1
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Gahan JM, Helfrich LW, Wetzel LA, Bhanu NV, Yuan ZF, Garcia BA, Klose R, Booth DS. Chromatin profiling identifies putative dual roles for H3K27me3 in regulating transposons and cell type-specific genes in choanoflagellates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.28.596151. [PMID: 38854040 PMCID: PMC11160669 DOI: 10.1101/2024.05.28.596151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Gene expression is tightly controlled during animal development to allow the formation of specialized cell types. Our understanding of how animals evolved this exquisite regulatory control remains elusive, but evidence suggests that changes in chromatin-based mechanisms may have contributed. To investigate this possibility, here we examine chromatin-based gene regulatory features in the closest relatives of animals, choanoflagellates. Using Salpingoeca rosetta as a model system, we examined chromatin accessibility and histone modifications at the genome scale and compared these features to gene expression. We first observed that accessible regions of chromatin are primarily associated with gene promoters and found no evidence of distal gene regulatory elements resembling the enhancers that animals deploy to regulate developmental gene expression. Remarkably, a histone modification deposited by polycomb repressive complex 2, histone H3 lysine 27 trimethylation (H3K27me3), appeared to function similarly in S. rosetta to its role in animals, because this modification decorated genes with cell type-specific expression. Additionally, H3K27me3 marked transposons, retaining what appears to be an ancestral role in regulating these elements. We further uncovered a putative new bivalent chromatin state at cell type-specific genes that consists of H3K27me3 and histone H3 lysine 4 mono-methylation (H3K4me1). Together, our discoveries support the scenario that gene-associated histone modification states that underpin development emerged before the evolution of animal multicellularity.
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Affiliation(s)
- James M. Gahan
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry, University of Oxford, Oxford, UK
- Present Address: Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway, Ireland
| | - Lily W. Helfrich
- Howard Hughes Medical Institute / University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720
- Present Address: Benchling
| | - Laura A. Wetzel
- Howard Hughes Medical Institute / University of California, Berkeley, Department of Molecular and Cell Biology, Berkeley, CA 94720
- Present Address: BioMarin Pharmaceutical Inc
| | - Natarajan V. Bhanu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Zuo-Fei Yuan
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Rob Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - David S. Booth
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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2
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Torres DE, Kramer HM, Tracanna V, Fiorin GL, Cook DE, Seidl MF, Thomma BPHJ. Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen. Nat Commun 2024; 15:1701. [PMID: 38402218 PMCID: PMC10894299 DOI: 10.1038/s41467-024-45884-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/05/2024] [Indexed: 02/26/2024] Open
Abstract
The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.
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Affiliation(s)
- David E Torres
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - H Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Vittorio Tracanna
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Gabriel L Fiorin
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - David E Cook
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Department of Plant Pathology, Kansas State University, 1712 Claflin Road, Manhattan, KS, USA
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands.
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany.
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3
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Kramer HM, Cook DE, Seidl MF, Thomma BP. Epigenetic regulation of nuclear processes in fungal plant pathogens. PLoS Pathog 2023; 19:e1011525. [PMID: 37535497 PMCID: PMC10399791 DOI: 10.1371/journal.ppat.1011525] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023] Open
Abstract
Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta-induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens.
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Affiliation(s)
- H. Martin Kramer
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
| | - David E. Cook
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Michael F. Seidl
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- Theoretical Biology & Bioinformatics, Department of Biology, Utrecht University, Utrecht, the Netherlands
| | - Bart P.H.J. Thomma
- Laboratory of Phytopathology, Wageningen University and Research, Wageningen, the Netherlands
- University of Cologne, Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
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4
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Torres DE, Reckard AT, Klocko AD, Seidl MF. Nuclear genome organization in fungi: from gene folding to Rabl chromosomes. FEMS Microbiol Rev 2023; 47:fuad021. [PMID: 37197899 PMCID: PMC10246852 DOI: 10.1093/femsre/fuad021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/28/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023] Open
Abstract
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.
