目的描绘弥漫型胃癌组织中组蛋白H3第27位赖氨酸的三甲基化(H3K27me3)修饰的全基因组分布图谱,通过鉴定H3K27me3所调控的关键靶基因,初步探究H3K27me3修饰重编程可能调控弥漫型胃癌细胞发生发展的作用机制。方法样本来源于2021-2023年...目的描绘弥漫型胃癌组织中组蛋白H3第27位赖氨酸的三甲基化(H3K27me3)修饰的全基因组分布图谱,通过鉴定H3K27me3所调控的关键靶基因,初步探究H3K27me3修饰重编程可能调控弥漫型胃癌细胞发生发展的作用机制。方法样本来源于2021-2023年在陆军特色医学中心消化内科内镜中心及手术室胃肠外科组接受检查或治疗的患者。共收集到正常组患者14例,其中男性6例,女性8例,平均年龄46岁;胃癌组患者14例,其中男性8例,女性6例,平均年龄63岁。采用染色质靶向剪切及转座酶技术(cleavage under target and tagmentation,CUT&Tag)捕获基因组H3K27me3修饰区域,分析H3K27me3修饰重编程特征。整合转录组(RNA‐Seq)测序数据、高通量染色体构象捕获技术(high‐throughput chromosome conformation capture,Hi‐C)及已发表的公共单细胞数据,分析H3K27me3修饰重编程在弥漫型胃癌细胞中所调控靶基因。结果CUT&Tag和RNA测序数据质量符合下游分析标准,正常胃黏膜组织和弥漫型胃癌组织的组蛋白H3K27me3修饰均主要分布于远端基因间区和内含子区。相较于正常组织,胃癌组织的H3K27me3修饰存在显著的重编程特征,表现为H3K27me3总体信号强度明显降低。其中缺失的2912个H3K27me3信号峰可能导致822个肿瘤相关基因的表达上调,这些基因中上调最显著(信号值强度的差异倍数≥2,P<0.05)的56个基因主要富集于哺乳动物雷帕霉素靶蛋白复合体1(mammalian target of rapamycin complex 1,mTORC1)信号通路,其中甲硫氨酸转运体SLC7A5和胱氨酸转运体SLC7A11在胃癌组织中的表达最高。单细胞数据提示,弥漫型胃癌组织中SLC7A11的异常高表达主要存在于肿瘤上皮细胞。利用公共数据和免疫组织化学实验进一步验证SLC7A11在弥漫型胃癌中高表达,且与胃癌患者的不良预后相关。结论组蛋白H3K27me3修饰重编程是弥漫型胃癌的重要表观遗传学特征;组蛋白H3K27me3修饰缺失可能上调肿瘤细胞SLC7A11表达,进而促进肿瘤进展。展开更多
The leaf is a major organ for photosynthesis,and its shape plays an important role in plant development and yield determination in rice(Oryza sativa L.).In this study,an adaxial curled leaf mutant,termed curly leaf 1-...The leaf is a major organ for photosynthesis,and its shape plays an important role in plant development and yield determination in rice(Oryza sativa L.).In this study,an adaxial curled leaf mutant,termed curly leaf 1-1(cul1-1),was obtained by chemical mutagenesis.The leaf rolling index of the cul1-1 mutant was higher than that of the wild-type,which was caused by the abnormal development of bulliform cells(BCs).We cloned the CUL1 gene by map-based cloning.A nonsense mutation was present in the cul1-1 mutant,converting a tryptophan codon into a stop codon.The CUL1 gene encodes a chromodomain,helicase/ATPase and DNA-binding domain containing protein.Genes related to leaf rolling and BC development,such as ADL1,REL1 and ROC5,were activated by the cul1-1 mutation.The trimethylation of lysine 27 in histone 3(H3K27me3),but not H3K4me3,at the ADL1,REL1 and ROC5 loci,was reduced in the cul1-1 mutant.High-throughput mRNA sequencing indicated that the cul1-1 mutation caused genome-wide differential gene expression.The differentially expressed genes were classified into a few gene ontology terms and Kyoto encyclopedia of genes and genomes pathways.In the natural population,22 missense genomic variations in the CUL1 locus were identified,which composed of 7 haplotypes.A haplotype network was also built with haplotype II as the ancestor.The findings revealed that CUL1 is essential for normal leaf development and regulates this process by inhibiting the expression of genes involved in leaf rolling and BC development.展开更多
