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Liu H, Marayati BF, de la Cerda D, Lemezis BM, Gao J, Song Q, Chen M, Reid KZ. The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe. PLoS Genet 2024; 20:e1011107. [PMID: 38181050 PMCID: PMC10795994 DOI: 10.1371/journal.pgen.1011107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/18/2024] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
Eukaryotic chromatin is organized into either silenced heterochromatin or relaxed euchromatin regions, which controls the accessibility of transcriptional machinery and thus regulates gene expression. In fission yeast, Schizosaccharomyces pombe, Set1 is the sole H3K4 methyltransferase and is mainly enriched at the promoters of actively transcribed genes. In contrast, Clr4 methyltransferase initiates H3K9 methylation, which has long been regarded as a hallmark of heterochromatic silencing. Lsd1 and Lsd2 are two highly conserved H3K4 and H3K9 demethylases. As these histone-modifying enzymes perform critical roles in maintaining histone methylation patterns and, consequently, gene expression profiles, cross-regulations among these enzymes are part of the complex regulatory networks. Thus, elucidating the mechanisms that govern their signaling and mutual regulations remains crucial. Here, we demonstrated that C-terminal truncation mutants, lsd1-ΔHMG and lsd2-ΔC, do not compromise the integrity of the Lsd1/2 complex but impair their chromatin-binding capacity at the promoter region of target genomic loci. We identified protein-protein interactions between Lsd1/2 and Raf2 or Swd2, which are the subunits of the Clr4 complex (CLRC) and Set1-associated complex (COMPASS), respectively. We showed that Clr4 and Set1 modulate the protein levels of Lsd1 and Lsd2 in opposite ways through the ubiquitin-proteasome-dependent pathway. During heat stress, the protein levels of Lsd1 and Lsd2 are upregulated in a Set1-dependent manner. The increase in protein levels is crucial for differential gene expression under stress conditions. Together, our results support a cross-regulatory model by which Set1 and Clr4 methyltransferases control the protein levels of Lsd1/2 demethylases to shape the dynamic chromatin landscape.
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Affiliation(s)
- Haoran Liu
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Bahjat Fadi Marayati
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - David de la Cerda
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Brendan Matthew Lemezis
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Jieyu Gao
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Qianqian Song
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, Florida, United States of America
| | - Minghan Chen
- Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Ke Zhang Reid
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
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Azemin WA, Alias N, Ali AM, Shamsir MS. In silico analysis prediction of HepTH1-5 as a potential therapeutic agent by targeting tumour suppressor protein networks. J Biomol Struct Dyn 2023; 41:1141-1167. [PMID: 34935583 DOI: 10.1080/07391102.2021.2017349] [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: 01/18/2023]
Abstract
Many studies reported that the activation of tumour suppressor protein, p53 induced the human hepcidin expression. However, its expression decreased when p53 was silenced in human hepatoma cells. Contrary to Tilapia hepcidin TH1-5, HepTH1-5 was previously reported to trigger the p53 activation through the molecular docking approach. The INhibitor of Growth (ING) family members are also shown to directly interact with p53 and promote cell cycle arrest, senescence, apoptosis and participate in DNA replication and DNA damage responses to suppress the tumour initiation and progression. However, the interrelation between INGs and HepTH1-5 remains unknown. Therefore, this study aims to identify the mechanism and their protein interactions using in silico approaches. The finding revealed that HepTH1-5 and its ligands had interacted mostly on hotspot residues of ING proteins which involved in histone modifications via acetylation, phosphorylation, and methylation. This proves that HepTH1-5 might implicate in an apoptosis signalling pathway and preserve the protein structure and function of INGs by reducing the perturbation of histone binding upon oxidative stress response. This study would provide theoretical guidance for the design and experimental studies to decipher the role of HepTH1-5 as a potential therapeutic agent for cancer therapy. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wan-Atirah Azemin
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia.,Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia
| | - Nadiawati Alias
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Abdul Manaf Ali
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
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3
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Chong ZS, Khong ZJ, Tay SH, Ng SY. Metabolic contributions to neuronal deficits caused by genomic disruption of schizophrenia risk gene SETD1A. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2022; 8:115. [PMID: 36581615 PMCID: PMC9800576 DOI: 10.1038/s41537-022-00326-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 12/20/2022] [Indexed: 12/30/2022]
Abstract
Regulation of neuronal metabolism during early brain development is crucial for directing synaptic plasticity and proper circuit formation. Alterations in neuronal glycolysis or mitochondrial function are associated with several neuropsychiatric disorders, including schizophrenia. Recently, loss-of-function mutations in SETD1A, a histone methyltransferase, have been linked to increased schizophrenia risk and global developmental delay. Here, we show that heterozygous disruption of SETD1A in human induced pluripotent stem cell (hiPSC)-derived neurons results in reduced neurite outgrowth and spontaneous activity, two phenotypes commonly associated with schizophrenia, as well as alterations in metabolic capacity. Furthermore, supplementing culture media with metabolic intermediates ameliorated changes in neurite outgrowth and spontaneous activity, suggesting that metabolic dysfunction contributes to neuronal phenotypes caused by SETD1A haploinsufficiency. These findings highlight a previously unknown connection between SETD1A function, metabolic regulation, and neuron development, and identifies alternative avenues for therapeutic development.