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Affiliation(s)
- David E Torres
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Laboratory of Phytopathology, Wageningen University and Research,Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands
| | - Andrew T Reckard
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, 234 Centennial Hall, 1420 Austin Bluffs Pkwy, Colorado Springs, CO 80918 USA
| | - Andrew D Klocko
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, 234 Centennial Hall, 1420 Austin Bluffs Pkwy, Colorado Springs, CO 80918 USA
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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5
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Chen H, Fang Y, Song W, Shu H, Li X, Ye W, Wang Y, Dong S. The SET domain protein PsKMT3 regulates histone H3K36 trimethylation and modulates effector gene expression in the soybean pathogen Phytophthora sojae. MOLECULAR PLANT PATHOLOGY 2023; 24:346-358. [PMID: 36748674 PMCID: PMC10013772 DOI: 10.1111/mpp.13301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
Plant pathogens secrete effector proteins to overcome host immunity and promote colonization. In oomycete plant pathogens, the expression of many effector genes is altered upon infection; however, the regulatory mechanisms are unclear. In this study, we identified a su(var)3-9, enhancer of zeste, and trithorax (SET) domain protein-encoding gene, PsKMT3, that was highly induced at early infection stages in Phytophthora sojae. Deletion of PsKMT3 led to asexual development and pathogenicity defects. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) and western blot analyses demonstrated that histone H3K36 trimethylation (H3K36me3) was significantly reduced genome-wide in mutants. RNA-seq analysis identified 374 genes encoding secreted proteins that were differentially expressed in pskmt3 at the mycelium stage. The significantly altered genes encompassed the RxLR (Arg-x-Lys-Arg) effector gene family, including the essential effector genes Avh23, Avh181, Avh240, and Avh241. Transcriptome analysis at early infection stages showed misregulation of effector gene expression waves in pskmt3. H3K36me3 was directly and indirectly associated with RxLR effector gene activation. Our results reveal a role of a SET domain protein in regulating effector gene expression and modulating histone methylation in P. sojae.
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Affiliation(s)
- Han Chen
- Department of Plant Pathology, the Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Yujie Fang
- Department of Plant Pathology, the Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Wenrui Song
- Department of Plant Pathology, the Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Haidong Shu
- Department of Plant Pathology, the Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Xi Li
- Department of Plant Pathology, the Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Wenwu Ye
- Department of Plant Pathology, the Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Yuanchao Wang
- Department of Plant Pathology, the Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
| | - Suomeng Dong
- Department of Plant Pathology, the Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, the Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjingChina
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6
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Heterochromatin and RNAi act independently to ensure genome stability in Mucorales human fungal pathogens. Proc Natl Acad Sci U S A 2023; 120:e2220475120. [PMID: 36745785 PMCID: PMC9963178 DOI: 10.1073/pnas.2220475120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Chromatin modifications play a fundamental role in controlling transcription and genome stability and yet despite their importance, are poorly understood in early-diverging fungi. We present a comprehensive study of histone lysine and DNA methyltransferases across the Mucoromycota, emphasizing heterochromatin formation pathways that rely on the Clr4 complex involved in H3K9-methylation, the Polycomb-repressive complex 2 driving H3K27-methylation, or DNMT1-like methyltransferases that catalyze 5mC DNA methylation. Our analysis uncovered H3K9-methylated heterochromatin as the major chromatin modification repressing transcription in these fungi, which lack both Polycomb silencing and cytosine methylation. Although small RNAs generated by RNA interference (RNAi) pathways facilitate the formation of heterochromatin in many eukaryotic organisms, we show that RNAi is not required to maintain either genomic or centromeric heterochromatin in Mucor. H3K9-methylation and RNAi act independently to control centromeric regions, suggesting a functional subspecialization. Whereas the H3K9 methyltransferase Clr4 and heterochromatin formation are essential for cell viability, RNAi is dispensable for viability yet acts as the main epigenetic, regulatory force repressing transposition of centromeric GremLINE1 elements. Mutations inactivating canonical RNAi lead to rampant transposition and insertional inactivation of targets resulting in antimicrobial drug resistance. This fine-tuned, Rdrp2-dependent RNAi activity is critical for genome stability, restricting GremLINE1 retroelements to the centromeres where they occupy long heterochromatic islands. Taken together, our results suggest that RNAi and heterochromatin formation are independent genome defense and regulatory mechanisms in the Mucorales, contributing to a paradigm shift from the cotranscriptional gene silencing observed in fission yeasts to models in which heterochromatin and RNAi operate independently in early-diverging fungi.
