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
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
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
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
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
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
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
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
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
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
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
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
基金supported by the Project of the Seed Industry Revitalization of Department of Agriculture and Rural Affairs of Guangdong Province(2022-XPY-05-001)the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program(2019BT02N630).
文摘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.
基金supported by the Yunnan Government(2009CI119)Modern Agricultural Industry Technology System(Honeybee)(CARS-45-kxj14)
文摘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.
基金Supported by Beijing Natural Science Foundation,No.7182182the Young Elite Scientist Sponsorship Program by Cast,No.YESS20170089+1 种基金the National Natural Science Foundation of China,No.81600865 and No.81970940the National Science and Technology Major Project of the Ministry of Science and Technology of China,No.2018ZX10302207。
文摘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.
文摘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.
基金973 project,National Natural Science Foundation of China,Transgenic Research Project
文摘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.
基金partially supported by the United States Department of Agriculture National Institute of Food and Agriculture Hatch Grant (Project No.OHO01304)。
文摘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.
文摘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 )
基金supported by the National Natural Science Foundation(Nos.81471958 and 31401258)the Natural Science Foundation of Shandong Province(No.ZR2012BM006),China
文摘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.
基金This work was supported by the National Key Research and Development Program of China(No.2016YFC0905103)the Chinese Academy of Medical Sciences(CAMS)Innovation Fund for Medical Sciences(CIFMS)(No.2016-I2M-1-004)the Strategic Priority Research Program of the Chinese Academy of Sciences(Nos.XDB39000000,XDB39040100).
文摘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.
基金supported by the National Natural Science Foundation of China(No.61872063)and Shenzhen Science and Technology Program(No.JCYJ20210324140407021).
文摘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.
基金National Key Research and Development Program of China,No.2016YFA0100800(to LC)International(Regional)Cooperation and Communication Program of the National Natural Science Foundation of China,No.81820108013(to LC)+3 种基金State Key Program of the National Natural Science Foundation of China,No.81330030(to LC)National Natural Science Foundation of China,Nos.82071370(to ZW),81301042(to LC)Shanghai Pujiang Program,No.19PJ1409200(to ZW)Shanghai Sailing Program,No.21YF1442400(to CL)。
文摘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.
文摘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.