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Affiliation(s)
- Zheng-Shan Chong
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore
| | - Zi Jian Khong
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Integrative Sciences and Engineering Programme, NUS Graduate School, National University of Singapore, Singapore, Singapore
| | - Shermaine Huiping Tay
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore
| | - Shi-Yan Ng
- grid.418812.60000 0004 0620 9243Cellular Basis of Neural Diseases Laboratory, Institute of Molecular and Cell Biology, A*STAR Research Entities, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431National University of Singapore, Yong Loo Lin School of Medicine (Department of Physiology, Singapore, Singapore ,grid.276809.20000 0004 0636 696XNational Neuroscience Institute, Singapore, Singapore
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4
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Edwardes LV, Caswell SJ, Giurrandino M, Zhai X, Gohlke A, Kostomiris DH, Pollard HK, Pflug A, Hamm GR, Jervis KV, Clarkson PN, Syson K. Dissecting the Kinetic Mechanism of Human Lysine Methyltransferase 2D and Its Interactions with the WRAD2 Complex. Biochemistry 2022; 61:1974-1987. [PMID: 36070615 PMCID: PMC9494746 DOI: 10.1021/acs.biochem.2c00385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human lysine methyltransferase 2D (hKMT2D) is an epigenetic writer catalyzing the methylation of histone 3 lysine 4. hKMT2D by itself has little catalytic activity and reaches full activation as part of the WRAD2 complex, additionally comprising binding partners WDR5, RbBP5, Ash2L, and DPY30. Here, a detailed mechanistic study of the hKMT2D SET domain and its WRAD2 interactions is described. We characterized the WRAD2 subcomplexes containing full-length components and the hKMT2D SET domain. By performing steady-state analysis as a function of WRAD2 concentration, we identified the inner stoichiometry and determined the binding affinities for complex formation. Ash2L and RbBP5 were identified as the binding partners critical for the full catalytic activity of the SET domain. Contrary to a previous report, product and dead-end inhibitor studies identified hKMT2D as a rapid equilibrium random Bi-Bi mechanism with EAP and EBQ dead-end complexes. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-ToF MS) analysis showed that hKMT2D uses a distributive mechanism and gives further insights into how the WRAD2 components affect mono-, di-, and trimethylation. We also conclude that the Win motif of hKMT2D is not essential in complex formation, unlike other hKMT2 proteins.
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Affiliation(s)
- Lucy V Edwardes
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Sarah J Caswell
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Mariacarmela Giurrandino
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Xiang Zhai
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Boston, Massachusetts 02210, United States
| | - Andrea Gohlke
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Demetrios H Kostomiris
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Boston, Massachusetts 02210, United States
| | - Hannah K Pollard
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Alexander Pflug
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Gregory R Hamm
- Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Kate V Jervis
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Paul N Clarkson
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Karl Syson
- Discovery Biology, Discovery Sciences, BioPharmaceuticals, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
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5
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Ki BS, Shim SH, Park C, Yoo H, La H, Lee OH, Kwon Y, Skalnik DG, Okada Y, Yoon HG, Kim JH, Hong K, Choi Y. Epigenetic regulator Cfp1 safeguards male meiotic progression by regulating meiotic gene expression. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1098-1108. [PMID: 35918532 PMCID: PMC9440128 DOI: 10.1038/s12276-022-00813-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/04/2022] [Accepted: 05/10/2022] [Indexed: 11/09/2022]
Abstract
Meiosis occurs specifically in germ cells to produce sperm and oocytes that are competent for sexual reproduction. Multiple factors are required for successful meiotic entry, progression, and termination. Among them, trimethylation of histone H3 on lysine 4 (H3K4me3), a mark of active transcription, has been implicated in spermatogenesis by forming double-strand breaks (DSBs). However, the role of H3K4me in transcriptional regulation during meiosis remains poorly understood. Here, we reveal that mouse CXXC finger protein 1 (Cfp1), a component of the H3K4 methyltransferase Setd1a/b, is dynamically expressed in differentiating male germ cells and safeguards meiosis by controlling gene expression. Genetic ablation of mouse CFP1 in male germ cells caused complete infertility with failure in prophase I of the 1st meiosis. Mechanistically, CFP1 binds to genes essential for spermatogenesis, and its loss leads to a reduction in H3K4me3 levels and gene expression. Importantly, CFP1 is highly enriched within the promoter/TSS of target genes to elevate H3K4me3 levels and gene expression at the pachytene stage of meiotic prophase I. The most enriched genes were associated with meiosis and homologous recombination during the differentiation of spermatocytes to round spermatids. Therefore, our study establishes a mechanistic link between CFP1-mediated transcriptional control and meiotic progression and might provide an unprecedented genetic basis for understanding human sterility. Details of the role of a protein in the development of sperm cells in mice could lead to new understanding of sterility in men. An international research team led by Youngsok Choi and Kwonho Hong at Konkuk University, Seoul, South Korea, investigated the role of protein Cfp1, which they found to be required for sperm formation in mice. The protein is a component of an enzyme complex that transfers methyl groups (CH3) onto other proteins involved in controlling gene activity. The researchers identified key aspects of the mechanism by which Cfp1 controls the activity of genes essential for sperm formation to proceed normally. Absence of Cfp1 specifically interferes with the process of meiosis, which generates sperm cells containing only one copy of each chromosome instead of the two copies found in other cells.