目的通过表观遗传组学技术,解析胃印戒细胞癌(signet-ring cell carcinoma of the stomach,SRCC)的H3K27me3沉默子的全基因组特征及其对基因转录的调控作用,以阐明SRCC恶性进展的表观调控机制。方法采集2021年1月至2023年12月陆军特色...目的通过表观遗传组学技术,解析胃印戒细胞癌(signet-ring cell carcinoma of the stomach,SRCC)的H3K27me3沉默子的全基因组特征及其对基因转录的调控作用,以阐明SRCC恶性进展的表观调控机制。方法采集2021年1月至2023年12月陆军特色医学中心消化内科35例胃镜样本(正常胃窦/胃体15例,SRCC 20例)。采用以下多组学分析:染色质可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)检测染色质开放区域;染色质靶向捕获测序(cleavage under targets and tagmentation,CUT&Tag)捕获H3K27me3沉默子区域;转录组测序(transcriptome sequencing,RNA-seq)分析转录组。测序于Illumina NovaSeq 6000平台完成(符合深度标准)。通过DESeq2筛选H3K27me3相关差异基因(|Log_(2)FC|>1,FDR<0.05),并通过基因本体论(Gene Oncology,GO)和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)分析进行功能富集,Homer鉴定转录因子基序,Cytoscape构建调控网络,并使用免疫组化进行验证,探讨其调控机制。结果SRCC沉默子主要分布于基因组远端基因间区(占37.06%)。与正常组织相比,SRCC中H3K27me3沉默子信号显著降低(95%CI:1.34~2.30,P=0.007),共鉴定出6257个丢失位点(FDR<0.01)。CUT&Tag和RNA-seq整合分析显示,380个因沉默子丢失而上调的基因显著富集于免疫相关通路,如T细胞受体信号通路(OR=4.2,95%CI:2.8~6.3,P=0.002)。免疫组化验证表明,转录因子EHF表达显著升高(P<0.05)。结论SRCC中存在H3K27me3沉默子重塑现象,转录因子EHF可能在SRCC恶性进展中发挥关键作用。展开更多
As the“fourth messenger”of epigenetic regulation,metabolites playa spatiotemporally specific regulatory role in kidney regeneration by dynamically reshaping the state of chromatin modifications.This review systemati...As the“fourth messenger”of epigenetic regulation,metabolites playa spatiotemporally specific regulatory role in kidney regeneration by dynamically reshaping the state of chromatin modifications.This review systematically expounds the coordinated mechanism of the dual axes of succinate/H3K9ac andα-ketoglutarate(α-KG)/TET enzymes:Succinate activates regeneration-related genes by regulating histone acetylation(H3K9ac),whileα-KG relieves the epigenetic repression of the Wnt pathway through TET-mediated DNA demethylation.The dynamic balance between the two maintains epigenetic plasticity.Multi-omics integration strategies(such as Gaussian graphical models and deep learning frameworks)and single-cell epigenetic tracking technologies(such as spatial metabolomics)have revealed the regulation of metabolite gradients on cellular heterogeneity and the immune microenvironment.The coordinated application of metabolite precursor supplementation(such as NAD precursors)and dynamic monitoring systems(such as isotope tracing and artifi cial intelligence models)has promoted the shift of metabolic medicine from the“static replacement”paradigm to the“dynamic reshaping”paradigm.However,technical bottlenecks(such as insuffi cient multimodal integration)and clinical translation pitfalls(such as challenges in standardized production)still need to be overcome.In the future,through the development of“metabolism-immunity”co-regulatory strategies and intelligent closed-loop systems,it is expected to achieve precise interventions for kidney regeneration and disease treatment.展开更多
卵母细胞成熟过程受组蛋白H3K4me3(trimethylation of lysine 4 on histone 3)和H3K27me3(trimethylation of lysine 27 on histone 3)及其相关的甲基化和去甲基化酶的调控,因此考虑对鸡的卵泡发育也存在一定的影响。选取“苏禽3号”配...卵母细胞成熟过程受组蛋白H3K4me3(trimethylation of lysine 4 on histone 3)和H3K27me3(trimethylation of lysine 27 on histone 3)及其相关的甲基化和去甲基化酶的调控,因此考虑对鸡的卵泡发育也存在一定的影响。选取“苏禽3号”配套系第一母本为研究对象,采用Western blot法探究组蛋白H3K4me3和H3K27me3在鸡卵泡不同发育阶段颗粒层中蛋白的表达模式。结果表明:在苏禽3号卵泡颗粒层中,组蛋白H3K4me3在卵泡发育不同阶段表达模式呈降低→升高→降低→升高的波浪形趋势,波浪变化较为平缓,在F5、F2和F13个表达高点的表达量与SWF(small white follicle)、LWF(large white follicle)、SYF(small yellow follicle)和F34个表达低点的表达差异显著(P<0.05)。组蛋白H3K27me3在不同发育阶段表达模式亦呈波浪形表达趋势,波浪变化起伏较明显,在SWF、SYF和F33个表达高点的表达量与F5、F4、F1和F24个表达低点的表达差异显著(P<0.05)。相关性分析显示,组蛋白H3K4me3与H3K27me3在不同发育阶段卵泡颗粒细胞中的表达呈较强的负线性相关(R=-0.808,P=0.000)。结果提示:组蛋白H3K4me3和H3K27me3在不同发育阶段卵泡颗粒层中的表达具有组织差异性,呈负相关的动态修饰性,可能共同协调卵泡生长过程中各基因的表达与功能,研究结果为鸡繁殖性状调控机理提供了理论依据。展开更多
