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Guiza Beltran D, Wan T, Zhang L. WhiB-like proteins: Diversity of structure, function and mechanism. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119787. [PMID: 38879133 DOI: 10.1016/j.bbamcr.2024.119787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/20/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
The WhiB-Like (Wbl) proteins are a large family of iron-sulfur (Fe-S) cluster-containing transcription factors exclusively found in the phylum Actinobacteria, including the notable genera like Mycobacteria, Streptomycetes and Corynebacteria. These proteins play pivotal roles in diverse biological processes, such as cell development, redox stress response and antibiotic resistance. Members of the Wbl family exhibit remarkable diversity in their sequences, structures and functions, attracting great attention since their first discovery. This review highlights the most recent breakthroughs in understanding the structural and mechanistic aspects of Wbl-dependent transcriptional regulation.
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Affiliation(s)
- Daisy Guiza Beltran
- Department of Biochemistry, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA
| | - Tao Wan
- Department of Biochemistry, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA
| | - LiMei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA; Redox Biology Center, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, N138 Beadle Center, 1901 Vine Street, Lincoln, NE 68588, USA.
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2
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Xu L, Zheng S, Witzel K, Van De Slijke E, Baekelandt A, Mylle E, Van Damme D, Cheng J, De Jaeger G, Inzé D, Jiang H. Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana. Nat Commun 2024; 15:1286. [PMID: 38346986 PMCID: PMC10861482 DOI: 10.1038/s41467-024-45577-5] [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: 07/03/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The nuclear matrix is a nuclear compartment that has diverse functions in chromatin regulation and transcription. However, how this structure influences epigenetic modifications and gene expression in plants is largely unknown. In this study, we show that a nuclear matrix binding protein, AHL22, together with the two transcriptional repressors FRS7 and FRS12, regulates hypocotyl elongation by suppressing the expression of a group of genes known as SMALL AUXIN UP RNAs (SAURs) in Arabidopsis thaliana. The transcriptional repression of SAURs depends on their attachment to the nuclear matrix. The AHL22 complex not only brings these SAURs, which contain matrix attachment regions (MARs), to the nuclear matrix, but it also recruits the histone deacetylase HDA15 to the SAUR loci. This leads to the removal of H3 acetylation at the SAUR loci and the suppression of hypocotyl elongation. Taken together, our results indicate that MAR-binding proteins act as a hub for chromatin and epigenetic regulators. Moreover, we present a mechanism by which nuclear matrix attachment to chromatin regulates histone modifications, transcription, and hypocotyl elongation.
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Affiliation(s)
- Linhao Xu
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Shiwei Zheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, 14979, Germany
| | - Eveline Van De Slijke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Evelien Mylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Daniel Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Jinping Cheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, 9052, Belgium
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, 06466, Germany.
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3
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Scadden AW, Graybill AS, Hull-Crew C, Lundberg TJ, Lande NM, Klocko AD. Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization of Neurospora crassa. Proc Natl Acad Sci U S A 2023; 120:e2311249120. [PMID: 37963248 PMCID: PMC10666030 DOI: 10.1073/pnas.2311249120] [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: 07/20/2023] [Accepted: 10/11/2023] [Indexed: 11/16/2023] Open
Abstract
Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes, including in the fungus Neurospora crassa, where chromatin fiber loops compact into Topologically Associated Domain-like structures formed by heterochromatic region aggregation. However, insufficient data exist on how histone posttranslational modifications (PTMs), including acetylation, affect genome organization. In Neurospora, the HCHC complex [composed of the proteins HDA-1, CDP-2 (Chromodomain Protein-2), Heterochromatin Protein-1, and CHAP (CDP-2 and HDA-1 Associated Protein)] deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation, and alters the methylation of cytosines in DNA. Here, we assess whether the HCHC complex affects genome organization by performing Hi-C in strains deleted of the cdp-2 or chap genes. CDP-2 loss increases intra- and interchromosomal heterochromatic region interactions, while loss of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different patterns of histone PTMs genome-wide, as CDP-2 deletion increases heterochromatic H4K16 acetylation, yet smaller heterochromatic regions lose H3K9 trimethylation and gain interheterochromatic region interactions; CHAP loss produces minimal acetylation changes but increases heterochromatic H3K9me3 enrichment. Loss of both CDP-2 and the DIM-2 DNA methyltransferase causes extensive genome disorder as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how the increased cytosine methylation in HCHC mutants ensures genome compartmentalization when heterochromatic regions become hyperacetylated without HDAC activity.