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Affiliation(s)
- Byeong Seong Ki
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Sung Han Shim
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyunjin Yoo
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyeonwoo La
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Ok-Hee Lee
- Department of Biomedical Science, CHA University, Gyeonggi-do, 13488, Republic of Korea
| | - Youngjoo Kwon
- College of Pharmacy, Graduate School of Pharmaceutical Sciences, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - David G Skalnik
- Department of Biology, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Yuki Okada
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Tokyo, 113-0032, Japan
| | - Ho-Geun Yoon
- Department of Biochemistry and Molecular Biology, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea.
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology, Humanized Pig Center, Konkuk University, Seoul, 05029, Republic of Korea.
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6
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Deshpande N, Jordan R, Henderson Pozzi M, Bryk M. Histone 3 lysine 4 monomethylation supports activation of transcription in S. cerevisiae during nutrient stress. Curr Genet 2022; 68:181-194. [PMID: 35041077 PMCID: PMC8976815 DOI: 10.1007/s00294-022-01226-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 12/17/2021] [Accepted: 12/31/2021] [Indexed: 12/11/2022]
Abstract
Mono-methylation of the fourth lysine on the N-terminal tail of histone H3 was found to support the induction of RNA polymerase II transcription in S. cerevisiae during nutrient stress. In S. cerevisiae, the mono-, di- and tri-methylation of lysine 4 on histone H3 (H3K4) is catalyzed by the protein methyltransferase, Set1. The three distinct methyl marks on H3K4 act in discrete ways to regulate transcription. Nucleosomes enriched with tri-methylated H3K4 are usually associated with active transcription whereas di-methylated H3K4 is associated with gene repression. Mono-methylated H3K4 has been shown to repress gene expression in S. cerevisiae and is detected at enhancers and promoters in eukaryotes. S. cerevisiae set1Δ mutants unable to methylate H3K4 exhibit growth defects during histidine starvation. The growth defects are rescued by either a wild-type allele of SET1 or partial-function alleles of set1, including a mutant that predominantly generates H3K4me1 and not H3K4me3. Rescue of the growth defect is associated with induction of the HIS3 gene. Growth defects observed when set1Δ cultures were starved for isoleucine and valine were also rescued by wild-type SET1 or partial-function set1 alleles. The results show that H3K4me1, in the absence of H3K4me3, supports transcription of the HIS3 gene and expression of one or more of the genes required for biosynthesis of isoleucine and valine during nutrient stress. Set1-like methyltransferases are evolutionarily conserved, and research has linked their functions to developmental gene regulation and several cancers in higher eukaryotes. Identification of mechanisms of H3K4me1-mediated activation of transcription in budding yeast will provide insight into gene regulation in all eukaryotes.
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Affiliation(s)
- Neha Deshpande
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Rachel Jordan
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
- iBio, 8800 HSC Blvd, Bryan, TX, 77807, USA
| | - Michelle Henderson Pozzi
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA
| | - Mary Bryk
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA.
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7
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Wang S, Bleeck A, Nadif Kasri N, Kleefstra T, van Rhijn JR, Schubert D. SETD1A Mediated H3K4 Methylation and Its Role in Neurodevelopmental and Neuropsychiatric Disorders. Front Mol Neurosci 2021; 14:772000. [PMID: 34803610 PMCID: PMC8595121 DOI: 10.3389/fnmol.2021.772000] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/12/2021] [Indexed: 01/07/2023] Open
Abstract
Posttranslational modification of histones and related gene regulation are shown to be affected in an increasing number of neurological disorders. SETD1A is a chromatin remodeler that influences gene expression through the modulation of mono- di- and trimethylation marks on Histone-H3-Lysine-4 (H3K4me1/2/3). H3K4 methylation is predominantly described to result in transcriptional activation, with its mono- di- and trimethylated forms differentially enriched at promoters or enhancers. Recently, dominant mostly de novo variants in SETD1A have clinically been linked to developmental delay, intellectual disability (DD/ID), and schizophrenia (SCZ). Affected individuals often display both developmental and neuropsychiatric abnormalities. The primary diagnoses are mainly dependent on the age at which the individual is assessed. Investigations in mouse models of SETD1A dysfunction have been able to recapitulate key behavioral features associated with ID and SCZ. Furthermore, functional investigations suggest disrupted synaptic and neuronal network function in these mouse models. In this review, we provide an overview of pre-clinical studies on the role of SETD1A in neuronal development. A better understanding of the pathobiology underlying these disorders may provide novel opportunities for therapeutic intervention. As such, we will discuss possible strategies to move forward in elucidating the genotype-phenotype correlation in SETD1A associated disorders.
