI Yong-Gang YAO 《Zoological Research》 CAS CSCD 北大核心 2014年第2期92-98,共7页
In honeybee (Apis mellifera) colonies, queens and workers are altemative forms of the adult female honeybee that develop from genetically identical zygotes but that depend on differential nourishment. Queens and wor... In honeybee (Apis mellifera) colonies, queens and workers are altemative forms of the adult female honeybee that develop from genetically identical zygotes but that depend on differential nourishment. Queens and workers display distinct morphologies, anatomies and behavior, better known as caste differentiation. Despite some basic insights, the exact mechanism responsible for this phenomenon, especially at the molecular level, remains unclear although some progress has been achieved. In this study, we examined mRNA levels of the TOR (target of rapamycin) and Dnmt3 (DNA methyltransferase 3) genes, closely related to caste differentiation in honeybees. We also investigated mRNA expression of the S6K (similar to RPS6-p70-protein kinase) gene linked closely to organismal growth and development in queen and worker larvae (1-day and 3-day old). Last, we investigated the methylation status of these three genes in corresponding castes. We found no difference in mRNA expression for the three genes between 1st instar queen and worker larvae; however, 3rd instar queen larvae had a higher level of TOR mRNA than worker larvae. Methylation levels of all three genes were lower in queen larvae than worker larvae but the differences were not statistically significant. These findings provide basic data for broadening our understanding of caste differentiation in female honeybees. 展开更多
关键词 Caste differentiation dna methylation dna methyltransferase 3 HONEYBEE Target of rapamycin
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DNA methylation and demethylation link the properties of mesenchymal stem cells: Regeneration and immunomodulation 被引量:3
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作者 Tian-Yi Xin Ting-Ting Yu Rui-Li Yang 《World Journal of Stem Cells》 SCIE CAS 2020年第5期351-358,共8页
Mesenchymal stem cells(MSCs)are a heterogeneous population that can be isolated from various tissues,including bone marrow,adipose tissue,umbilical cord blood,and craniofacial tissue.MSCs have attracted increasingly m... Mesenchymal stem cells(MSCs)are a heterogeneous population that can be isolated from various tissues,including bone marrow,adipose tissue,umbilical cord blood,and craniofacial tissue.MSCs have attracted increasingly more attention over the years due to their regenerative capacity and function in immunomodulation.The foundation of tissue regeneration is the potential of cells to differentiate into multiple cell lineages and give rise to multiple tissue types.In addition,the immunoregulatory function of MSCs has provided insights into therapeutic treatments for immune-mediated diseases.DNA methylation and demethylation are important epigenetic mechanisms that have been shown to modulate embryonic stem cell maintenance,proliferation,differentiation and apoptosis by activating or suppressing a number of genes.In most studies,DNA hypermethylation is associated with gene suppression,while hypomethylation or demethylation is associated with gene activation.The dynamic balance of DNA methylation and demethylation is required for normal mammalian development and inhibits the onset of abnormal phenotypes.However,the exact role of DNA methylation and demethylation in MSC-based tissue regeneration and immunomodulation requires further investigation.In this review,we discuss how DNA methylation and demethylation function in multi-lineage cell differentiation and immunomodulation of MSCs based on previously published work.Furthermore,we discuss the implications of the role of DNA methylation and demethylation in MSCs for the treatment of metabolic or immune-related diseases. 展开更多
