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
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
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
目的:探讨DNA结合抑制因子4(inhibitor of DNA binding 4,ID4)基因核心启动子区甲基化及其蛋白表达与儿童急性白血病(acute leukemia,AL)的关系。方法:采用甲基化特异性聚合酶链反应(methylation-specific polymerase chain reaction,MS...目的:探讨DNA结合抑制因子4(inhibitor of DNA binding 4,ID4)基因核心启动子区甲基化及其蛋白表达与儿童急性白血病(acute leukemia,AL)的关系。方法:采用甲基化特异性聚合酶链反应(methylation-specific polymerase chain reaction,MS-PCR)对32例初发白血病患儿、34例同期非肿瘤疾病儿童(对照组)及白血病细胞株Jurkat和Molt4进行ID4基因启动子区甲基化状况分析,并进行测序。RT-PCR检测ID4 mRNA的表达,免疫组织化学法检测ID4蛋白的表达。结果:ID4基因启动子区在Jurkat和Molt4细胞中均呈完全甲基化状态,而初发急性淋巴细胞及非淋巴细胞白血病患儿中完全甲基化率显著高于对照组患儿(81.0%vs17.6%,P<0.001;63.6%vs17.6%,P<0.005)。测序分析显示在完全甲基化状态的ID4基因核心启动子区所有CpG岛均呈甲基化状态。呈完全甲基化状态的白血病患儿和Jurkat、Molt4细胞中均无ID4 mRNA表达,而白血病组ID4蛋白表达显著低于对照组(P<0.001)。结论:儿童白血病及某些白血病细胞株存在ID4基因核心启动子区高程度的甲基化。完全的甲基化状态可使ID4基因表达沉默,ID4蛋白表达缺失。展开更多
鸡繁殖性能近交衰退是地方鸡遗传资源活体保种过程中面临的重要问题之一,本研究旨在探讨全基因组CpG岛(CpG island, CGI)区DNA甲基化在鸡繁殖性能近交衰退中的作用。分别从狼山鸡高近交组和低近交组中各选取健康母鸡3只,即试验分2个组,...鸡繁殖性能近交衰退是地方鸡遗传资源活体保种过程中面临的重要问题之一,本研究旨在探讨全基因组CpG岛(CpG island, CGI)区DNA甲基化在鸡繁殖性能近交衰退中的作用。分别从狼山鸡高近交组和低近交组中各选取健康母鸡3只,即试验分2个组,每组3个重复,然后采用全基因组重亚硫酸盐测序(WGBS)技术,检测分析两组个体性腺轴组织(包括卵巢和下丘脑)全基因组DNA甲基化差异,筛选差异甲基化区域(DMRs),并对CpG岛区差异甲基化基因进行功能注释和富集分析。结果表明,狼山鸡高近交组和低近交组比较,其卵巢和下丘脑基因组整体甲基化水平均不存在显著差异(P>0.05);高、低近交组间差异甲基化区域检测发现,下丘脑和卵巢中分别检测到5 948和4 593个差异甲基化区域,其中1 798和995个差异甲基化区域位于基因组CpG岛区,分别注释到1 020和552个基因;下丘脑中,这些CpG岛区差异甲基化基因显著富集在信号转导、神经系统发育、生殖系统发育和卵母细胞成熟调控等繁殖相关的GO条目,以及转化生长因子β信号通路、乙型肝炎、脂肪酸代谢、胰岛素信号通路等19条KEGG信号通路(P<0.05);卵巢中,CpG岛区差异甲基化基因显著富集于12条信号通路(P<0.05),包括慢性骨髓白血病、流感A、精氨酸和脯氨酸代谢、粘着连接等,一些与卵子发育和性激素分泌相关的信号通路也被富集到,如黄体酮介导的卵母细胞成熟、卵母细胞减数分裂、GnRH信号通路、雌激素信号通路等,其中包含CDC27、ADCY8、AKT3等10个差异甲基化基因。因此,本研究在狼山鸡高、低近交组间检测到了大量差异甲基化区域,并发现大量差异甲基化基因与繁殖性状相关,推测这些基因CpG岛区DNA甲基化可能在狼山鸡繁殖性能近交衰退调控中发挥重要作用,研究结果为进一步深入探索鸡繁殖性能近交衰退调控机制奠定了基础,为物种资源保护和家禽育种工作提供了理论参考依据。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: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
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.
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.
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.