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Affiliation(s)
- Shan Wang
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Anna Bleeck
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Nael Nadif Kasri
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands.,Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands.,Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, Netherlands
| | - Jon-Ruben van Rhijn
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
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Enhanced H3K4 Trimethylation in TNF- α Promoter Gene Locus with Cell Apoptosis in the Ventral-Medial Striatum following Opioid Withdrawal of Neonatal Rat Offspring from Morphine-Addicted Mothers. Mediators Inflamm 2021; 2021:9828995. [PMID: 34220336 PMCID: PMC8221879 DOI: 10.1155/2021/9828995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/12/2021] [Accepted: 05/31/2021] [Indexed: 12/03/2022] Open
Abstract
Prenatal opioid exposure might disturb epigenetic programming in the brain of neonatal offspring with various consequences for gene expressions and behaviors. This study determined whether altered trimethylation of histone 3 at lysine 4 (H3K4me3) in the promoter of the tumor necrosis factor-α (tnf-α) gene with neural cell apoptosis was involved in the ventral-medial striatum, an important brain region for withdrawal symptoms, of neonatal rat offspring from morphine-addicted mothers. Female adult rats were injected with morphine before gestation and until 14 days after giving birth. On postnatal day 14 (P14), rat offspring from morphine-addicted mothers were subjected to an opioid-withdrawal protocol and were analyzed 2 or 8 h after administration of that protocol. Expressions of the TNF-α protein, H3K4me3 in the tnf-α promoter gene, and neural cell apoptosis within the ventral-medial striatum of neonatal rat offspring were evaluated. In the absence of significant opioid withdrawal (2 h after initiation of the opioid-withdrawal protocol on P14), prenatal morphine exposure led to increased levels of H3K4me3 in the tnf-α promoter gene, of the TNF-α protein, and of neural cell apoptosis within the ventral-medial striatum of neonatal rat offspring. Following opioid withdrawal (8 h after initiation of the opioid-withdrawal protocol on P14), differential expression of H3K4me3 in the tnf-α promoter gene locus and upregulation of the level of TNF-α protein expression were further enhanced in these offspring. In addition, increased levels of caspase-3 and neural cell apoptosis were also observed. Taken together, this study revealed that prenatal opioid exposure can activate an epigenetic histone mechanism which regulates proinflammatory factor generation, which hence, led to cell apoptotic damage within the ventral-medial striatum of neonatal rat offspring from morphine-addicted mothers. More importantly, the opioid-withdrawal episode may provide augmented effects for the abovementioned alterations and could lead to deleterious effects in the neonatal brain of such offspring.
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9
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The Role of H3K4 Trimethylation in CpG Islands Hypermethylation in Cancer. Biomolecules 2021; 11:biom11020143. [PMID: 33499170 PMCID: PMC7912453 DOI: 10.3390/biom11020143] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/30/2020] [Accepted: 01/15/2021] [Indexed: 01/01/2023] Open
Abstract
CpG methylation in transposons, exons, introns and intergenic regions is important for long-term silencing, silencing of parasitic sequences and alternative promoters, regulating imprinted gene expression and determining X chromosome inactivation. Promoter CpG islands, although rich in CpG dinucleotides, are unmethylated and remain so during all phases of mammalian embryogenesis and development, except in specific cases. The biological mechanisms that contribute to the maintenance of the unmethylated state of CpG islands remain elusive, but the modification of established DNA methylation patterns is a common feature in all types of tumors and is considered as an event that intrinsically, or in association with genetic lesions, feeds carcinogenesis. In this review, we focus on the latest results describing the role that the levels of H3K4 trimethylation may have in determining the aberrant hypermethylation of CpG islands in tumors.
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10
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Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194567. [PMID: 32360393 PMCID: PMC7294231 DOI: 10.1016/j.bbagrm.2020.194567] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/24/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The precise regulation of gene transcription is required to establish and maintain cell type-specific gene expression programs during multicellular development. In addition to transcription factors, chromatin, and its chemical modification, play a central role in regulating gene expression. In vertebrates, DNA is pervasively methylated at CG dinucleotides, a modification that is repressive to transcription. However, approximately 70% of vertebrate gene promoters are associated with DNA elements called CpG islands (CGIs) that are refractory to DNA methylation. CGIs integrate the activity of a range of chromatin-regulating factors that can post-translationally modify histones and modulate gene expression. This is exemplified by the trimethylation of histone H3 at lysine 4 (H3K4me3), which is enriched at CGI-associated gene promoters and correlates with transcriptional activity. Through studying H3K4me3 at CGIs it has become clear that CGIs shape the distribution of H3K4me3 and, in turn, H3K4me3 influences the chromatin landscape at CGIs. Here we will discuss our understanding of the emerging relationship between CGIs, H3K4me3, and gene expression.