关键词 Mesenchymal stem cells dna methylation and demethylation Multi-lineage differentiation REGENERATION IMMUNOMODULATION Immune disease
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Effects of DNA Methylation and Histone Modification on Differentiation-associated Gene Expression in ES,NIH3T3,and NIT-1
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作者 方爱平 张悦 +4 位作者 李明岳 郭辉 余小舫 李富荣 胡泓 《Journal of Huazhong University of Science and Technology(Medical Sciences)》 SCIE CAS 2011年第1期10-16,共7页
The effects of epigenetic modification on the differentiation of islet cells and the expression of associated genes(Pdx-1,Pax4,MafA,and Nkx6.1,etc) were investigated.The promoter methylation status of islet differen... The effects of epigenetic modification on the differentiation of islet cells and the expression of associated genes(Pdx-1,Pax4,MafA,and Nkx6.1,etc) were investigated.The promoter methylation status of islet differentiation-associated genes(Pdx-1,Pax4,MafA and Nkx6.1),Oct4 and MLH1 genes of mouse embryonic stem cells,NIH3T3 cells and NIT-1 cells were profiled by methylated DNA immunoprecipitation,real-time quantitative PCR(MeDIP-qPCR) techniques.The histone modification status of these genes promoter region in different cell types was also measured by using chromatin immunoprecipitation real-time quantitative PCR methods.The expression of these genes in these cells was detected by using real-time quantitative PCR.The relationship between the epigenetic modification(DNA methylation,H3 acetylation,H3K4m3 and H3K9m3) of these genes and their expression was analyzed.The results showed that:(1) the transcription-initiation-sites of Pdx-1,MafA and Nkx6.1 were highly methylated in NIH3T3 cells; (2) NIH3T3 cells showed a significantly higher level of DNA methylation modification in the transcription-initiation-site of Pdx-1,Pax4,MafA and Nkx6.1 genes than that in mES cells and NIT-1 cells(P〈0.05); (3) NIT-1 cells had a significantly higher level of H3K4m3 modification in the transcription-initiation-site of Pdx-1,Pax4,MafA and Nkx6.1 genes than that in mES cells and NIH3T3 cells(P〈0.05),with significantly increased level of gene expression; (4) NIH3T3 cell had a significantly higher level of H3K9m3 modification in the transcription-initiation-site of Pdx-1,Pax4,MafA and Nkx6.1 genes than that in mES cells and with NIT-1 cell(P〈0.05),with no detectable mRNA expression of these genes.It was concluded that histone modification(H3K4m3 and H3K9m3) and DNA methylation might have an intimate communication between each other in the differentiation process from embryonic stem cells into islet cells. 展开更多
关键词 dna methylation histone 3 lysine 4 trimethylation histone 3 lysine 9 trimethylation histone 3 acetylation gene expression islet DIFFERENTIATION
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miR-214-5p通过DNMT1介导的AXIN2基因DNA甲基化修饰在皮肤基底细胞癌中的作用机制
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作者 熊斯颖 邵蕾 +2 位作者 杨艳 高爱莉 揭丽云 《新疆医科大学学报》 CAS 2024年第1期27-32,共6页
目的探讨皮肤基底细胞癌中轴抑制蛋白2(Axis inhibition protein 2,AXIN2)基因启动子甲基化对基因转录的影响及miR-214-5p通过靶向DNA甲基转移酶1(DNA methyltransferase1,DNMT1)对AXIN2甲基化率的调控机制。方法收集2022年1月-2023年6... 目的探讨皮肤基底细胞癌中轴抑制蛋白2(Axis inhibition protein 2,AXIN2)基因启动子甲基化对基因转录的影响及miR-214-5p通过靶向DNA甲基转移酶1(DNA methyltransferase1,DNMT1)对AXIN2甲基化率的调控机制。方法收集2022年1月-2023年6月在广州市皮肤病防治所就诊治疗的102例皮肤基底细胞癌(Cutaneous basal cell carcinoma,BCC)患者作为研究对象,提取癌组织和癌旁正常组织标本及基线资料。焦磷酸测序法检测AXIN2基因启动子区甲基化率。实时荧光定量PCR检测AXIN2、DNMT1基因mRNA和miR-214-5p的表达水平。将miR-214-5p模拟物(mimic)、抑制物(inhibitor)及其阴性对照(mimic NC和inhibitor NC)分别对基底细胞癌A431细胞进行转染,48 h后检测DNMT1基因mRNA表达水平和AXIN2基因甲基化率。结果BCC癌组织的AXIN2基因甲基化率显著高于癌旁正常组织(t=5.128,P<0.001),AXIN2基因mRNA相对表达水平显著低于癌旁正常组织(t=7.826,P<0.001),DNMT1基因mRNA表达水平显著高于癌旁正常组织(t=4.838,P<0.001),miR-214-5p表达水平显著低于癌旁正常组织(t=5.426,P<0.001)。BCC癌组织的AXIN2基因甲基化率与其mRNA表达水平呈负相关(r=-0.793,P<0.001),DNMT1基因mRNA水平与AXIN2基因甲基化率呈正相关(r=0.814,P<0.001),miR-214-5p表达水平与DNMT1基因mRNA水平呈负相关(r=-0.747,P<0.001)。双荧光素酶报告基因实验结果证实,DNMT1是miR-214-5p的靶基因。细胞转染后,与mimic NC、inhibitor和inhibitor NC比较,mimic的DNMT1基因mRNA水平、AXIN2基因甲基化率显著降低(P<0.001);而inhibitor的DNMT1基因mRNA水平和AXIN2基因甲基化率相较于其他三组明显上升(P<0.001)。结论miR-214-5p可通过调控下游靶蛋白DNMT1表达,影响AXIN2基因的DNA甲基化率,调控AXIN2基因的表达水平,参与皮肤基底细胞癌的发生机制。 展开更多