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Affiliation(s)
- Ashley W. Scadden
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Alayne S. Graybill
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Clayton Hull-Crew
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Tiffany J. Lundberg
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Nickolas M. Lande
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
| | - Andrew D. Klocko
- Department of Chemistry and Biochemistry, University of Colorado Colorado Springs, Colorado Springs, CO80918
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4
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Scadden AW, Graybill AS, Hull-Crew C, Lundberg TJ, Lande NM, Klocko AD. Histone deacetylation and cytosine methylation compartmentalize heterochromatic regions in the genome organization of Neurospora crassa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.03.547530. [PMID: 37461718 PMCID: PMC10349943 DOI: 10.1101/2023.07.03.547530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Chromosomes must correctly fold in eukaryotic nuclei for proper genome function. Eukaryotic organisms hierarchically organize their genomes, including in the fungus Neurospora crassa, where chromatin fiber loops compact into Topologically Associated Domain (TAD)-like structures formed by heterochromatic region aggregation. However, insufficient data exists on how histone post-translational modifications, including acetylation, affect genome organization. In Neurospora, the HCHC complex (comprised of the proteins HDA-1, CDP-2, HP1, and CHAP) deacetylates heterochromatic nucleosomes, as loss of individual HCHC members increases centromeric acetylation and alters the methylation of cytosines in DNA. Here, we assess if the HCHC complex affects genome organization by performing Hi-C in strains deleted of the cdp-2 or chap genes. CDP-2 loss increases intra- and inter-chromosomal heterochromatic region interactions, while loss of CHAP decreases heterochromatic region compaction. Individual HCHC mutants exhibit different patterns of histone post-translational modifications genome-wide: without CDP-2, heterochromatic H4K16 acetylation is increased, yet smaller heterochromatic regions lose H3K9 trimethylation and gain inter-heterochromatic region interactions; CHAP loss produces minimal acetylation changes but increases heterochromatic H3K9me3 enrichment. Loss of both CDP-2 and the DIM-2 DNA methyltransferase causes extensive genome disorder, as heterochromatic-euchromatic contacts increase despite additional H3K9me3 enrichment. Our results highlight how the increased cytosine methylation in HCHC mutants ensures genome compartmentalization when heterochromatic regions become hyperacetylated without HDAC activity.
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Affiliation(s)
- Ashley W. Scadden
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Alayne S. Graybill
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Clayton Hull-Crew
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Tiffany J. Lundberg
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Nickolas M. Lande
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
| | - Andrew D. Klocko
- University of Colorado Colorado Springs, Department of Chemistry & Biochemistry, Colorado Springs, CO 80918, USA
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5
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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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6
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Meng S, Huang S, Liu J, Gai Y, Li M, Duan S, Zhang S, Sun X, Yang Q, Wang Y, Xu K, Ma H. Histone Methylation Is Required for Virulence, Conidiation, and Multi-Stress Resistance of Alternaria alternata. Front Microbiol 2022; 13:924476. [PMID: 35783406 PMCID: PMC9245015 DOI: 10.3389/fmicb.2022.924476] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/24/2022] [Indexed: 11/22/2022] Open
Abstract
Histone methylation, which is critical for transcriptional regulation and various biological processes in eukaryotes, is a reversible dynamic process regulated by histone methyltransferases (HMTs) and histone demethylases (HDMs). This study determined the function of 5 HMTs (AaDot1, AaHMT1, AaHnrnp, AaSet1, and AaSet2) and 1 HDMs (AaGhd2) in the phytopathogenic fungus Alternaria alternata by analyzing targeted gene deletion mutants. The vegetative growth, conidiation, and pathogenicity of ∆AaSet1 and ∆AaSet2 were severely inhibited indicating that AaSet1 and AaSet2 play critical roles in cell development in A. alternata. Multiple stresses analysis revealed that both AaSet1 and AaSet2 were involved in the adaptation to cell wall interference agents and osmotic stress. Meanwhile, ∆AaSet1 and ∆AaSet2 displayed serious vegetative growth defects in sole carbon source medium, indicating that AaSet1 and AaSet2 play an important role in carbon source utilization. In addition, ∆AaSet2 colony displayed white in color, while the wild-type colony was dark brown, indicating AaSet2 is an essential gene for melanin biosynthesis in A. alternata. AaSet2 was required for the resistance to oxidative stress. On the other hand, all of ∆AaDot1, ∆AaHMT1, and ∆AaGhd2 mutants displayed wild-type phenotype in vegetative growth, multi-stress resistance, pathogenicity, carbon source utilization, and melanin biosynthesis. To explore the regulatory mechanism of AaSet1 and AaSet2, RNA-seq of these mutants and wild-type strain was performed. Phenotypes mentioned above correlated well with the differentially expressed genes in ∆AaSet1 and ∆AaSet2 according to the KEGG and GO enrichment results. Overall, our study provides genetic evidence that defines the central role of HMTs and HDMs in the pathological and biological functions of A. alternata.