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11
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H3K4me3 Is a Potential Mediator for Antiproliferative Effects of Calcitriol (1α,25(OH)2D3) in Ovarian Cancer Biology. Int J Mol Sci 2020; 21:ijms21062151. [PMID: 32245092 PMCID: PMC7139961 DOI: 10.3390/ijms21062151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/12/2020] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
Posttranslational histone modification plays an important role in tumorigenesis. Histone modification is a dynamic response of chromatin to various signals, such as the exposure to calcitriol (1α,25(OH)2D3). Recent studies suggested that histone modification levels could be used to predict patient outcomes in various cancers. Our study evaluated the expression level of histone 3 lysine 4 trimethylation (H3K4me3) in a cohort of 156 epithelial ovarian cancer (EOC) cases by immunohistochemical staining and analyzed its correlation to patient prognosis. The influence of 1α,25(OH)2D3 on the proliferation of ovarian cancer cells was measured by BrdU proliferation assay in vitro. We could show that higher levels of H3K4me3 were correlated with improved overall survival (median overall survival (OS) not reached vs. 37.0 months, p = 0.047) and identified H3K4me3 as a potential prognostic factor for the present cohort. Ovarian cancer cell 1α,25(OH)2D3 treatment induced H3K4me3 protein expression and exhibited antiproliferative effects. By this, the study suggests a possible impact of H3K4me3 expression on EOC progression as well as its relation to calcitriol (1α,25(OH)2D3) treatment. These results may serve as an explanation on how 1α,25(OH)2D3 mediates its known antiproliferative effects. In addition, they further underline the potential benefit of 1α,25(OH)2D3 supplementation in context of ovarian cancer care.
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Domínguez‐Andrés J, Ferreira AV, Jansen T, Smithers N, Prinjha RK, Furze RC, Netea MG. Bromodomain inhibitor I-BET151 suppresses immune responses during fungal-immune interaction. Eur J Immunol 2019; 49:2044-2050. [PMID: 31206650 PMCID: PMC6899658 DOI: 10.1002/eji.201848081] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/06/2019] [Accepted: 06/12/2019] [Indexed: 12/29/2022]
Abstract
Changes in the epigenetic landscape of immune cells are a crucial component of gene activation during the induction of inflammatory responses, therefore it has been hypothesized that epigenetic modulation could be employed to restore homeostasis in inflammatory scenarios. Fungal pathogens cause a large burden of morbidity and even mortality due to the hyperinflammatory processes that induce mucosal, allergic or systemic infections. Bromodomain and extraterminal domain (BET) proteins are considered as one as the most tantalizing pharmacological targets for the modulation of inflammatory responses at the epigenetic level. Nothing is known of the role of BET inhibitors on the inflammation induced by fungal pathogens. In the present study, we assessed the in vitro efficacy of the small molecular histone mimic BET inhibitor I-BET151 to modulate innate immune responses during fungal-immune interaction with the clinically relevant fungal pathogens Candida albicans and Aspergillus fumigatus. Our results prove that BET inhibitors (I-BETs) represent an important modulator of inflammation induced by fungal pathogens: both direct production of proinflammatory cytokines and the induction of trained immunity were inhibited by I-BET151. These modulatory effects are likely to have important potential implications in clinically relevant situations.
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Affiliation(s)
- Jorge Domínguez‐Andrés
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI)Radboud University Nijmegen Medical Centre6500HBNijmegenthe Netherlands
| | - Anaísa V Ferreira
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI)Radboud University Nijmegen Medical Centre6500HBNijmegenthe Netherlands
- Instituto de Ciências Biomédicas Abel Salazar (ICBAS)Universidade do Porto4050‐313PortoPortugal
| | - Trees Jansen
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI)Radboud University Nijmegen Medical Centre6500HBNijmegenthe Netherlands
| | - Nicholas Smithers
- Epigenetics DPU, Immuno‐Inflammation Therapy AreaGlaxoSmithKline R&D, Medicines Research CentreStevenageSG1 2NYUK
| | - Rab K. Prinjha
- Epigenetics DPU, Immuno‐Inflammation Therapy AreaGlaxoSmithKline R&D, Medicines Research CentreStevenageSG1 2NYUK
| | - Rebecca C. Furze
- Epigenetics DPU, Immuno‐Inflammation Therapy AreaGlaxoSmithKline R&D, Medicines Research CentreStevenageSG1 2NYUK
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious diseases (RCI)Radboud University Nijmegen Medical Centre6500HBNijmegenthe Netherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES)University of Bonn53115BonnGermany
- Human Genomics LaboratoryCraiova University of Medicine and PharmacyCraiovaRomania
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13
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Brown DA, Di Cerbo V, Feldmann A, Ahn J, Ito S, Blackledge NP, Nakayama M, McClellan M, Dimitrova E, Turberfield AH, Long HK, King HW, Kriaucionis S, Schermelleh L, Kutateladze TG, Koseki H, Klose RJ. The SET1 Complex Selects Actively Transcribed Target Genes via Multivalent Interaction with CpG Island Chromatin. Cell Rep 2018; 20:2313-2327. [PMID: 28877467 PMCID: PMC5603731 DOI: 10.1016/j.celrep.2017.08.030] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 07/19/2017] [Accepted: 08/06/2017] [Indexed: 12/24/2022] Open