关键词 基底细胞癌 miR-214-5p dna甲基化转移酶1 轴抑制蛋白2 启动子区甲基化
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Genome-Wide Analysis of DNA Methylation in Soybean 被引量:7
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作者 Qing-Xin Song Xiang Lu +6 位作者 Qing-Tian Li Hui Chen Xing-Yu Hu Biao Ma Wan-Ke Zhang Shou-Yi Chen Jin-Song Zhang 《Molecular Plant》 SCIE CAS CSCD 2013年第6期1961-1974,共14页
Cytosine methylation is an important mechanism for dynamical regulation of gene expression and trans- posable element (TE) mobility during plant developmental processes. Here, we identified the transcription start s... Cytosine methylation is an important mechanism for dynamical regulation of gene expression and trans- posable element (TE) mobility during plant developmental processes. Here, we identified the transcription start sites of genes using high-throughput sequencing and then analyzed the DNA methylation status in soybean roots, stems, leaves, and cotyledons of developing seeds at single-base resolution. Profiling of DNA methylation in different organs revealed 2162 differentially methylated regions among organs, and a portion of hypomethylated regions were correlated with high expression of neighboring genes. Because of the different distribution of class I TEs (retrotransposons) and class II TEs (DNA transposons), the promoters of the lowest-expressed genes showed higher levels of CG and CHG methyla- tion but a lower level of CHH methylation. We further found that the CHH methylation level of class II TEs was higher than class I TEs, possibly due to the presence of more smRNAs in class II TEs. In cotyledons of developing seeds, smRNA abundance was roughly positively correlated with hypermethylated regions but negatively related to hypomethylated regions. These studies provide significant insights into the complicated interplays among DNA methylation, smRNA abundance, TE distribution, and gene expression in soybean. 展开更多
关键词 SOYBEAN dna methylation differentially methylated regions organs.
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Imprinting at the KBTBD6 locus involves species-specific m ternal methylation and monoallelic expression in livestock animals
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作者 Jinsoo Ahn In-Sul Hwang +2 位作者 Mi-Ryung Park Seongsoo Hwang Kichoon Lee 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2024年第1期127-145,共19页
Background The primary differentially methylated regions(DMRs) which are maternally hypermethylated serve as imprinting control regions(ICRs) that drive monoallelic gene expression, and these ICRs have been investigat... Background The primary differentially methylated regions(DMRs) which are maternally hypermethylated serve as imprinting control regions(ICRs) that drive monoallelic gene expression, and these ICRs have been investigated due to their implications in mammalian development. Although a subset of genes has been identified as imprinted, in-depth comparative approach needs to be developed for identification of species-specific imprinted genes. Here, we examined DNA methylation status and allelic expression at the KBTBD6 locus across species and tissues and explored potential mechanisms of imprinting.Results Using whole-genome bisulfite sequencing and RNA-sequencing on parthenogenetic and normal porcine embryos, we identified a maternally hypermethylated DMR between the embryos at the KBTBD6 promoter Cp G island and paternal monoallelic expression of KBTBD6. Also, in analyzed domesticated mammals but not in humans, non-human primates and mice, the KBTBD6 promoter Cp G islands were methylated in oocytes and/or allelically methyl-ated in tissues, and monoallelic KBTBD6 expression was observed, indicating livestock-specific imprinting. Further analysis revealed that these Cp G islands were embedded within transcripts in porcine and bovine oocytes which coexisted with an active transcription mark and DNA methylation, implying the presence of transcription-dependent imprinting.Conclusions In this study, our comparative approach revealed an imprinted expression of the KBTBD6 gene in domesticated mammals, but not in humans, non-human primates, and mice which implicates species-specific evolution of genomic imprinting. 展开更多
