目的·研究Apc^(min/+)小鼠自发结肠肿瘤的空间表观遗传特征。方法·使用8月龄雄性Apc^(min/+)小鼠自发结肠肿瘤模型,搭建空间染色质可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,A...目的·研究Apc^(min/+)小鼠自发结肠肿瘤的空间表观遗传特征。方法·使用8月龄雄性Apc^(min/+)小鼠自发结肠肿瘤模型,搭建空间染色质可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)技术平台。摘取一颗小鼠结肠肿瘤,经冷冻包埋后,进行连续切片;一张组织切片使用苏木精-伊红染色观察其组织学特征,另一张相邻的组织切片进行空间ATAC-seq技术处理,得到带有空间位置信息的DNA文库后进行测序,得到该小鼠结肠肿瘤的空间染色质可及性数据。取同一只小鼠的另一颗肿瘤组织,经消化后得到细胞悬液,通过流式细胞术分选有活性的单细胞悬液,进行单细胞转录组测序,与空间染色质可及性数据联合分析此小鼠的结肠肿瘤微环境表观遗传学特征。结果·成功搭建稳定的空间ATAC-seq技术体系,并据此将小鼠的肿瘤分为恶性区域、非恶性区域以及恶性-非恶性边界区域;恶性区域富集到的转录因子包括NK2同源框转录因子5(NK2 homeobox 5,NKX2-5)、转录因子3(transcription factor 3,TCF3)等。在3个区域分别对转录因子进行富集,得到2种不同的表达趋势:一种为表达水平自恶性‒边界‒非恶性区域逐步降低;另一种为在恶性和边界区域表达水平高,在非恶性区域表达水平低。对不同区域的基因分析显示恶性区域的缺氧反应明显上调,转化生长因子(transforming growth factor,TGF)、Kirsten大鼠肉瘤病毒癌基因同源物(Kirsten rat sarcoma viral oncogene homolog,KRAS)信号通路显著上调,与细胞周期相关的功能明显增强。对肿瘤微环境中细胞间的相互作用分析发现不同区域的细胞互作强度具有显著差别,非恶性区域内部细胞的相互作用强,边界区与非恶性区以及恶性与非恶性区域的相互作用中等,恶性区与边界区的相互作用弱。结论·Apc^(min/+)小鼠结肠肿瘤呈高度空间异质性;肿瘤恶性区域富集了Tcf3等多种转录因子,恶性区域与边界、非恶性区域之间细胞相互作用相对较弱。展开更多
Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economic...Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in China.In the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents.Analysis identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between them.Notably,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen content.These loci corresponded to 241 genes,63 of which were categorized as both DEGs and DCAGs.This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C.ariakensis.展开更多
染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)是利用Tn5转座酶研究染色质可及性的高通量测序技术。ATAC-seq可以在全基因组范围内绘制染色质可及性图谱,揭示转录因...染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)是利用Tn5转座酶研究染色质可及性的高通量测序技术。ATAC-seq可以在全基因组范围内绘制染色质可及性图谱,揭示转录因子结合位点以及核小体的位置。在医学领域,ATAC-seq技术是研究重大疾病发病机制、药物作用机制、新药研发和生物标志物功能等的新一代有力工具。本文对ATAC-seq技术的优势及其在复杂疾病研究中的应用和前景进行了综述,以期为人类复杂疾病基因表达调控机制等相关研究的开展提供借鉴与参考。展开更多
2025年7月8日,浙江大学医学院/良渚实验室郭国骥教授团队在《细胞》(Cell)上发表了题为“Modeling the vertebrate regulatory sequence landscape by UUATAC-seq and deep learning”的研究论文(DOI:10.1016/j.cell.2025.06.020)。该...2025年7月8日,浙江大学医学院/良渚实验室郭国骥教授团队在《细胞》(Cell)上发表了题为“Modeling the vertebrate regulatory sequence landscape by UUATAC-seq and deep learning”的研究论文(DOI:10.1016/j.cell.2025.06.020)。该研究建立了超高通量、超灵敏的单核ATAC测序技术(UUATAC-seq)。展开更多
Molybdenum cofactor(Moco)biosynthesis is linked to c-Jun N-terminal kinase(JNK)signaling in Drosophila through MoaE,a molybdopterin(MPT)synthase subunit that is also acomponent of theAdaTwoAcontaining(ATAC)acetyltrans...Molybdenum cofactor(Moco)biosynthesis is linked to c-Jun N-terminal kinase(JNK)signaling in Drosophila through MoaE,a molybdopterin(MPT)synthase subunit that is also acomponent of theAdaTwoAcontaining(ATAC)acetyltransferasecomplex.Here,weshow thathumanMPTsynthase and ATAC inhibited PKR,a double-stranded RNA-dependent protein kinase,to facilitate translation initiation of iron-responsive mRNA.MPT synthase and ATAC directly interacted with PKR and suppressed latent autophosphorylation of PKR and its downstream phosphorylation of JNK and eukaryotic initiation factor 2a(eIF2a).The suppression of eIF2a phosphorylation via MPT synthase and ATAC prevented sequestration of the guanine nucleotide exchange factor eIF2B,which recycles eIF2-GDP to eIF2-GTP,resulting in the promotion of translation initiation.Indeed,translation of the iron storage protein,ferritin,was reduced in the absence of MPT synthase or ATAC subunits.Thus,MPT synthase and ATAC regulate latent PKR signaling and link transcription and translation initiation.展开更多