Abstract
Chromatin modifications and the promoter-associated epigenome are important for the regulation of gene expression. However, the mechanisms by which chromatin-modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live-cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed gene promoters through CFP1, which engages in a form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). CFP1 defines SET1 complex occupancy on chromatin, and its multivalent interactions are required for the SET1 complex to place H3K4me3. In the absence of CFP1, gene expression is perturbed, suggesting that normal targeting and function of the SET1 complex are central to creating an appropriately functioning vertebrate promoter-associated epigenome. The CFP1/SET1 complex engages in dynamic and stable chromatin-binding events CFP1 uses multivalent chromatin interactions to select active CpG island promoters SET1A occupancy at CpG island promoters is predominately defined by CFP1 CFP1 targets SET1 to shape promoter-associated H3K4me3 and gene expression
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Affiliation(s)
- David A Brown
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Vincenzo Di Cerbo
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Angelika Feldmann
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Jaewoo Ahn
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Shinsuke Ito
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-2 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Neil P Blackledge
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Manabu Nakayama
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-2 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Michael McClellan
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Emilia Dimitrova
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Hannah K Long
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Hamish W King
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Skirmantas Kriaucionis
- Ludwig Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-2 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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Chang AYF, Liao BY. Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution. Genome Res 2017; 27:1513-1524. [PMID: 28720579 PMCID: PMC5580711 DOI: 10.1101/gr.221739.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/05/2017] [Indexed: 12/24/2022]
Abstract
Following gene duplication, mRNA expression of the duplicated gene is reduced to maintain mRNA dosage. In mammals, this process is achieved with increased cytosine DNA methylation of the promoters of duplicated genes to suppress transcriptional initiation. However, not all animal species possess a full apparatus for cytosine DNA methylation. For such species, such as the roundworm (Caenorhabditis elegans, "worm" hereafter) or fruit fly (Drosophila melanogaster, "fly" hereafter), it is unclear how reduced expression of duplicated genes has been achieved evolutionarily. Here, we hypothesize that in the absence of a classical cytosine DNA methylation pathway, histone modifications play an increasing role in maintaining mRNA dosage following gene duplication. We initially verified that reduced gene expression of duplicated genes had occurred in the worm, fly, and mouse (Mus musculus). Next, several histone marks, with the capacity to control mRNA abundance in the models studied, were examined. In the worm and fly, but not in the mouse, multiple histone modifications were found to assist mRNA dosage maintenance following gene duplication events and the possible involvement of adenine DNA methylation in this process was excluded. Furthermore, the histone marks and acting regions that mediated the reduction in duplicated gene expression were found to be largely organism specific. Thus, it appears that many of the histone marks that maintain mRNA dosage were independently recruited during the evolution of worms and flies to compensate for the loss of cytosine DNA methylation machinery from their genomes.
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Affiliation(s)
- Andrew Ying-Fei Chang
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County 350, Taiwan, Republic of China
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County 350, Taiwan, Republic of China
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15
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Eckstein M, Eleazer R, Rea M, Fondufe-Mittendorf Y. Epigenomic reprogramming in inorganic arsenic-mediated gene expression patterns during carcinogenesis. REVIEWS ON ENVIRONMENTAL HEALTH 2017; 32:93-103. [PMID: 27701139 DOI: 10.1515/reveh-2016-0025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/08/2016] [Indexed: 05/22/2023]
Abstract
Arsenic is a ubiquitous metalloid that is not mutagenic but is carcinogenic. The mechanism(s) by which arsenic causes cancer remain unknown. To date, several mechanisms have been proposed, including the arsenic-induced generation of reactive oxygen species (ROS). However, it is also becoming evident that inorganic arsenic (iAs) may exert its carcinogenic effects by changing the epigenome, and thereby modifying chromatin structure and dynamics. These epigenetic changes alter the accessibility of gene regulatory factors to DNA, resulting in specific changes in gene expression both at the levels of transcription initiation and gene splicing. In this review, we discuss recent literature reports describing epigenetic changes induced by iAs exposure and the possible epigenetic mechanisms underlying these changes.