关键词 differentially methylated region Domesticated mammal IMPRINTING KBTBD6 PARTHENOGENETIC
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A differentially methylated region of the DAZ1 gene in spermatic and somatic cells 被引量:3
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作者 Zuo-Xiang Li Xu Ma Zhao-Hui Wang 《Asian Journal of Andrology》 SCIE CAS CSCD 2006年第1期61-67,共7页
Aim: To investigate the methylation status of the deleted in azoospermia 1(DAZ1) gene promoter region in different cell types. Methods: Using CpG island Searcher software, a CpG island was found in the promoter re... Aim: To investigate the methylation status of the deleted in azoospermia 1(DAZ1) gene promoter region in different cell types. Methods: Using CpG island Searcher software, a CpG island was found in the promoter region of the DAZ1 gene. The methylation status of this region was analyzed in sperm and leukocytes by bisulfited sequencing. Results: The methylation status of the CpG island in the DAZ1 gene promoter region differed in leukocytes and sperm: it was methylated in leukocytes, but unmethylated in sperm. Conclusion: A differentially methylated region of the DAZ1 gene exists in spermatic and somatic cells, suggesting that methylation of this region may regulate DAZ1 gene expression in different tissues. (Asian J Androl 2006 Jan; 8:61-67 ) 展开更多
关键词 DAZ1 gene dna methylation CpG island methylated region SPERMATOGENESIS
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DNA methylation level of promoter region of activating transcription factor 5 in glioma 被引量:3
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作者 Xiao-min HUA Juan WANG +10 位作者 Dong-meng QIAN Jing-yi SONG Hao CHEN Xiu-li ZHU Rui ZHOU Yu-dan ZHAO Xiu-zhi ZHOU Ling LI Li ZHANG Xu-xia SONG Bin WANG 《Journal of Zhejiang University-Science B(Biomedicine & Biotechnology)》 SCIE CAS CSCD 2015年第9期757-762,共6页
Transcription factors, which represent an important class of proteins that play key roles in controlling cellular proliferation and cell cycle modulation, are attractive targets for cancer therapy. Previous researches... Transcription factors, which represent an important class of proteins that play key roles in controlling cellular proliferation and cell cycle modulation, are attractive targets for cancer therapy. Previous researches have shown that the expression level of activating transcription factor 5 (ATF5) was frequently increased in glioma and its acetylation level was related to glioma. The purposes of this study were to explore the methylation level of ATF5 in clinical glioma tissues and to explore the effect of ATF5 methylation on the expression of ATF5 in glioma. Methylation of the promoter region of ATF5 was assayed by bisulflte-specific polymerase chain reaction (PCR) sequencing analysis in 35 cases of glioma and 5 normal tissues. Quantitative real-time PCR (qRT-PCR) was also performed to detect ATF5 mRNA expression in 35 cases of glioma and 5 normal tissues. Clinical data were collected from the patients and analyzed. The percentages of methylation of the ATF5 gene in the promoter region in healthy control, patients with well-differentiated glioma, and those with poorly differentiated glioma were 87.78%, 73.89%, and 47.70%, respectively. Analysis of the methylation status of the promoter region of the ATF5 gene showed a gradually de- creased methylation level in poorly differentiated glioma, well-differentiated glioma, and normal tissues (P〈0.05). There was also a significant difference between well-differentiated glioma and poorly differentiated glioma (P〈0.05). ATF5 mRNA expression in glioma was significantly higher than that in the normal tissues (P〈0.05). This study provides the first evidence that the methylation level of ATF5 decreased, and its mRNA expression was evidently up-regulated in glioma. 展开更多