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Affiliation(s)
- Shuai Meng
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Suya Huang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Jinhua Liu
- Natural Medicine Institute of Zhejiang YangShengTang Co., LTD, Hangzhou, China
| | - Yunpeng Gai
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Min Li
- China-USA Citrus Huanglongbing Joint Laboratory (GNU-UF Joint Lab), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, China
| | - Shuo Duan
- China-USA Citrus Huanglongbing Joint Laboratory (GNU-UF Joint Lab), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, China
| | - Shuting Zhang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Qi Yang
- Linyi Inspection and Testing Center, Linyi, China
| | - Yuchun Wang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Kai Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
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7
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Yao Y, Wen Q, Zhang T, Yu C, Chan KM, Gan H. Advances in Approaches to Study Chromatin-Mediated Epigenetic Memory. ACS Synth Biol 2022; 11:16-25. [PMID: 34965084 DOI: 10.1021/acssynbio.1c00394] [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: 11/28/2022]
Abstract
Chromatin structure contains critical epigenetic information in various forms, such as histone post-translational modifications (PTMs). The deposition of certain histone PTMs can remodel the chromatin structure, resulting in gene expression alteration. The epigenetic information carried by histone PTMs could be inherited by daughter cells to maintain the gene expression status. Recently, studies revealed that several conserved replisome proteins regulate the recycling of parental histones carrying epigenetic information in Saccharomyces cerevisiae. Hence, the proper recycling and deposition of parental histones onto newly synthesized DNA strands is presumed to be essential for epigenetic inheritance. Here, we first reviewed the fundamental mechanisms of epigenetic modification establishment and maintenance discovered within fungal models. Next, we discussed the functions of parental histone chaperones and the potential impacts of the parental histone recycling process on heterochromatin-mediated transcriptional silencing inheritance. Subsequently, we summarized novel synthetic biology approaches developed to analyze individual epigenetic components during epigenetic inheritance in fungal and mammalian systems. These newly emerged research paradigms enable us to dissect epigenetic systems in a bottom-up manner. Furthermore, we highlighted the approaches developed in this emerging field and discussed the potential applications of these engineered regulators to building synthetic epigenetic systems.