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Evolving Catalytic Properties of the MLL Family SET Domain. Structure 2015; 23:1921-1933. [PMID: 26320581 PMCID: PMC4597100 DOI: 10.1016/j.str.2015.07.018] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/20/2015] [Accepted: 07/27/2015] [Indexed: 12/25/2022]
Abstract
Methylation of histone H3 lysine-4 is a hallmark of chromatin associated with active gene expression. The activity of H3K4-specific modification enzymes, in higher eukaryotes the MLL (or KMT2) family, is tightly regulated. The MLL family has six members, each with a specialized function. All contain a catalytic SET domain that associates with a core multiprotein complex for activation. These SET domains segregate into three classes that correlate with the arrangement of targeting domains that populate the rest of the protein. Here we show that, unlike MLL1, the MLL4 SET domain retains significant activity without the core complex. We also present the crystal structure of an inactive MLL4-tagged SET domain construct and describe conformational changes that account for MLL4 intrinsic activity. Finally, our structure explains how the MLL SET domains are able to add multiple methyl groups to the target lysine, despite having the sequence characteristics of a classical monomethylase. MLL4 SET domain has significant H3K4 methyltransferase activity without WRAD MLL4 SET domain structure (inactivated by tag) reveals differences to MLL1 The postSET loop region contributes to the intrinsic methyltransferase activity MLL4 can catalyze multiple methylations on H3K4 but prefers monomethylation
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17
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The cancer COMPASS: navigating the functions of MLL complexes in cancer. Cancer Genet 2015; 208:178-91. [PMID: 25794446 DOI: 10.1016/j.cancergen.2015.01.005] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 12/13/2022]
Abstract
The mixed-lineage leukemia family of histone methyltransferases (MLL1-4, or KMT2A-D) were previously linked to cancer through the founding member, MLL1/KMT2A, which is often involved in translocation-associated gene fusion events in childhood leukemias. However, in recent years, a multitude of tumor exome sequencing studies have revealed that orthologues MLL3/KMT2C and MLL2/KMT2D are mutated in a significant percentage of a large variety of malignancies, particularly solid tumors. These unexpected findings necessitate a deeper inspection into the activities and functional differences between the MLL/KMT2 family members. This review provides an overview of this protein family and its relation to cancers, focusing on the recent links between MLL3/KMT2C and MLL2/4/KMT2D and their potential roles as tumor suppressors in an assortment of cell types.
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18
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Lorenz DR, Meyer LF, Grady PJR, Meyer MM, Cam HP. Heterochromatin assembly and transcriptome repression by Set1 in coordination with a class II histone deacetylase. eLife 2014; 3:e04506. [PMID: 25497836 PMCID: PMC4383021 DOI: 10.7554/elife.04506] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 12/12/2014] [Indexed: 12/20/2022] Open
Abstract
Histone modifiers play essential roles in controlling transcription and organizing
eukaryotic genomes into functional domains. Here, we show that Set1, the catalytic
subunit of the highly conserved Set1C/COMPASS complex responsible for histone H3K4
methylation (H3K4me), behaves as a repressor of the transcriptome largely independent
of Set1C and H3K4me in the fission yeast Schizosaccharomyces pombe.
Intriguingly, while Set1 is enriched at highly expressed and repressed loci, Set1
binding levels do not generally correlate with the levels of transcription. We show
that Set1 is recruited by the ATF/CREB homolog Atf1 to heterochromatic loci and
promoters of stress-response genes. Moreover, we demonstrate that Set1 coordinates
with the class II histone deacetylase Clr3 in heterochromatin assembly at prominent
chromosomal landmarks and repression of the transcriptome that includes
Tf2 retrotransposons, noncoding RNAs, and regulators of
development and stress-responses. Our study delineates a molecular framework for
elucidating the functional links between transcriptome control and chromatin
organization. DOI:http://dx.doi.org/10.7554/eLife.04506.001 Genes can be turned on or off at different times in an organism's life. In humans,
yeast and other eukaryotes, this is mainly controlled by the way DNA is packaged with
proteins—known as histones—in a structure called chromatin. Genes that
are switched on, or only temporarily switched off, are associated with areas of the
genome where the chromatin is loosely packed. In contrast, genes that remain switched
off for long periods of time are found in regions—known as
heterochromatin—where the chromatin is tightly packed. There are many enzymes that can modify histones to change the structure of chromatin.
One enzyme—called Set1—adds a methyl tag to chromatin, which is known
to be associated with genes being switched on. However, Lorenz et al. found that Set1
also has other roles in modifying chromatin in the yeast Schizosaccharomyces
pombe. The experiments found that Set1 helps to keep genes switched off and that this role
is largely independent of its ability to add the methyl tag to chromatin. Set1 is
recruited to many sites across the genome by another protein called Atf1, which is
involved in the cell's response to environmental stresses. Lorenz et al. believe that
this helps to put these genes in a ‘poised’ off state so that they are
ready to be switched on rapidly if needed. Set1 also works with another protein that removes acetyl tags—which encourage
chromatin to be less tightly packed—from histones. Together, both proteins
contribute to the assembly of heterochromatin and keep genes involved in development
and stress responses switched off when they are not required. Collectively, these experiments reveal unexpected and important insights into how
Set1—which plays critical roles in many aspects of human health including
aging and cancer—works in cells. DOI:http://dx.doi.org/10.7554/eLife.04506.002
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Affiliation(s)
- David R Lorenz
- Department of Biology, Boston College, Chestnut Hill, United States