关键词 dna methylation Activating transcription factor Promoter region EPIGENETIC GLIOMA
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Epigenome-wide DNA methylation study of whole blood in patients with sporadic amyotrophic lateral sclerosis 被引量:1
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作者 Zhengyi Cai Xinmiao Jia +2 位作者 Mingsheng Liu Xunzhe Yang Liying Cui 《Chinese Medical Journal》 SCIE CAS CSCD 2022年第12期1466-1473,共8页
Background:Epigenetics,and especially DNA methylation,contributes to the pathogenesis of sporadic amyotrophic lateral sclerosis(SALS).This study aimed to investigate the role of DNA methylation in SALS using whole blo... Background:Epigenetics,and especially DNA methylation,contributes to the pathogenesis of sporadic amyotrophic lateral sclerosis(SALS).This study aimed to investigate the role of DNA methylation in SALS using whole blood of SALS patients.Methods::In total,32 SALS patients and 32 healthy controls were enrolled in this study.DNA was isolated from whole blood collected from the participants.DNA methylation profiles were generated using Infinium MethylationEPIC BeadChip.Results:We identified 34 significant differentially methylated positions(DMPs)in whole blood from SALS patients,compared with the healthy controls.Of these DMPs,five were hypermethylated and 29 were hypomethylated;they corresponded to 13 genes.For the DMPs,ATAD3B and BLK were hypermethylated,whereas DDO,IQCE,ABCB1,DNAH9,FIGN,NRP1,TMEM87B,CCSAP,ST6GALNAC5,MYOM2,and RUSC1-AS1 were hypomethylated.We also identified 12 differentially methylated regions(DMRs),related to 12 genes(NWD1,LDHD,CIS,IQCE,TNF,PDE1C,LGALS1,CSNK1E,LRRC23,ENO2,ELOVL2,and ELOVL2-AS1).According to data from the Kyoto Encyclopedia of Genes and Genomes database,DNAH9 and TNF are involved in the amyotrophic lateral sclerosis(ALS)pathway.Correlation analysis between clinical features and DNA methylation profiling indicated that the methylation level of ELOVL2 and ARID1B was positively associated with the age of onset(r=0.86,adjust P=0.001)and disease duration(r=0.83,adjust P=0.01),respectively.Conclusions:We found aberrant methylation in DMP-and DMR-related genes,implying that many epigenetic alterations,such as the hypomethylation of DNAH9 and TNF,play important roles in ALS etiology.These findings can be helpful for developing new therapeutic interventions. 展开更多
关键词 Amyotrophic lateral sclerosis dna methylation differentially methylated positions differentially methylated regions Whole blood
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水稻幼苗期低温胁迫DNA甲基化特征分析 被引量:1
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作者 郭慧 李树杏 +4 位作者 甘雨 张宏伟 郝留根 杨占烈 向关伦 《植物遗传资源学报》 CAS CSCD 北大核心 2023年第2期376-387,共12页
为探索低温胁迫下幼苗期水稻全基因组DNA甲基化调控机制,通过对3个耐冷性不同的水稻品种进行3~4℃低温处理试验,利用全基因组DNA甲基化测序(WGBS,whole genome bisulfite sequencing)技术分析低温处理后全基因组DNA甲基化水平及模式变... 为探索低温胁迫下幼苗期水稻全基因组DNA甲基化调控机制,通过对3个耐冷性不同的水稻品种进行3~4℃低温处理试验,利用全基因组DNA甲基化测序(WGBS,whole genome bisulfite sequencing)技术分析低温处理后全基因组DNA甲基化水平及模式变化。结果显示:低温处理后,日本晴和9311的胞嘧啶甲基化(mC)都表现下降,而P427的mC值上升。针对启动子区和转录区发生甲基化的基因进行锚定,发现启动子区锚定的基因数远高于转录区,材料P427锚定的基因最多,9311锚定的基因最少。GO、KEGG富集分析发现,低温处理后P427差异甲基化基因主要富集在二萜生物合成、淀粉和蔗糖代谢、苯丙烷类生物合成等代谢通路。结果表明:基因启动子区甲基化对低温胁迫响应基因的调控作用更为重要,甲基化调控基因表达不仅与甲基化程度有关,与甲基化类型也可能存在一定的关系。P427可能通过二萜生物合成、淀粉和蔗糖代谢等代谢通路及激素信号转导通路上的基因影响苗期水稻的耐冷性。本研究进一步加深了对水稻耐冷性响应机制的理解。 展开更多
关键词 水稻 dna甲基化 低温胁迫 差异表达基因 差异甲基化区域
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The progress on the estimation of DNA methylation level and the detection of abnormal methylation
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作者 Shicai Fan Likun Wang +3 位作者 Liang Liang Xiaohong Cao Jianxiong Tang Qi Tian 《Quantitative Biology》 CSCD 2022年第1期55-66,共12页