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Affiliation(s)
- Yuan Yao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qing Wen
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianjun Zhang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Chuanhe Yu
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Kui Ming Chan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR 999077, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518172, China
| | - Haiyun Gan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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8
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Wan T, Horová M, Beltran DG, Li S, Wong HX, Zhang LM. Structural insights into the functional divergence of WhiB-like proteins in Mycobacterium tuberculosis. Mol Cell 2021; 81:2887-2900.e5. [PMID: 34171298 DOI: 10.1016/j.molcel.2021.06.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/12/2021] [Accepted: 05/31/2021] [Indexed: 12/12/2022]
Abstract
WhiB7 represents a distinct subclass of transcription factors in the WhiB-Like (Wbl) family, a unique group of iron-sulfur (4Fe-4S] cluster-containing proteins exclusive to the phylum of Actinobacteria. In Mycobacterium tuberculosis (Mtb), WhiB7 interacts with domain 4 of the primary sigma factor (σA4) in the RNA polymerase holoenzyme and activates genes involved in multiple drug resistance and redox homeostasis. Here, we report crystal structures of the WhiB7:σA4 complex alone and bound to its target promoter DNA at 1.55-Å and 2.6-Å resolution, respectively. These structures show how WhiB7 regulates gene expression by interacting with both σA4 and the AT-rich sequence upstream of the -35 promoter DNA via its C-terminal DNA-binding motif, the AT-hook. By combining comparative structural analysis of the two high-resolution σA4-bound Wbl structures with molecular and biochemical approaches, we identify the structural basis of the functional divergence between the two distinct subclasses of Wbl proteins in Mtb.
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Affiliation(s)
- Tao Wan
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Magdaléna Horová
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Daisy Guiza Beltran
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Shanren Li
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Huey-Xian Wong
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Li-Mei Zhang
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Redox Biology Center, University of Nebraska-Lincoln, Lincoln, NE 68588, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
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9
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Nai YS, Huang YC, Yen MR, Chen PY. Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns. Front Microbiol 2021; 11:616922. [PMID: 33552027 PMCID: PMC7862722 DOI: 10.3389/fmicb.2020.616922] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/28/2020] [Indexed: 11/24/2022] Open
Abstract
DNA methyltransferases (DNMTs) are a group of proteins that catalyze DNA methylation by transferring a methyl group to DNA. The genetic variation in DNMTs results in differential DNA methylation patterns associated with various biological processes. In fungal species, DNMTs and their DNA methylation profiles were found to be very diverse and have gained many research interests. We reviewed fungal DNMTs in terms of their biological functions, protein domain structures, and their associated epigenetic regulations compared to those known in plant and animal systems. In addition, we summarized recent reports on potential RNA-directed DNA methylation (RdDM) related to DNMT5 in fungi. We surveyed up to 40 fungal species with published genome-wide DNA methylation profiles (methylomes) and presented the associations between the specific patterns of fungal DNA methylation and their DNMTs based on a phylogenetic tree of protein domain structures. For example, the main DNMTs in Basidiomycota, DNMT1 with RFD domain + DNMT5, contributing to CG methylation preference, were distinct from RID + Dim-2 in Ascomycota, resulting in a non-CG methylation preference. Lastly, we revealed that the dynamic methylation involved in fungal life stage changes was particularly low in mycelium and DNA methylation was preferentially located in transposable elements (TEs). This review comprehensively discussed fungal DNMTs and methylomes and their connection with fungal development and taxonomy to present the diverse usages of DNA methylation in fungal genomes.
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Affiliation(s)
- Yu-Shin Nai
- Department of Entomology, National Chung Hsing University, Taichung, Taiwan.,Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chun Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan.,Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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10
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Storck WK, Bicocca VT, Rountree MR, Honda S, Ormsby T, Selker EU. LSD1 prevents aberrant heterochromatin formation in Neurospora crassa. Nucleic Acids Res 2020; 48:10199-10210. [PMID: 32946564 PMCID: PMC7544195 DOI: 10.1093/nar/gkaa724] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 08/17/2020] [Accepted: 09/16/2020] [Indexed: 12/25/2022] Open
Abstract
Heterochromatin is a specialized form of chromatin that restricts access to DNA and inhibits genetic processes, including transcription and recombination. In Neurospora crassa, constitutive heterochromatin is characterized by trimethylation of lysine 9 on histone H3, hypoacetylation of histones, and DNA methylation. We explored whether the conserved histone demethylase, lysine-specific demethylase 1 (LSD1), regulates heterochromatin in Neurospora, and if so, how. Though LSD1 is implicated in heterochromatin regulation, its function is inconsistent across different systems; orthologs of LSD1 have been shown to either promote or antagonize heterochromatin expansion by removing H3K4me or H3K9me respectively. We identify three members of the Neurospora LSD complex (LSDC): LSD1, PHF1, and BDP-1. Strains deficient for any of these proteins exhibit variable spreading of heterochromatin and establishment of new heterochromatin domains throughout the genome. Although establishment of H3K9me3 is typically independent of DNA methylation in Neurospora, instances of DNA methylation-dependent H3K9me3 have been found outside regions of canonical heterochromatin. Consistent with this, the hyper-H3K9me3 phenotype of Δlsd1 strains is dependent on the presence of DNA methylation, as well as HCHC-mediated histone deacetylation, suggesting that spreading is dependent on some feedback mechanism. Altogether, our results suggest LSD1 works in opposition to HCHC to maintain proper heterochromatin boundaries.