| | - Lauren F Meyer
- Department of Biology, Boston College, Chestnut Hill, United States
| | | | - Michelle M Meyer
- Department of Biology, Boston College, Chestnut Hill, United States
| | - Hugh P Cam
- Department of Biology, Boston College, Chestnut Hill, United States
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19
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Mikheyeva IV, Grady PJR, Tamburini FB, Lorenz DR, Cam HP. Multifaceted genome control by Set1 Dependent and Independent of H3K4 methylation and the Set1C/COMPASS complex. PLoS Genet 2014; 10:e1004740. [PMID: 25356590 PMCID: PMC4214589 DOI: 10.1371/journal.pgen.1004740] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/08/2014] [Indexed: 12/21/2022] Open
Abstract
Histone modifiers are critical regulators of chromatin-based processes in eukaryotes. The histone methyltransferase Set1, a component of the Set1C/COMPASS complex, catalyzes the methylation at lysine 4 of histone H3 (H3K4me), a hallmark of euchromatin. Here, we show that the fission yeast Schizosaccharomyces pombe Set1 utilizes distinct domain modules to regulate disparate classes of repetitive elements associated with euchromatin and heterochromatin via H3K4me-dependent and -independent pathways. Set1 employs its RNA-binding RRM2 and catalytic SET domains to repress Tf2 retrotransposons and pericentromeric repeats while relying on its H3K4me function to maintain transcriptional repression at the silent mating type (mat) locus and subtelomeric regions. These repressive functions of Set1 correlate with the requirement of Set1C components to maintain repression at the mat locus and subtelomeres while dispensing Set1C in repressing Tf2s and pericentromeric repeats. We show that the contributions of several Set1C subunits to the states of H3K4me diverge considerably from those of Saccharomyces cerevisiae orthologs. Moreover, unlike S. cerevisiae, the regulation of Set1 protein level is not coupled to the status of H3K4me or histone H2B ubiquitination by the HULC complex. Intriguingly, we uncover a genome organization role for Set1C and H3K4me in mediating the clustering of Tf2s into Tf bodies by antagonizing the acetyltransferase Mst1-mediated H3K4 acetylation. Our study provides unexpected insights into the regulatory intricacies of a highly conserved chromatin-modifying complex with diverse roles in genome control. Methylation of histone H3 at lysine 4 (H3K4me) is a well-documented mark associated with euchromatin. In this study, we investigate the contributions of the histone methyltransferase Set1 (KMT2) and its associated Set1C/COMPASS complex in the fission yeast Schizosaccharomyces pombe to histone H3 lysine 4 methylation (H3K4me), transcriptional repression, and genome organization. We show that Set1 exhibits multiple modes of transcriptional repression at different types of repetitive elements, requiring distinct domains of Set1 and other Set1C subunits. Despite high conservation of subunits between the S. pombe and S. cerevisiae Set1C complexes, there are considerable differences in contributions to H3K4me by several individual subunits. Furthermore, unlike a recent report in S. cerevisiae, the abundance of Set1 proteins in S. pombe is generally not coupled to either the status of H3K4 methylation or H2B ubiquitination, further highlighting critical differences in Set1 regulation between the two yeast species. We describe a role for the Set1C complex in the nuclear organization of dispersed retrotransposons into Tf bodies. Set1C maintains Tf body integrity by employing H3K4me to antagonize the activities of the H3K4 acetyltransferase Mst1. Collectively, our findings dramatically expand the regulatory landscape controlled by the Set1C complex, an important and highly conserved chromatin-modifying complex with diverse roles in genome control and development.
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Affiliation(s)
- Irina V. Mikheyeva
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Patrick J. R. Grady
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Fiona B. Tamburini
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - David R. Lorenz
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Hugh P. Cam
- Biology Department, Boston College, Chestnut Hill, Massachusetts, United States of America
- * E-mail:
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Histone H3 lysine 4 trimethylation regulates cotranscriptional H2A variant exchange by Tip60 complexes to maximize gene expression. Proc Natl Acad Sci U S A 2014; 111:4850-5. [PMID: 24639513 DOI: 10.1073/pnas.1320337111] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) and the acetylated H2A variant, H2A.Z/v (H2Avac), are enriched at promoters of highly transcribed loci including the stress response genes. Using the inducible Drosophila hsp70 loci as a model, we study here the roles of the dSet1 and dTip60 complexes in the generation of these two chromatin modifications. We find that Heat Shock Factor recruits the dTip60 complex to the hsp70 loci in cells treated with salicylate, which triggers chromatin remodeling at these loci without transcription activation. Under these conditions, H2Avac or H3K4me3 are not enriched at the hsp70 promoter. By contrast, heat shock-induced hsp70 transcription induces dSet1-dependent H3K4me3 and H2Avac deposition by the dTip60 complex. The loss of dSet1 or dTip60 abolishes H2Avac incorporation, impairs Pol II release from the hsp70 promoter, and causes a stalling of mRNA production during phases of transcription maximization. Biochemical assays confirm that nucleosomal H3K4me3 stimulates the histone acetyltransferase and H2Av exchange activities of dTip60 complexes. H2Avac contributes to nucleosome destabilization at promoters, and H3K4me3 restricts its incorporation to phases of acute transcription. The process uncouples cotranscriptional chromatin remodeling by dTip60 complexes from their role in the activation of PARP, which is responsible for the removal of transcription-incompatible or damaged chromatin during the initial stress response. The control of the multifunctional dTip60 complex by H3K4me3 ensures optimal stress response and cell survival by mediating the rapid maximization of hsp70 expression. Furthermore, this mechanism prevents the accumulation of epigenetic noise caused by random complex-nucleosome collisions.
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