Background:DNA methylation is a key heritable epigenetic modification that plays a crucial role in transcriptional regulation and therefore a broad range of biological processes.The complex patterns of DNA methylation... Background:DNA methylation is a key heritable epigenetic modification that plays a crucial role in transcriptional regulation and therefore a broad range of biological processes.The complex patterns of DNA methylation highlight the significance of the profiling the DNA methylation landscape.Results:In this review,the main high-throughput detection technologies are summarized,and then the three trends of computational estimation of DNA methylation levels were analyzed,especially the expanding of the methylation data with lower coverage.Furthermore,the detection methods of differential methylation patterns for sequencing and array data were presented.Conclusions:More and more research indicated the great importance of DNA methylation changes across different diseases,such as cancers.Although a lot of enormous progress has been made in understanding the role of DNA methylation,only few methylated genes or functional elements serve as clinically relevant cancer biomarkers.The bottleneck in DNA methylation advances has shifted from data generation to data analysis.Therefore,it is meaningful to develop machine learning models for computational estimation of methylation profiling and identify the potential biomarkers. 展开更多
关键词 dna methylation genome-wide profiling computational estimation single-cell methylome differential methylation detection
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Reduced non-CpG methylation is a potential epigenetic target after spinal cord injury
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作者 Zhourui Wu Chen Li +3 位作者 Ran Zhu Yiqiu Cao Thomas C.Chen Liming Cheng 《Neural Regeneration Research》 SCIE CAS CSCD 2023年第11期2489-2496,共8页
DNA methylation is a critical epigenetic regulator in the occurrence and development of diseases and is closely related to various functional responses in relation to spinal cord injury.To investigate the role of DNA ... DNA methylation is a critical epigenetic regulator in the occurrence and development of diseases and is closely related to various functional responses in relation to spinal cord injury.To investigate the role of DNA methylation in spinal cord injury,we constructed a library with reduced-representation bisulfite sequencing data obtained at various time points(day 0-42)after spinal cord injury in mice.Global DNA methylation levels,specifically non-CpG(CHG and CHH)methylation levels,decreased modestly following spinal cord injury.Stages post-spinal cord injury were classified as early(day 0-3),intermediate(day7-14),and late(day 28-42)based on similarity and hie rarchical cluste ring of global DNA methylation patterns.The non-CpG methylation level,which included CHG and CHH methylation levels,was markedly reduced despite accounting for a minor proportion of total methylation abundance.At multiple genomic sites,including the 5’untranslated regions,promoter,exon,intron,and 3’untranslated regions,the non-CpG methylation level was markedly decreased following spinal cord injury,whereas the CpG methylation level remained unchanged at these locations.Approximately one-half of the differentially methylated regions were located in intergenic areas;the other differentially methylated regions in both CpG and non-CpG regions were cluste red in intron regions,where the DNA methylation level was highest.The function of genes associated with differentially methylated regions in promoter regions was also investigated.From Gene Ontology analysis results,DNA methylation was implicated in a number of essential functional responses to spinal cord injury,including neuronal synaptic connection creation and axon regeneration.Notably,neither CpG methylation nor non-CpG methylation was implicated in the functional response of glial or inflammatory cells.In summary,our work elucidated the dynamic pattern of DNA methylation in the spinal co rd following injury and identified reduced nonCpG methylation as an epigenetic target after spinal cord injury in mice. 展开更多