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Affiliation(s)
- William K Storck
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Vincent T Bicocca
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Michael R Rountree
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Shinji Honda
- Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Tereza Ormsby
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA
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11
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Klocko AD, Summers CA, Glover ML, Parrish R, Storck WK, McNaught KJ, Moss ND, Gotting K, Stewart A, Morrison AM, Payne L, Hatakeyama S, Selker EU. Selection and Characterization of Mutants Defective in DNA Methylation in Neurospora crassa. Genetics 2020; 216:671-688. [PMID: 32873602 PMCID: PMC7648584 DOI: 10.1534/genetics.120.303471] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/25/2020] [Indexed: 01/05/2023] Open
Abstract
DNA methylation, a prototypical epigenetic modification implicated in gene silencing, occurs in many eukaryotes and plays a significant role in the etiology of diseases such as cancer. The filamentous fungus Neurospora crassa places DNA methylation at regions of constitutive heterochromatin such as in centromeres and in other A:T-rich regions of the genome, but this modification is dispensable for normal growth and development. This and other features render N. crassa an excellent model to genetically dissect elements of the DNA methylation pathway. We implemented a forward genetic selection on a massive scale, utilizing two engineered antibiotic-resistance genes silenced by DNA methylation, to isolate mutants d efective i n m ethylation (dim). Hundreds of potential mutants were characterized, yielding a rich collection of informative alleles of 11 genes important for DNA methylation, most of which were already reported. In parallel, we characterized the pairwise interactions in nuclei of the DCDC, the only histone H3 lysine 9 methyltransferase complex in Neurospora, including those between the DIM-5 catalytic subunit and other complex members. We also dissected the N- and C-termini of the key protein DIM-7, required for DIM-5 histone methyltransferase localization and activation. Lastly, we identified two alleles of a novel gene, dim-10 - a homolog of Clr5 in Schizosaccharomyces pombe - that is not essential for DNA methylation, but is necessary for repression of the antibiotic-resistance genes used in the selection, which suggests that both DIM-10 and DNA methylation promote silencing of constitutive heterochromatin.
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Affiliation(s)
- Andrew D Klocko
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Calvin A Summers
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Marissa L Glover
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Robert Parrish
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - William K Storck
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Kevin J McNaught
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Nicole D Moss
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Kirsten Gotting
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Aurelian Stewart
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Ariel M Morrison
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Laurel Payne
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
| | - Shin Hatakeyama
- Laboratory of Genetics, Faculty of Science, Shimo-ohkubo 255, Saitama University, Sakura-ward, 338-8570, JAPAN
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403
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12
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Ridenour JB, Möller M, Freitag M. Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi. Genes (Basel) 2020; 11:E638. [PMID: 32527036 PMCID: PMC7348808 DOI: 10.3390/genes11060638] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Genome integrity is essential to maintain cellular function and viability. Consequently, genome instability is frequently associated with dysfunction in cells and associated with plant, animal, and human diseases. One consequence of relaxed genome maintenance that may be less appreciated is an increased potential for rapid adaptation to changing environments in all organisms. Here, we discuss evidence for the control and function of facultative heterochromatin, which is delineated by methylation of histone H3 lysine 27 (H3K27me) in many fungi. Aside from its relatively well understood role in transcriptional repression, accumulating evidence suggests that H3K27 methylation has an important role in controlling the balance between maintenance and generation of novelty in fungal genomes. We present a working model for a minimal repressive network mediated by H3K27 methylation in fungi and outline challenges for future research.
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Affiliation(s)
| | | | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis OR 97331, USA; (J.B.R.); (M.M.)
