1
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Ouyang Z, Liu F, Li W, Wang J, Chen B, Zheng Y, Li Y, Tao H, Xu X, Li C, Cong Y, Li H, Bo X, Chen H. The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model. Nucleic Acids Res 2024; 52:7610-7626. [PMID: 38813828 PMCID: PMC11260490 DOI: 10.1093/nar/gkae441] [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: 01/22/2024] [Revised: 04/26/2024] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Gene expression is temporally and spatially regulated by the interaction of transcription factors (TFs) and cis-regulatory elements (CREs). The uneven distribution of TF binding sites across the genome poses challenges in understanding how this distribution evolves to regulate spatio-temporal gene expression and consequent heritable phenotypic variation. In this study, chromatin accessibility profiles and gene expression profiles were collected from several species including mammals (human, mouse, bovine), fish (zebrafish and medaka), and chicken. Transcription factor binding sites clustered regions (TFCRs) at different embryonic stages were characterized to investigate regulatory evolution. The study revealed dynamic changes in TFCR distribution during embryonic development and species evolution. The synchronization between TFCR complexity and gene expression was assessed across species using RegulatoryScore. Additionally, an explainable machine learning model highlighted the importance of the distance between TFCR and promoter in the coordinated regulation of TFCRs on gene expression. Our results revealed the developmental and evolutionary dynamics of TFCRs during embryonic development from fish, chicken to mammals. These data provide valuable resources for exploring the relationship between transcriptional regulation and phenotypic differences during embryonic development.
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Affiliation(s)
- Zhangyi Ouyang
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Feng Liu
- College of Medical Informatics, Chongqing Medical University, Chongqing 400016, China
| | - Wanying Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Junting Wang
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Bijia Chen
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Yang Zheng
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Yaru Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Huan Tao
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiang Xu
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Yuwen Cong
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hao Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiaochen Bo
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hebing Chen
- Academy of Military Medical Sciences, Beijing 100850, China
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2
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Kealy L, Runting J, Thiele D, Scheer S. An emerging maestro of immune regulation: how DOT1L orchestrates the harmonies of the immune system. Front Immunol 2024; 15:1385319. [PMID: 38962004 PMCID: PMC11219580 DOI: 10.3389/fimmu.2024.1385319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/04/2024] [Indexed: 07/05/2024] Open
Abstract
The immune system comprises a complex yet tightly regulated network of cells and molecules that play a critical role in protecting the body from infection and disease. The activity and development of each immune cell is regulated in a myriad of ways including through the cytokine milieu, the availability of key receptors, via tailored intracellular signalling cascades, dedicated transcription factors and even by directly modulating gene accessibility and expression; the latter is more commonly known as epigenetic regulation. In recent years, epigenetic regulators have begun to emerge as key players involved in modulating the immune system. Among these, the lysine methyltransferase DOT1L has gained significant attention for its involvement in orchestrating immune cell formation and function. In this review we provide an overview of the role of DOT1L across the immune system and the implications of this role on health and disease. We begin by elucidating the general mechanisms of DOT1L-mediated histone methylation and its impact on gene expression within immune cells. Subsequently, we provide a detailed and comprehensive overview of recent studies that identify DOT1L as a crucial regulator of immune cell development, differentiation, and activation. Next, we discuss the potential mechanisms of DOT1L-mediated regulation of immune cell function and shed light on how DOT1L might be contributing to immune cell homeostasis and dysfunction. We then provide food for thought by highlighting some of the current obstacles and technical limitations precluding a more in-depth elucidation of DOT1L's role. Finally, we explore the potential therapeutic implications of targeting DOT1L in the context of immune-related diseases and discuss ongoing research efforts to this end. Overall, this review consolidates the current paradigm regarding DOT1L's role across the immune network and emphasises its critical role in governing the healthy immune system and its potential as a novel therapeutic target for immune-related diseases. A deeper understanding of DOT1L's immunomodulatory functions could pave the way for innovative therapeutic approaches which fine-tune the immune response to enhance or restore human health.