关键词 CpG methylation cytosine fraction differentially methylated regions dna methylation dna methyltransferases dynamic signatures Gene Ontology non-CpG methylation single-cell RNA-Seq spinal cord injury
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Identification of differentially expressed genes regulated by methylation in colon cancer based on bioinformatics analysis 被引量:7
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作者 Yu Liang Cheng Zhang Dong-Qiu Dai 《World Journal of Gastroenterology》 SCIE CAS 2019年第26期3392-3407,共16页
BACKGROUND DNA methylation, acknowledged as a key modification in the field of epigenetics, regulates gene expression at the transcriptional level. Aberrant methylation in DNA regulatory regions could upregulate oncog... BACKGROUND DNA methylation, acknowledged as a key modification in the field of epigenetics, regulates gene expression at the transcriptional level. Aberrant methylation in DNA regulatory regions could upregulate oncogenes and downregulate tumor suppressor genes without changing the sequences.However, studies of methylation in the control of gene expression are still inadequate. In the present research, we performed bioinformatics analysis to clarify the function of methylation and supply candidate methylation-related biomarkers and drivers for colon cancer.AIM To identify and analyze methylation-regulated differentially expressed genes(MeDEGs) in colon cancer by bioinformatics analysis.METHODS We downloaded RNA expression profiles, Illumina Human Methylation 450 K BeadChip data, and clinical data of colon cancer from The Cancer Genome Atlas project. MeDEGs were identified by analyzing the gene expression and methylation levels using the edgeR and limma package in R software. Gene ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analyses were performed in the DAVID database and KEGG Orthology-Based Annotation System 3.0, respectively. We then conducted Kaplan–Meier survival analysis to explore the relationship between methylation and expression and prognosis. Gene set enrichment analysis(GSEA) and investigation of protein-protein interactions(PPI) were performed to clarify the function of prognosis-related genes.RESULTS A total of 5 up-regulated and 81 down-regulated genes were identified asMeDEGs. GO and KEGG pathway analyses indicated that MeDEGs were enriched in multiple cancer-related terms. Furthermore, Kaplan–Meier survival analysis showed that the prognosis was negatively associated with the methylation status of glial cell-derived neurotrophic factor(GDNF) and reelin(RELN). In PPI networks, GDNF and RELN interact with neural cell adhesion molecule 1. Besides, GDNF can interact with GDNF family receptor alpha(GFRA1), GFRA2, GFRA3, and RET. RELN can interact with RAFAH1 B1,disabled homolog 1, very low-density lipoprotein receptor, lipoprotein receptorrelated protein 8, and NMDA 2 B. Based on GSEA, hypermethylation of GDNF and RELN were both significantly associated with pathways including "RNA degradation," "ribosome," "mismatch repair," "cell cycle" and "base excision repair."CONCLUSION Aberrant DNA methylation plays an important role in colon cancer progression.MeDEGs that are associated with the overall survival of patients may be potential targets in tumor diagnosis and treatment. 展开更多
关键词 COLON CANCER Bioinformatics analysis The CANCER Genome Atlas project dna methylation methylation-regulated differentially EXPRESSED genes Overall survival
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DNA甲基化在解析毛竹自然变异中的应用
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作者 李英 岳祥华 《生物技术通报》 CAS CSCD 北大核心 2023年第7期48-55,共8页