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13
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A Light-Inducible Strain for Genome-Wide Histone Turnover Profiling in Neurospora crassa. Genetics 2020; 215:569-578. [PMID: 32357961 DOI: 10.1534/genetics.120.303217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 04/30/2020] [Indexed: 01/14/2023] Open
Abstract
In chromatin, nucleosomes are composed of ∼146 bp of DNA wrapped around a histone octamer, and are highly dynamic structures subject to remodeling and exchange. Histone turnover has previously been implicated in various processes including the regulation of chromatin accessibility, segregation of chromatin domains, and dilution of histone marks. Histones in different chromatin environments may turnover at different rates, possibly with functional consequences. Neurospora crassa sports a chromatin environment that is more similar to that of higher eukaryotes than yeasts, which have been utilized in the past to explore histone exchange. We constructed a simple light-inducible system to profile histone exchange in N. crassa on a 3xFLAG-tagged histone H3 under the control of the rapidly inducible vvd promoter. After induction with blue light, incorporation of tagged H3 into chromatin occurred within 20 min. Previous studies of histone turnover involved considerably longer incubation periods and relied on a potentially disruptive change of medium for induction. We used this reporter to explore replication-independent histone turnover at genes and examine changes in histone turnover at heterochromatin domains in different heterochromatin mutant strains. In euchromatin, H3-3xFLAG patterns were almost indistinguishable from that observed in wild-type in all mutant backgrounds tested, suggesting that loss of heterochromatin machinery has little effect on histone turnover in euchromatin. However, turnover at heterochromatin domains increased with loss of trimethylation of lysine 9 of histone H3 or HP1, but did not depend on DNA methylation. Our reporter strain provides a simple yet powerful tool to assess histone exchange across multiple chromatin contexts.
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14
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Bewick AJ, Hofmeister BT, Powers RA, Mondo SJ, Grigoriev IV, James TY, Stajich JE, Schmitz RJ. Diversity of cytosine methylation across the fungal tree of life. Nat Ecol Evol 2019; 3:479-490. [PMID: 30778188 PMCID: PMC6533610 DOI: 10.1038/s41559-019-0810-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/13/2019] [Indexed: 12/22/2022]
Abstract
The generation of thousands of fungal genomes is leading to a better understanding of genes and genomic organization within the kingdom. However, the epigenome, which includes DNA and chromatin modifications, remains poorly investigated in fungi. Large comparative studies in animals and plants have deepened our understanding of epigenomic variation, particularly of the modified base 5-methylcytosine (5mC), but taxonomic sampling of disparate groups is needed to develop unifying explanations for 5mC variation. Here we utilize the largest phylogenetic resolution of 5mC methyltransferases (5mC MTases) and genome evolution to better understand levels and patterns of 5mC across fungi. We show that extant 5mC MTase genotypes are descendent from ancestral maintenance and de novo genotypes, whereas the 5mC MTases DIM-2 and RID are more recently derived, and that 5mC levels are correlated with 5mC MTase genotype and transposon content. Our survey also revealed that fungi lack canonical gene body methylation, which distinguishes fungal epigenomes from certain insect and plant species. However, some fungal species possess independently derived clusters of contiguous 5mC encompassing many genes. In some cases, DNA repair pathways and the N6-methyladenine (6mA) DNA modification negatively coevolved with 5mC pathways, which additionally contributed to interspecific epigenomic variation across fungi.
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Affiliation(s)
- Adam J Bewick
- Department of Genetics, University of Georgia, Athens, GA, USA.