在真核生物中,染色质作为遗传物质DNA的载体,直接参与基因的表达调控。染色质的可及性是指染色质中的DNA能与转录因子等蛋白复合物结合的区域,对染色质可及性的测定可为获取开放区域的信息、核小体定位信息以及转录因子结合信息提供基...在真核生物中,染色质作为遗传物质DNA的载体,直接参与基因的表达调控。染色质的可及性是指染色质中的DNA能与转录因子等蛋白复合物结合的区域,对染色质可及性的测定可为获取开放区域的信息、核小体定位信息以及转录因子结合信息提供基础依据。随着高通量测序技术的进步以及测序成本的降低,研究者已开发多种研究染色质可及性的测序方法,该文介绍4种常见的染色质可及性测序方法,对其中的染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)的原理和数据分析方法进行重点描述,讨论ATAC-seq的应用与发展趋势,为染色质可及性以及基因表达调控的研究提供参考。展开更多
基金supported by the National Key R&D Program of China(2022YFD2400105,2018YFD0900104)Central Publicinterest Scientific Institution Basal Research Fund,CAFS(2021XT0102,2023TD30)+2 种基金Marine S&T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology(Qingdao)(2021QNLM050103)Key Research and Development Project of Shandong Province(2021LZGC028)National Marine Genetic Resource Center。
文摘Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters.The Jinjiang oyster(Crassostrea ariakensis)is an economically and ecologically important species in China.In the present study,RNA sequencing(RNA-seq)and assay for transposase-accessible chromatin using sequencing(ATAC-seq)were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents.Analysis identified 9483 differentially expressed genes(DEGs)and 7215 genes with significantly differential chromatin accessibility(DCAGs)were obtained,with an overlap of 2600 genes between them.Notably,a significant proportion of these genes were enriched in pathways related to glycogen metabolism,including“Glycogen metabolic process”and“Starch and sucrose metabolism”.In addition,genome-wide association study(GWAS)identified 526 single nucleotide polymorphism(SNP)loci associated with glycogen content.These loci corresponded to 241 genes,63 of which were categorized as both DEGs and DCAGs.This study enriches basic research data and provides insights into the molecular mechanisms underlying the regulation of glycogen metabolism in C.ariakensis.
文摘染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)是利用Tn5转座酶研究染色质可及性的高通量测序技术。ATAC-seq可以在全基因组范围内绘制染色质可及性图谱,揭示转录因子结合位点以及核小体的位置。在医学领域,ATAC-seq技术是研究重大疾病发病机制、药物作用机制、新药研发和生物标志物功能等的新一代有力工具。本文对ATAC-seq技术的优势及其在复杂疾病研究中的应用和前景进行了综述,以期为人类复杂疾病基因表达调控机制等相关研究的开展提供借鉴与参考。
文摘2025年7月8日,浙江大学医学院/良渚实验室郭国骥教授团队在《细胞》(Cell)上发表了题为“Modeling the vertebrate regulatory sequence landscape by UUATAC-seq and deep learning”的研究论文(DOI:10.1016/j.cell.2025.06.020)。该研究建立了超高通量、超灵敏的单核ATAC测序技术(UUATAC-seq)。
基金supported by private funding fromthe Stowers Institute for Medical Research to the Workman laboratory.
文摘Molybdenum cofactor(Moco)biosynthesis is linked to c-Jun N-terminal kinase(JNK)signaling in Drosophila through MoaE,a molybdopterin(MPT)synthase subunit that is also acomponent of theAdaTwoAcontaining(ATAC)acetyltransferasecomplex.Here,weshow thathumanMPTsynthase and ATAC inhibited PKR,a double-stranded RNA-dependent protein kinase,to facilitate translation initiation of iron-responsive mRNA.MPT synthase and ATAC directly interacted with PKR and suppressed latent autophosphorylation of PKR and its downstream phosphorylation of JNK and eukaryotic initiation factor 2a(eIF2a).The suppression of eIF2a phosphorylation via MPT synthase and ATAC prevented sequestration of the guanine nucleotide exchange factor eIF2B,which recycles eIF2-GDP to eIF2-GTP,resulting in the promotion of translation initiation.Indeed,translation of the iron storage protein,ferritin,was reduced in the absence of MPT synthase or ATAC subunits.Thus,MPT synthase and ATAC regulate latent PKR signaling and link transcription and translation initiation.
文摘在真核生物中,染色质作为遗传物质DNA的载体,直接参与基因的表达调控。染色质的可及性是指染色质中的DNA能与转录因子等蛋白复合物结合的区域,对染色质可及性的测定可为获取开放区域的信息、核小体定位信息以及转录因子结合信息提供基础依据。随着高通量测序技术的进步以及测序成本的降低,研究者已开发多种研究染色质可及性的测序方法,该文介绍4种常见的染色质可及性测序方法,对其中的染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)的原理和数据分析方法进行重点描述,讨论ATAC-seq的应用与发展趋势,为染色质可及性以及基因表达调控的研究提供参考。