DNA甲基化能够在不改变DNA序列的情况下改变基因的表达和引起可变剪切等,进而改变细胞的表型甚至功能;并且这种修饰能够随着DNA的复制过程遗传给子代DNA,因而在植物体细胞突变过程发挥重要调控作用。虽然长期以无性繁殖为主,毛竹(Phyllo... DNA甲基化能够在不改变DNA序列的情况下改变基因的表达和引起可变剪切等,进而改变细胞的表型甚至功能;并且这种修饰能够随着DNA的复制过程遗传给子代DNA,因而在植物体细胞突变过程发挥重要调控作用。虽然长期以无性繁殖为主,毛竹(Phyllostachys edulis)却存在丰富的自然突变类型,但是至今其遗传调控机制尚不清晰。本文综述了毛竹自然变异研究现状、植物DNA甲基化及其转录调控机制在植物发育过程中的研究进展,展望了DNA甲基化在解析毛竹自然变异现象的潜在应用,以期为竹类植物精准育种提供理论指导与技术支持。 展开更多
关键词 表观转录调控 dna甲基化 分化和发育 自然变异 竹类植物
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舌黏膜癌变基因组甲基化分析
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作者 刘华 岳万远 +3 位作者 邵帅 孙家平 杨莹 代晓明 《华西口腔医学杂志》 CAS CSCD 北大核心 2024年第3期319-328,共10页
目的研究舌黏膜癌变过程中基因组甲基化特征,探讨舌癌中DNA甲基化的规律。方法用50 mg/L的4-硝基喹啉-1-氧化物(4NQO)饮水诱导C57BL/6J小鼠舌黏膜癌变,分别取第0、12、28周的舌黏膜(分别代表正常、癌前病变和癌变)进行基因芯片检测和甲... 目的研究舌黏膜癌变过程中基因组甲基化特征,探讨舌癌中DNA甲基化的规律。方法用50 mg/L的4-硝基喹啉-1-氧化物(4NQO)饮水诱导C57BL/6J小鼠舌黏膜癌变,分别取第0、12、28周的舌黏膜(分别代表正常、癌前病变和癌变)进行基因芯片检测和甲基化DNA免疫沉淀测序(MeDIP-Seq),在人舌黏膜组织和人舌癌细胞系中,用实时定量逆转录聚合酶链反应(qRT-PCR)和飞行质谱检测验证转化生长因子贝塔信号蛋白1(SMAD1)的表达和启动子的甲基化。结果28周较12周和0周舌黏膜的胞嘧啶鸟嘌呤岛(CGI)甲基化水平均升高,12周时启动子甲基化水平高于0周。在0、12和28周期间,208个差异表达基因与启动子中的差异甲基化呈负相关。与正常黏膜相比,细胞系中SMAD1的mRNA上调,同时启动子甲基化水平降低。结论舌黏膜癌变中伴随DNA甲基化修饰异常,舌癌中SMAD1高表达伴启动子低甲基化。 展开更多
关键词 舌癌 发病机制 甲基化 动物模型 甲基化dna免疫沉淀测序 差异表达基因
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5-azaC对萝卜茎尖DNA甲基化和开花的影响 被引量:23
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作者 汪炳良 李水凤 +1 位作者 曾广文 邓俭英 《核农学报》 CAS CSCD 北大核心 2005年第4期265-268,共4页
本文研究了去甲基化因子5氮杂胞苷(5azaC)对萝卜开花及幼苗茎尖DNA甲基化水平的影响。用0(对照)、0.10、0.25、0.50和1.00mmolL5azaC处理‘短叶13’萝卜种子6d,除对照外,茎尖组织DNA甲基化水平均有所降低,并与春化后茎尖组织DNA甲基化... 本文研究了去甲基化因子5氮杂胞苷(5azaC)对萝卜开花及幼苗茎尖DNA甲基化水平的影响。用0(对照)、0.10、0.25、0.50和1.00mmolL5azaC处理‘短叶13’萝卜种子6d,除对照外,茎尖组织DNA甲基化水平均有所降低,并与春化后茎尖组织DNA甲基化水平相当;茎尖组织DNA甲基化水平随着处理浓度的提高而下降。同时,5azaC处理明显促进春性品种萝卜‘短叶13’的开花。结果表明5azaC可以部分代替低温诱导萝卜开花。 展开更多
关键词 萝卜 5-azaC 花芽分化 开花 dna甲基化 茎尖 甲基化水平 萝卜种子 5-氮杂胞苷 去甲基化
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菜心茎尖DNA甲基化水平及GA、蛋白质含量的变化与花芽分化 被引量:14
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作者 李梅兰 曾广文 朱祝军 《浙江大学学报(农业与生命科学版)》 CAS CSCD 北大核心 2002年第2期161-164,共4页
研究了菜心花芽分化起始前后茎尖部位 DNA甲基化水平、赤霉素 (GA)含量和蛋白质 (Pr)含量的变化 .结果表明 :花芽分化前夕 ,即一级分化之前 DNA甲基化水平就开始下降 ,且随着花芽分化的进行进一步下降 ;GA含量在花芽将要分化时 ,稍有下... 研究了菜心花芽分化起始前后茎尖部位 DNA甲基化水平、赤霉素 (GA)含量和蛋白质 (Pr)含量的变化 .结果表明 :花芽分化前夕 ,即一级分化之前 DNA甲基化水平就开始下降 ,且随着花芽分化的进行进一步下降 ;GA含量在花芽将要分化时 ,稍有下降 ,但花芽开始分化后又有所回升 ; 展开更多
关键词 dna甲基化 赤霉素 蛋白质 花芽分化 菜心 茎尖 GA 含量 春性植物
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骨髓增生异常综合征患者血浆DNA中FHIT基因启动子区甲基化状态及地西他滨的去甲基化作用 被引量:11
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作者 邓银芬 张磊 +4 位作者 张秀群 胡明秋 戴丹 张学忠 徐燕丽 《中国实验血液学杂志》 CAS CSCD 北大核心 2012年第5期1144-1148,共5页
本研究旨在检测骨髓增生异常综合征(MDS)患者血浆DNA中FHIT基因启动子区域甲基化状况及地西他滨对其甲基化的影响。采用甲基化特异性聚合酶链反应法检测1例初治的MDS患者、3例MDS转化而来的AML患者在地西他滨序贯半量CAG方案化疗前后血... 本研究旨在检测骨髓增生异常综合征(MDS)患者血浆DNA中FHIT基因启动子区域甲基化状况及地西他滨对其甲基化的影响。采用甲基化特异性聚合酶链反应法检测1例初治的MDS患者、3例MDS转化而来的AML患者在地西他滨序贯半量CAG方案化疗前后血浆DNA中FHIT基因启动子区域CPG岛甲基化情况,并分析其临床疗效。结果表明,3例患者治疗前有FHIT基因甲基化。治疗1个疗程后其中2例患者FHIT基因甲基化得到逆转,4例患者中有2例获得临床缓解,2例无效。结论:MDS的发生可能与FHIT基因甲基化相关,地西他滨对MDS患者血浆DNA中FHIT基因高甲基化具有明显的去甲基化作用。血浆DNA的FHIT基因甲基化检测可能成为MDS辅助诊断和预后判断的分子标记。 展开更多
关键词 MDS FHIT基因 FHIT基因启动子区 dna甲基化 血浆
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参茸补血丸对去势大鼠生殖器官和DNA甲基化水平的影响 被引量:8
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作者 王蕾 胡元会 +5 位作者 王萍 何忠效 方素萍 陈玉英 吕新霞 吴志奎 《中国中医基础医学杂志》 CAS CSCD 2003年第10期48-50,共3页
目的 :为探讨参茸补血丸 (SRBXW )补肾填精 ,提高机体生命活力的分子机理 ,观察SRBXW对去势大鼠生殖器官及肝肾组织DNA甲基化水平的影响。方法 :建立摘除双侧卵巢的雌性大鼠模型 ,观察生殖器官的组织形态 ,采用3 H SAM法测定肝、肾组织D... 目的 :为探讨参茸补血丸 (SRBXW )补肾填精 ,提高机体生命活力的分子机理 ,观察SRBXW对去势大鼠生殖器官及肝肾组织DNA甲基化水平的影响。方法 :建立摘除双侧卵巢的雌性大鼠模型 ,观察生殖器官的组织形态 ,采用3 H SAM法测定肝、肾组织DNA 甲基化酶活力 ,HPLC法分析DNA甲基化水平 ,3 H UTP掺入检测RNA聚合酶活力。结果 :大鼠摘除卵巢后 ,雌激素分泌障碍 ,生殖器官萎缩 ,整体效应明显下降 ,肝、肾组织甲基化酶活力、甲基化水平升高 ,处于高甲基化 ,对应组织RNA聚合酶活力明显降低 ,处于低表达 ;雌二醇组大鼠由于补充外源性雌激素 ,生殖器官组织发育得到了代偿 ,肝、肾组织甲基化酶活力、甲基化水平趋于降低 ,RNA聚合酶活力上升 ;SRBXW大、小剂量组大鼠子宫和阴道组织结构与模型组对比有明显改善 ,肝肾组织甲基化酶活力、甲基化水平呈规律性低下 ,呈剂量依赖性 ,RNA聚合酶活力明显提高。结论 :参茸补血丸能促进去势大鼠生殖器官的发育 ,明显降低肝、肾组织DNA甲基化酶活力 ,DNA甲基化水平 ,提高对应组织中RNA聚合酶活力 ,能使受损机体肝、肾组织低甲基化 ,高表达以代偿因切除卵巢带来整体效应低下。 展开更多
关键词 参茸补血丸 去势大鼠 生殖器官 dna甲基化 HPLC 分子机理
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