| | | | - Rob A Powers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Stephen J Mondo
- US Department of Energy Joint Genome Institute, Walnut Creek, Berkeley, CA, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA
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15
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Nucleosome Positioning by an Evolutionarily Conserved Chromatin Remodeler Prevents Aberrant DNA Methylation in Neurospora. Genetics 2018; 211:563-578. [PMID: 30554169 DOI: 10.1534/genetics.118.301711] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 12/11/2018] [Indexed: 01/04/2023] Open
Abstract
In the filamentous fungus Neurospora crassa, constitutive heterochromatin is marked by tri-methylation of histone H3 lysine 9 (H3K9me3) and DNA methylation. We identified mutations in the Neurospora defective in methylation-1 (dim-1) gene that cause defects in cytosine methylation and implicate a putative AAA-ATPase chromatin remodeler. Although it was well-established that chromatin remodelers can affect transcription by influencing DNA accessibility with nucleosomes, little was known about the role of remodelers on chromatin that is normally not transcribed, including regions of constitutive heterochromatin. We found that dim-1 mutants display both reduced DNA methylation in heterochromatic regions as well as increased DNA methylation and H3K9me3 in some intergenic regions associated with highly expressed genes. Deletion of dim-1 leads to atypically spaced nucleosomes throughout the genome and numerous changes in gene expression. DIM-1 localizes to both heterochromatin and intergenic regions that become hyper-methylated in dim-1 strains. Our findings indicate that DIM-1 normally positions nucleosomes in both heterochromatin and euchromatin and that the standard arrangement and density of nucleosomes is required for the proper function of heterochromatin machinery.
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16
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Wang Z, Gudibanda A, Ugwuowo U, Trail F, Townsend JP. Using evolutionary genomics, transcriptomics, and systems biology to reveal gene networks underlying fungal development. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2018.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Dutta B, Park JE, Qing ITY, Kon OL, Sze SK. Soy-Derived Phytochemical Genistein Modifies Chromatome Topology to Restrict Cancer Cell Proliferation. Proteomics 2018; 18:e1700474. [PMID: 29963755 DOI: 10.1002/pmic.201700474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/22/2018] [Indexed: 12/18/2022]
Abstract
Epidemiological data indicate that human cancer risk is significantly reduced by the consumption of soy-based foods containing the "phytoestrogen" genistein, which can signal via host cell estrogen receptors. While additional chemoprotective effects of genistein induced by epigenetic factors have also been reported, the key molecules and mechanisms involved are poorly defined. We therefore investigated genistein effects on chromatin-bound proteins in the estrogen receptor-deficient cell line MDA-MB-231 which is insensitive to phytoestrogen signaling. After exposure to low-dose genistein for >1 month, MDA-MB-231 cells exhibited stable epigenetic alterations that are analyzed via partial MNase digestion and TMT-based quantitative proteomics. 3177 chromatin-bound proteins are identified with high confidence, including 882 molecules that displayed altered binding topology after cell conditioning with genistein. Prolonged phytochemical exposure conferred heritable changes in the binding topology of key epigenetic regulators including ATRX, SUV39H1/H2, and HP1BP3 that are preserved in untreated progeny, resulting in sustained downregulation of proliferation genes and reduced cell growth. These data indicate that soy derivative genistein exerts complex estrogen receptor-independent effects on the epigenome likely to influence tumorigenesis by restricting cell growth.
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Affiliation(s)
- Bamaprasad Dutta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jung Eun Park
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Ivan Toh Yi Qing
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Oi Lian Kon
- Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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18
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Bhat J, Kouakanou L, Peters C, Yin Z, Kabelitz D. Immunotherapy With Human Gamma Delta T Cells-Synergistic Potential of Epigenetic Drugs? Front Immunol 2018; 9:512. [PMID: 29593742 PMCID: PMC5859364 DOI: 10.3389/fimmu.2018.00512] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 02/27/2018] [Indexed: 12/28/2022] Open
Affiliation(s)
- Jaydeep Bhat
- Institute of Immunology, University of Kiel, Kiel, Germany
| | | | | | - Zhinan Yin
- The First Affiliated Hospital, Biomedical Translational Research Institute, Guangdong Province Key Laboratory of Molecular Immunology and Antibody Engineering, Jinan University, Guangzhou, China
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19
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Abstract
Transposable elements have colonized the genomes of nearly all organisms, including fungi. Although transposable elements may sometimes provide beneficial functions to their hosts their overall impact is considered deleterious. As a result, the activity of transposable elements needs to be counterbalanced by the host genome defenses. In fungi, the primary genome defense mechanisms include repeat-induced point mutation (RIP) and methylation induced premeiotically, meiotic silencing by unpaired DNA, sex-induced silencing, cosuppression (also known as somatic quelling), and cotranscriptional RNA surveillance. Recent studies of the filamentous fungus Neurospora crassa have shown that the process of repeat recognition for RIP apparently involves interactions between coaligned double-stranded segments of chromosomal DNA. These studies have also shown that RIP can be mediated by the conserved pathway that establishes transcriptional (heterochromatic) silencing of repetitive DNA. In light of these new findings, RIP emerges as a specialized case of the general phenomenon of heterochromatic silencing of repetitive DNA.