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Affiliation(s)
- Liam Kealy
- Immunity Program, The Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jessica Runting
- Immunity Program, The Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Daniel Thiele
- Immunity Program, The Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sebastian Scheer
- Immunity Program, The Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
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3
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Cuamatzi-Flores J, Colón-González M, Requena-Romo F, Quiñones-Galeana S, Cervantes-Chávez JA, Morales L. Enhanced oxidative stress resistance in Ustilago maydis and its implications on the virulence. Int Microbiol 2024:10.1007/s10123-024-00489-8. [PMID: 38401003 DOI: 10.1007/s10123-024-00489-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/26/2024]
Abstract
The phytopathogenic fungus Ustilago maydis causes corn smut by suppressing host plant defenses, including the oxidative burst response. While many studies have investigated how U. maydis responds to oxidative stress during infection, the consequences of heightened resistance to oxidative stress on virulence remain understudied. This study aimed to identify the effects on virulence in U. maydis strains exhibiting enhanced resistance to hydrogen peroxide (H2O2).To achieve this, we exposed U. maydis SG200 to 20 escalating H2O2 shocks, resulting in an adapted strain resistant to concentrations as high as 60 mM of H2O2, a lethal dose for the initial strain. Genetic analysis of the adapted strain revealed five nucleotide substitutions, two minor copy number variants, and a large amplification event on chromosome nine (1-149 kb) encompassing the sole catalase gene. Overexpressing catalase increased resistance to H2O2; however, this resistance was lower than that observed in the adapted strain. Additionally, virulence was reduced in both strains with enhanced H2O2 resistance.In summary, enhanced H2O2 resistance, achieved through either continuous exposure to the oxidative agent or through catalase overexpression, decreased virulence. This suggests that the response to the oxidative stress burst in U. maydis is optimal and that increasing the resistance to H2O2 does not translate into increased virulence. These findings illuminate the intricate relationship between oxidative stress resistance and virulence in U. maydis, offering insights into its infection mechanisms.
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Affiliation(s)
- Jorge Cuamatzi-Flores
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Queretaro, 76230, Querétaro, México.
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, 76230, Querétaro, México.
| | - Maritrini Colón-González
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, 76230, Querétaro, México
| | - Fernanda Requena-Romo
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, 76230, Querétaro, México
- Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, 76230, Querétaro, México
| | - Samuel Quiñones-Galeana
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, 76230, Querétaro, México
- Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, 76230, Querétaro, México
| | - José Antonio Cervantes-Chávez
- Unit for Basic and Applied Microbiology, Faculty of Natural Sciences, Autonomous University of Queretaro, 76230, Querétaro, México.
| | - Lucia Morales
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, 76230, Querétaro, México.
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4
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Robert F, Jeronimo C. Transcription-coupled nucleosome assembly. Trends Biochem Sci 2023; 48:978-992. [PMID: 37657993 DOI: 10.1016/j.tibs.2023.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
Abstract
Eukaryotic transcription occurs on chromatin, where RNA polymerase II encounters nucleosomes during elongation. These nucleosomes must unravel for the DNA to enter the active site. However, in most transcribed genes, nucleosomes remain intact due to transcription-coupled chromatin assembly mechanisms. These mechanisms primarily involve the local reassembly of displaced nucleosomes to prevent (epi)genomic instability and the emergence of cryptic transcription. As a fail-safe mechanism, cells can assemble nucleosomes de novo, particularly in highly transcribed genes, but this may result in the loss of epigenetic information. This review examines transcription-coupled chromatin assembly, with an emphasis on studies in yeast and recent structural studies. These studies shed light on how elongation factors and histone chaperones coordinate to enable nucleosome recycling during transcription.
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Affiliation(s)
- François Robert
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Département de Médecine, Faculté de Médecine, Université de Montréal, 2900 Boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Canada; Faculty of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC H3A 1A3, Canada.
| | - Célia Jeronimo
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
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5
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Fields JK, Hicks CW, Wolberger C. Diverse modes of regulating methyltransferase activity by histone ubiquitination. Curr Opin Struct Biol 2023; 82:102649. [PMID: 37429149 PMCID: PMC10527252 DOI: 10.1016/j.sbi.2023.102649] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/29/2023] [Accepted: 06/11/2023] [Indexed: 07/12/2023]
Abstract
Post-translational modification of histones plays a central role in regulating transcription. Methylation of histone H3 at lysines 4 (H3K4) and 79 (H3K79) play roles in activating transcription whereas methylation of H3K27 is a repressive mark. These modifications, in turn, depend upon prior monoubiquitination of specific histone residues in a phenomenon known as histone crosstalk. Earlier work had provided insights into the mechanism by which monoubiquitination histone H2BK120 stimulates H3K4 methylation by COMPASS/MLL1 and H3K79 methylation by DOT1L, and monoubiquitinated H2AK119 stimulates methylation of H3K27 by the PRC2 complex. Recent studies have shed new light on the role of individual subunits and paralogs in regulating the activity of PRC2 and how additional post-translational modifications regulate yeast Dot1 and human DOT1L, as well as provided new insights into the regulation of MLL1 by H2BK120ub.