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7
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Lin C, Wu Z, Shi H, Yu J, Xu M, Lin F, Kou Y, Tao Z. The additional PRC2 subunit and Sin3 histone deacetylase complex are required for the normal distribution of H3K27me3 occupancy and transcriptional silencing in Magnaporthe oryzae. THE NEW PHYTOLOGIST 2022; 236:576-589. [PMID: 35842786 DOI: 10.1111/nph.18383] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Development in higher organisms requires proper gene silencing, partially achieved through trimethylation of lysine 27 on histone H3 (H3K27me3). However, how the normal distribution of this modification is established and maintained and how it affects gene expression remains unclear, especially in fungi. Polycomb repressive complex 2 (PRC2) catalyses H3K27me3 to assemble transcriptionally repressed facultative heterochromatin and is crucial in animals, plants, and fungi. Here, we report on the critical role of an additional PRC2 subunit in the normal distribution of H3K27me3 occupancy and the stable maintenance of gene repression in the rice fungal pathogen Magnaporthe oryzae. P55, identified as an additional PRC2 subunit, is physically associated with core subunits of PRC2 and is required for a complete level of H3K27me3 modification. Loss of P55 caused severe global defects in the normal distribution of H3K27me3 and transcriptional reprogramming on the H3K27me3-occupied genes. Furthermore, we found that the Sin3 histone deacetylase complex was required to sustain H3K27me3 occupancy and stably maintain gene repression by directly interacting with P55. Our results revealed a novel mechanism by which P55 and Sin3 participate in the normal distribution of facultative heterochromatic modifications and the stable maintenance of gene repression in eukaryotes.
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Affiliation(s)
- Chuyu Lin
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Zhongling Wu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Huanbin Shi
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310021, China
| | - Jinwei Yu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mengting Xu
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fucheng Lin
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Yanjun Kou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310021, China
| | - Zeng Tao
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
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8
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Zhang X, Noberini R, Bonaldi T, Collemare J, Seidl MF. The histone code of the fungal genus Aspergillus uncovered by evolutionary and proteomic analyses. Microb Genom 2022; 8. [PMID: 36129736 PMCID: PMC9676040 DOI: 10.1099/mgen.0.000856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chemical modifications of DNA and histone proteins impact the organization of chromatin within the nucleus. Changes in these modifications, catalysed by different chromatin-modifying enzymes, influence chromatin organization, which in turn is thought to impact the spatial and temporal regulation of gene expression. While combinations of different histone modifications, the histone code, have been studied in several model species, we know very little about histone modifications in the fungal genus Aspergillus, whose members are generally well studied due to their importance as models in cell and molecular biology as well as their medical and biotechnological relevance. Here, we used phylogenetic analyses in 94 Aspergilli as well as other fungi to uncover the occurrence and evolutionary trajectories of enzymes and protein complexes with roles in chromatin modifications or regulation. We found that these enzymes and complexes are highly conserved in Aspergilli, pointing towards a complex repertoire of chromatin modifications. Nevertheless, we also observed few recent gene duplications or losses, highlighting Aspergillus species to further study the roles of specific chromatin modifications. SET7 (KMT6) and other components of PRC2 (Polycomb Repressive Complex 2), which is responsible for methylation on histone H3 at lysine 27 in many eukaryotes including fungi, are absent in Aspergilli as well as in closely related Penicillium species, suggesting that these lost the capacity for this histone modification. We corroborated our computational predictions by performing untargeted MS analysis of histone post-translational modifications in Aspergillus nidulans. This systematic analysis will pave the way for future research into the complexity of the histone code and its functional implications on genome architecture and gene regulation in fungi.
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Affiliation(s)
- Xin Zhang
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.,Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy.,Department of Oncology and Haematology-Oncology, University of Milano, Via Santa Sofia 9/1, 20122 Milano, Italy
| | - Jerome Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Michael F Seidl
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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9
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Schüller A, Studt-Reinhold L, Strauss J. How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances. Pharmaceutics 2022; 14:1837. [PMID: 36145585 PMCID: PMC9505985 DOI: 10.3390/pharmaceutics14091837] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Fungal species have the capability of producing an overwhelming diversity of bioactive substances that can have beneficial but also detrimental effects on human health. These so-called secondary metabolites naturally serve as antimicrobial "weapon systems", signaling molecules or developmental effectors for fungi and hence are produced only under very specific environmental conditions or stages in their life cycle. However, as these complex conditions are difficult or even impossible to mimic in laboratory settings, only a small fraction of the true chemical diversity of fungi is known so far. This also implies that a large space for potentially new pharmaceuticals remains unexplored. We here present an overview on current developments in advanced methods that can be used to explore this chemical space. We focus on genetic and genomic methods, how to detect genes that harbor the blueprints for the production of these compounds (i.e., biosynthetic gene clusters, BGCs), and ways to activate these silent chromosomal regions. We provide an in-depth view of the chromatin-level regulation of BGCs and of the potential to use the CRISPR/Cas technology as an activation tool.