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20
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Induction of H3K9me3 and DNA methylation by tethered heterochromatin factors in Neurospora crassa. Proc Natl Acad Sci U S A 2017; 114:E9598-E9607. [PMID: 29078403 DOI: 10.1073/pnas.1715049114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Functionally different chromatin domains display distinct chemical marks. Constitutive heterochromatin is commonly associated with trimethylation of lysine 9 on histone H3 (H3K9me3), hypoacetylated histones, and DNA methylation, but the contributions of and interplay among these features are not fully understood. To dissect the establishment of heterochromatin, we investigated the relationships among these features using an in vivo tethering system in Neurospora crassa Artificial recruitment of the H3K9 methyltransferase DIM-5 (defective in methylation-5) induced H3K9me3 and DNA methylation at a normally active, euchromatic locus but did not bypass the requirement of DIM-7, previously implicated in the localization of DIM-5, indicating additional DIM-7 functionality. Tethered heterochromatin protein 1 (HP1) induced H3K9me3, DNA methylation, and gene silencing. The induced heterochromatin required histone deacetylase 1 (HDA-1), with an intact catalytic domain, but HDA-1 was not essential for de novo heterochromatin formation at native heterochromatic regions. Silencing did not require H3K9me3 or DNA methylation. However, DNA methylation contributed to establishment of H3K9me3 induced by tethered HP1. Our analyses also revealed evidence of regulatory mechanisms, dependent on HDA-1 and DIM-5, to control the localization and catalytic activity of the DNA methyltransferase DIM-2. Our study clarifies the interrelationships among canonical aspects of heterochromatin and supports a central role of HDA-1-mediated histone deacetylation in heterochromatin spreading and gene silencing.
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21
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Affiliation(s)
- Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331
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22
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Normal chromosome conformation depends on subtelomeric facultative heterochromatin in Neurospora crassa. Proc Natl Acad Sci U S A 2016; 113:15048-15053. [PMID: 27856763 DOI: 10.1073/pnas.1615546113] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High-throughput chromosome conformation capture (Hi-C) analyses revealed that the 3D structure of the Neurospora crassa genome is dominated by intra- and interchromosomal links between regions of heterochromatin, especially constitutive heterochromatin. Elimination of trimethylation of lysine 9 on histone H3 (H3K9me3) or its binding partner Heterochromatin Protein 1 (HP1)-both prominent features of constitutive heterochromatin-have little effect on the Hi-C pattern. It remained possible that di- or trimethylation of lysine 27 on histone H3 (H3K27me2/3), which becomes localized in regions of constitutive heterochromatin when H3K9me3 or HP1 are lost, plays a critical role in the 3D structure of the genome. We found that H3K27me2/3, catalyzed by the Polycomb Repressive Complex 2 (PRC2) member SET-7 (SET domain protein-7), does indeed play a prominent role in the Hi-C pattern of WT, but that its presence in regions normally occupied by H3K9me3 is not responsible for maintenance of the genome architecture when H3K9me3 is lost. The Hi-C pattern of a mutant defective in the PRC2 member N. crassa p55 (NPF), which is predominantly required for subtelomeric H3K27me2/3, was equivalent to that of the set-7 deletion strain, suggesting that subtelomeric facultative heterochromatin is paramount for normal chromosome conformation. Both PRC2 mutants showed decreased heterochromatin-heterochromatin contacts and increased euchromatin-heterochromatin contacts. Cytological observations suggested elimination of H3K27me2/3 leads to partial displacement of telomere clusters from the nuclear periphery. Transcriptional profiling of Δdim-5, Δset-7, Δset-7; Δdim-5, and Δnpf strains detailed anticipated changes in gene expression but did not support the idea that global changes in genome architecture, per se, led to altered transcription.
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