文摘目的描绘弥漫型胃癌组织中组蛋白H3第27位赖氨酸的三甲基化(H3K27me3)修饰的全基因组分布图谱,通过鉴定H3K27me3所调控的关键靶基因,初步探究H3K27me3修饰重编程可能调控弥漫型胃癌细胞发生发展的作用机制。方法样本来源于2021-2023年在陆军特色医学中心消化内科内镜中心及手术室胃肠外科组接受检查或治疗的患者。共收集到正常组患者14例,其中男性6例,女性8例,平均年龄46岁;胃癌组患者14例,其中男性8例,女性6例,平均年龄63岁。采用染色质靶向剪切及转座酶技术(cleavage under target and tagmentation,CUT&Tag)捕获基因组H3K27me3修饰区域,分析H3K27me3修饰重编程特征。整合转录组(RNA‐Seq)测序数据、高通量染色体构象捕获技术(high‐throughput chromosome conformation capture,Hi‐C)及已发表的公共单细胞数据,分析H3K27me3修饰重编程在弥漫型胃癌细胞中所调控靶基因。结果CUT&Tag和RNA测序数据质量符合下游分析标准,正常胃黏膜组织和弥漫型胃癌组织的组蛋白H3K27me3修饰均主要分布于远端基因间区和内含子区。相较于正常组织,胃癌组织的H3K27me3修饰存在显著的重编程特征,表现为H3K27me3总体信号强度明显降低。其中缺失的2912个H3K27me3信号峰可能导致822个肿瘤相关基因的表达上调,这些基因中上调最显著(信号值强度的差异倍数≥2,P<0.05)的56个基因主要富集于哺乳动物雷帕霉素靶蛋白复合体1(mammalian target of rapamycin complex 1,mTORC1)信号通路,其中甲硫氨酸转运体SLC7A5和胱氨酸转运体SLC7A11在胃癌组织中的表达最高。单细胞数据提示,弥漫型胃癌组织中SLC7A11的异常高表达主要存在于肿瘤上皮细胞。利用公共数据和免疫组织化学实验进一步验证SLC7A11在弥漫型胃癌中高表达,且与胃癌患者的不良预后相关。结论组蛋白H3K27me3修饰重编程是弥漫型胃癌的重要表观遗传学特征;组蛋白H3K27me3修饰缺失可能上调肿瘤细胞SLC7A11表达,进而促进肿瘤进展。
基金supported by the National Natural Science Foundation of China(32070642 and 31371222 to Dr.Xiaoxue Wang)the National Key Research and Development Program from the Ministry of Science and Technology of China(2016YFD0100406 and 2017YFD0300107 to Dr.Xiaoxue Wang)the Science and Technology Department of Liaoning province(2022JH6/100100039 to Dr.Xiaoxue Wang)。
文摘The leaf is a major organ for photosynthesis,and its shape plays an important role in plant development and yield determination in rice(Oryza sativa L.).In this study,an adaxial curled leaf mutant,termed curly leaf 1-1(cul1-1),was obtained by chemical mutagenesis.The leaf rolling index of the cul1-1 mutant was higher than that of the wild-type,which was caused by the abnormal development of bulliform cells(BCs).We cloned the CUL1 gene by map-based cloning.A nonsense mutation was present in the cul1-1 mutant,converting a tryptophan codon into a stop codon.The CUL1 gene encodes a chromodomain,helicase/ATPase and DNA-binding domain containing protein.Genes related to leaf rolling and BC development,such as ADL1,REL1 and ROC5,were activated by the cul1-1 mutation.The trimethylation of lysine 27 in histone 3(H3K27me3),but not H3K4me3,at the ADL1,REL1 and ROC5 loci,was reduced in the cul1-1 mutant.High-throughput mRNA sequencing indicated that the cul1-1 mutation caused genome-wide differential gene expression.The differentially expressed genes were classified into a few gene ontology terms and Kyoto encyclopedia of genes and genomes pathways.In the natural population,22 missense genomic variations in the CUL1 locus were identified,which composed of 7 haplotypes.A haplotype network was also built with haplotype II as the ancestor.The findings revealed that CUL1 is essential for normal leaf development and regulates this process by inhibiting the expression of genes involved in leaf rolling and BC development.
