David E Torres, Andrew T Reckard, Andrew D Klocko, Michael F Seidl
{"title":"真菌的核基因组组织:从基因折叠到 Rabl 染色体。","authors":"David E Torres, Andrew T Reckard, Andrew D Klocko, Michael F Seidl","doi":"10.1093/femsre/fuad021","DOIUrl":null,"url":null,"abstract":"<p><p>Comparative genomics has recently provided unprecedented insights into the biology and evolution of the fungal lineage. In the postgenomics era, a major research interest focuses now on detailing the functions of fungal genomes, i.e. how genomic information manifests into complex phenotypes. Emerging evidence across diverse eukaryotes has revealed that the organization of DNA within the nucleus is critically important. Here, we discuss the current knowledge on the fungal genome organization, from the association of chromosomes within the nucleus to topological structures at individual genes and the genetic factors required for this hierarchical organization. Chromosome conformation capture followed by high-throughput sequencing (Hi-C) has elucidated how fungal genomes are globally organized in Rabl configuration, in which centromere or telomere bundles are associated with opposite faces of the nuclear envelope. Further, fungal genomes are regionally organized into topologically associated domain-like (TAD-like) chromatin structures. We discuss how chromatin organization impacts the proper function of DNA-templated processes across the fungal genome. Nevertheless, this view is limited to a few fungal taxa given the paucity of fungal Hi-C experiments. We advocate for exploring genome organization across diverse fungal lineages to ensure the future understanding of the impact of nuclear organization on fungal genome function.</p>","PeriodicalId":12201,"journal":{"name":"FEMS microbiology reviews","volume":"47 3","pages":""},"PeriodicalIF":10.1000,"publicationDate":"2023-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246852/pdf/","citationCount":"0","resultStr":"{\"title\":\"Nuclear genome organization in fungi: from gene folding to Rabl chromosomes.\",\"authors\":\"David E Torres, Andrew T Reckard, Andrew D Klocko, Michael F Seidl\",\"doi\":\"10.1093/femsre/fuad021\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Comparative genomics has recently provided unprecedented insights into the biology and evolution of the fungal lineage. In the postgenomics era, a major research interest focuses now on detailing the functions of fungal genomes, i.e. how genomic information manifests into complex phenotypes. Emerging evidence across diverse eukaryotes has revealed that the organization of DNA within the nucleus is critically important. Here, we discuss the current knowledge on the fungal genome organization, from the association of chromosomes within the nucleus to topological structures at individual genes and the genetic factors required for this hierarchical organization. Chromosome conformation capture followed by high-throughput sequencing (Hi-C) has elucidated how fungal genomes are globally organized in Rabl configuration, in which centromere or telomere bundles are associated with opposite faces of the nuclear envelope. Further, fungal genomes are regionally organized into topologically associated domain-like (TAD-like) chromatin structures. We discuss how chromatin organization impacts the proper function of DNA-templated processes across the fungal genome. Nevertheless, this view is limited to a few fungal taxa given the paucity of fungal Hi-C experiments. We advocate for exploring genome organization across diverse fungal lineages to ensure the future understanding of the impact of nuclear organization on fungal genome function.</p>\",\"PeriodicalId\":12201,\"journal\":{\"name\":\"FEMS microbiology reviews\",\"volume\":\"47 3\",\"pages\":\"\"},\"PeriodicalIF\":10.1000,\"publicationDate\":\"2023-05-19\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10246852/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"FEMS microbiology reviews\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/femsre/fuad021\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"FEMS microbiology reviews","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/femsre/fuad021","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
比较基因组学最近为真菌的生物学和进化提供了前所未有的洞察力。在后基因组学时代,主要的研究兴趣集中在详细研究真菌基因组的功能,即基因组信息如何表现为复杂的表型。各种真核生物的新证据表明,DNA在细胞核内的组织结构至关重要。在这里,我们将讨论目前关于真菌基因组组织的知识,从细胞核内染色体的关联到单个基因的拓扑结构,以及这种分级组织所需的遗传因素。染色体构象捕获和高通量测序(Hi-C)阐明了真菌基因组如何以 Rabl 构型进行全局组织,其中中心粒或端粒束与核膜的相对面相关联。此外,真菌基因组在区域上被组织成拓扑相关域样(TAD-like)染色质结构。我们讨论了染色质组织如何影响整个真菌基因组中 DNA 模板过程的正常功能。然而,由于真菌 Hi-C 实验很少,这一观点仅限于少数真菌类群。我们主张探索不同真菌品系的基因组组织,以确保未来能了解核组织对真菌基因组功能的影响。
Nuclear genome organization in fungi: from gene folding to Rabl chromosomes.
Comparative genomics has recently provided unprecedented insights into the biology and evolution of the fungal lineage. In the postgenomics era, a major research interest focuses now on detailing the functions of fungal genomes, i.e. how genomic information manifests into complex phenotypes. Emerging evidence across diverse eukaryotes has revealed that the organization of DNA within the nucleus is critically important. Here, we discuss the current knowledge on the fungal genome organization, from the association of chromosomes within the nucleus to topological structures at individual genes and the genetic factors required for this hierarchical organization. Chromosome conformation capture followed by high-throughput sequencing (Hi-C) has elucidated how fungal genomes are globally organized in Rabl configuration, in which centromere or telomere bundles are associated with opposite faces of the nuclear envelope. Further, fungal genomes are regionally organized into topologically associated domain-like (TAD-like) chromatin structures. We discuss how chromatin organization impacts the proper function of DNA-templated processes across the fungal genome. Nevertheless, this view is limited to a few fungal taxa given the paucity of fungal Hi-C experiments. We advocate for exploring genome organization across diverse fungal lineages to ensure the future understanding of the impact of nuclear organization on fungal genome function.
期刊介绍:
Title: FEMS Microbiology Reviews
Journal Focus:
Publishes reviews covering all aspects of microbiology not recently surveyed
Reviews topics of current interest
Provides comprehensive, critical, and authoritative coverage
Offers new perspectives and critical, detailed discussions of significant trends
May contain speculative and selective elements
Aimed at both specialists and general readers
Reviews should be framed within the context of general microbiology and biology
Submission Criteria:
Manuscripts should not be unevaluated compilations of literature
Lectures delivered at symposia must review the related field to be acceptable