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Affiliation(s)
| | | | - Joseph Strauss
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, A-3430 Tulln/Donau, Austria
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10
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Zhang F, Luo H, Peng W, Wang L, Wang T, Xie Z, Zhang J, Dong W, Zheng X, Liu G, Zhu X, Kang Q, Tian X. Hypoxic condition induced H3K27me3 modification of the LncRNA Tmem235 promoter thus supporting apoptosis of BMSCs. Apoptosis 2022; 27:762-777. [PMID: 35779185 PMCID: PMC9482900 DOI: 10.1007/s10495-022-01747-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2022] [Indexed: 02/06/2023]
Abstract
Bone marrow mesenchymal stem cells (BMSCs) have strong regenerative potential and show good application prospects for treating clinical diseases. However, in the process of BMSC transplantation for treating ischemic and hypoxic diseases, BMSCs have high rates of apoptosis in the hypoxic microenvironment of transplantation, which significantly affects the transplantation efficacy. Our previous studies have confirmed the key role of long non-coding RNA Tmem235 (LncRNA Tmem235) in the process of hypoxia-induced BMSC apoptosis and its downstream regulatory mechanism, but the upstream mechanism by which hypoxia regulates LncRNA Tmem235 expression to induce BMSC apoptosis is still unclear. Under hypoxic conditions, we found that the level of LncRNA Tmem235 promoter histone H3 lysine 27 trimethylation modification (H3K27me3) was significantly increased by CHIP-qPCR. Moreover, H3K27me3 cooperated with LncRNA Tmem235 promoter DNA methylation to inhibit the expression of LncRNA Tmem235 and promote apoptosis of BMSCs. To study the mechanism of hypoxia-induced modification of LncRNA Tmem235 promoter H3K27me3 in the hypoxia model of BMSCs, we detected the expression of H3K27 methylase and histone demethylase and found that only histone methylase enhancer of zeste homolog 2 (EZH2) expression was significantly upregulated. Knockdown of EZH2 significantly decreased the level of H3K27me3 modification in the LncRNA Tmem235 promoter. The EZH2 promoter region contains a hypoxia-responsive element (HRE) that interacts with hypoxia-inducible factor-1alpha (HIF-1α), which is overexpressed under hypoxic conditions, thereby promoting its overexpression. In summary, hypoxia promotes the modification of the LncRNA Tmem235 promoter H3K27me3 through the HIF-1α/EZH2 signaling axis, inhibits the expression of LncRNA Tmem235, and leads to hypoxic apoptosis of BMSCs. Our findings improve the regulatory mechanism of LncRNA Tmem235 during hypoxic apoptosis of BMSCs and provide a more complete theoretical pathway for targeting LncRNA to inhibit hypoxic apoptosis of BMSCs.
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Affiliation(s)
- Fei Zhang
- Department of Orthopedics, The Affliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.,School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Hong Luo
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Wuxun Peng
- Department of Orthopedics, The Affliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China. .,School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China.
| | - Lei Wang
- Department of Orthopedics, The Affliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.,School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Tao Wang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Zhihong Xie
- School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jian Zhang
- Department of Orthopedics, The Affliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.,School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Wentao Dong
- Department of Orthopedics, The Affliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.,School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaohan Zheng
- Department of Orthopedics, The Affliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.,School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Gang Liu
- Department of Orthopedics, The Affliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.,School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xuesong Zhu
- Department of Orthopedics, The First Affliated Hospital of Soochow University, Suzhou, 215000, Jiangsu, China
| | - Qinglin Kang
- Department of Orthopedics, The Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai, 200233, China
| | - Xiaobin Tian
- Department of Orthopedics, The Affliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou, China.,School of Clinical Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
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