文摘目的通过表观遗传组学技术,解析胃印戒细胞癌(signet-ring cell carcinoma of the stomach,SRCC)的H3K27me3沉默子的全基因组特征及其对基因转录的调控作用,以阐明SRCC恶性进展的表观调控机制。方法采集2021年1月至2023年12月陆军特色医学中心消化内科35例胃镜样本(正常胃窦/胃体15例,SRCC 20例)。采用以下多组学分析:染色质可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)检测染色质开放区域;染色质靶向捕获测序(cleavage under targets and tagmentation,CUT&Tag)捕获H3K27me3沉默子区域;转录组测序(transcriptome sequencing,RNA-seq)分析转录组。测序于Illumina NovaSeq 6000平台完成(符合深度标准)。通过DESeq2筛选H3K27me3相关差异基因(|Log_(2)FC|>1,FDR<0.05),并通过基因本体论(Gene Oncology,GO)和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)分析进行功能富集,Homer鉴定转录因子基序,Cytoscape构建调控网络,并使用免疫组化进行验证,探讨其调控机制。结果SRCC沉默子主要分布于基因组远端基因间区(占37.06%)。与正常组织相比,SRCC中H3K27me3沉默子信号显著降低(95%CI:1.34~2.30,P=0.007),共鉴定出6257个丢失位点(FDR<0.01)。CUT&Tag和RNA-seq整合分析显示,380个因沉默子丢失而上调的基因显著富集于免疫相关通路,如T细胞受体信号通路(OR=4.2,95%CI:2.8~6.3,P=0.002)。免疫组化验证表明,转录因子EHF表达显著升高(P<0.05)。结论SRCC中存在H3K27me3沉默子重塑现象,转录因子EHF可能在SRCC恶性进展中发挥关键作用。
基金funded by Medical Science Research Project of Hebei(No.20220364).
文摘As the“fourth messenger”of epigenetic regulation,metabolites playa spatiotemporally specific regulatory role in kidney regeneration by dynamically reshaping the state of chromatin modifications.This review systematically expounds the coordinated mechanism of the dual axes of succinate/H3K9ac andα-ketoglutarate(α-KG)/TET enzymes:Succinate activates regeneration-related genes by regulating histone acetylation(H3K9ac),whileα-KG relieves the epigenetic repression of the Wnt pathway through TET-mediated DNA demethylation.The dynamic balance between the two maintains epigenetic plasticity.Multi-omics integration strategies(such as Gaussian graphical models and deep learning frameworks)and single-cell epigenetic tracking technologies(such as spatial metabolomics)have revealed the regulation of metabolite gradients on cellular heterogeneity and the immune microenvironment.The coordinated application of metabolite precursor supplementation(such as NAD precursors)and dynamic monitoring systems(such as isotope tracing and artifi cial intelligence models)has promoted the shift of metabolic medicine from the“static replacement”paradigm to the“dynamic reshaping”paradigm.However,technical bottlenecks(such as insuffi cient multimodal integration)and clinical translation pitfalls(such as challenges in standardized production)still need to be overcome.In the future,through the development of“metabolism-immunity”co-regulatory strategies and intelligent closed-loop systems,it is expected to achieve precise interventions for kidney regeneration and disease treatment.
文摘卵母细胞成熟过程受组蛋白H3K4me3(trimethylation of lysine 4 on histone 3)和H3K27me3(trimethylation of lysine 27 on histone 3)及其相关的甲基化和去甲基化酶的调控,因此考虑对鸡的卵泡发育也存在一定的影响。选取“苏禽3号”配套系第一母本为研究对象,采用Western blot法探究组蛋白H3K4me3和H3K27me3在鸡卵泡不同发育阶段颗粒层中蛋白的表达模式。结果表明:在苏禽3号卵泡颗粒层中,组蛋白H3K4me3在卵泡发育不同阶段表达模式呈降低→升高→降低→升高的波浪形趋势,波浪变化较为平缓,在F5、F2和F13个表达高点的表达量与SWF(small white follicle)、LWF(large white follicle)、SYF(small yellow follicle)和F34个表达低点的表达差异显著(P<0.05)。组蛋白H3K27me3在不同发育阶段表达模式亦呈波浪形表达趋势,波浪变化起伏较明显,在SWF、SYF和F33个表达高点的表达量与F5、F4、F1和F24个表达低点的表达差异显著(P<0.05)。相关性分析显示,组蛋白H3K4me3与H3K27me3在不同发育阶段卵泡颗粒细胞中的表达呈较强的负线性相关(R=-0.808,P=0.000)。结果提示:组蛋白H3K4me3和H3K27me3在不同发育阶段卵泡颗粒层中的表达具有组织差异性,呈负相关的动态修饰性,可能共同协调卵泡生长过程中各基因的表达与功能,研究结果为鸡繁殖性状调控机理提供了理论依据。