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Affiliation(s)
- James K Fields
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Chad W Hicks
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
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6
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Zhao X, Li X, Sun H, Zhao X, Gao T, Shi P, Chen F, Liu L, Lu X. Dot1l cooperates with Npm1 to repress endogenous retrovirus MERVL in embryonic stem cells. Nucleic Acids Res 2023; 51:8970-8986. [PMID: 37522386 PMCID: PMC10516645 DOI: 10.1093/nar/gkad640] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/06/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023] Open
Abstract
Dot1l is a histone methyltransferase without a SET domain and is responsible for H3K79 methylation, which marks active transcription. In contradiction, Dot1l also participates in silencing gene expression. The target regions and mechanism of Dot1l in repressing transcription remain enigmatic. Here, we show that Dot1l represses endogenous retroviruses in embryonic stem cells (ESCs). Specifically, the absence of Dot1l led to the activation of MERVL, which is a marker of 2-cell-like cells. In addition, Dot1l deletion activated the 2-cell-like state and predisposed ESCs to differentiate into trophectoderm lineage. Transcriptome analysis revealed activation of 2-cell genes and meiotic genes by Dot1l deletion. Mechanistically, Dot1l interacted with and co-localized with Npm1 on MERVL, and depletion of Npm1 similarly augmented MERVL expression. The catalytic activity and AT-hook domain of Dot1l are important to suppress MERVL. Notably, Dot1l-Npm1 restricts MERVL by regulating protein level and deposition of histone H1. Furthermore, Dot1l is critical for Npm1 to efficiently interact with histone H1 and inhibit ubiquitination of H1 whereas Npm1 is essential for Dot1l to interact with MERVL. Altogether, we discover that Dot1l represses MERVL through chaperoning H1 by collaborating with Npm1. Importantly, our findings shed light on the non-canonical transcriptional repressive role of Dot1l in ESCs.
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Affiliation(s)
- Xin Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
| | - Xiaomin Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
| | - Haiyang Sun
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
| | - Xuan Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
| | - Tingting Gao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
| | - Panpan Shi
- State Key Laboratory of Medicinal Chemical Biology, College of Life Science, Nankai University, Tianjin, Tianjin 300071, China
| | - Fuquan Chen
- State Key Laboratory of Medicinal Chemical Biology, College of Life Science, Nankai University, Tianjin, Tianjin 300071, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Science, Nankai University, Tianjin, Tianjin 300071, China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, Tianjin 300350, China
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7
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Tsirigka A, Theodosiou E, Patsios SI, Tsoureki A, Andreadelli A, Papa E, Aggeli A, Karabelas AJ, Makris AM. Novel evolved Yarrowia lipolytica strains for enhanced growth and lipid content under high concentrations of crude glycerol. Microb Cell Fact 2023; 22:62. [PMID: 37004109 PMCID: PMC10067222 DOI: 10.1186/s12934-023-02072-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023] Open
Abstract
BACKGROUND Yarrowia lipolytica is a well-studied oleaginous yeast known for its ability to accumulate and store intracellular lipids, while growing on diverse, non-conventional substrates. Amongst them, crude glycerol, a low-cost by-product of the biodiesel industry, appears to be an interesting option for scaling up a sustainable single-cell oil production process. Adaptive laboratory evolution (ALE) is a powerful tool to force metabolic adaptations endowing tolerance to stressful environmental conditions, generating superior phenotypes with industrial relevance. RESULTS Y. lipolytica MUCL 28849 underwent ALE in a synthetic medium with increasing concentration of pure or crude glycerol as a stressing factor (9-20% v/v) for 520 generations. In one case of pure glycerol, chemical mutagenesis with ethyl methanesulfonate (EMS) was applied prior to ALE. Growth profile, biomass production and lipid content of 660 evolved strains (EVS), revealed 5 superior isolates; exhibiting from 1.9 to 3.6-fold increase of dry biomass and from 1.1 to 1.6-fold increase of lipid concentration compared to the parental strain, when grown in 15% v/v crude glycerol. NGS for differential gene expression analysis, showed induced expression in all EVS affecting nucleosomal structure and regulation of transcription. As strains differentiated, further changes accumulated in membrane transport and protein transport processes. Genes involved in glycerol catabolism and triacylglycerol biosynthesis were overexpressed in two EVS. Mismatches and gaps in the expressed sequences identified altered splicing and mutations in the EVS, with most of them, affecting different components of septin ring formation in the budding process. The selected YLE155 EVS, used for scale-up cultivation in a 3L benchtop bioreactor with 20% v/v crude glycerol, achieved extended exponential phase, twofold increase of dry biomass and lipid yields at 48 h, while citric acid secretion and glycerol consumption rates were 40% and 50% lower, respectively, compared to the parental strain, after 24 h of cultivation. CONCLUSION ALE and EMS-ALE under increasing concentrations of pure or crude glycerol generated novel Y. lipolytica strains with enhanced biomass and lipid content. Differential gene expression analysis and scale-up of YLE155, illustrated the potential of the evolved strains to serve as suitable "chassis" for rational engineering approaches towards both increased lipid accumulation, and production of high-added value compounds, through efficient utilization of crude glycerol.
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Affiliation(s)
- Asimina Tsirigka
- Laboratory of Natural Resources and Renewable Energies, Chemical Process and Energy Resources Institute, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
- Department of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Theodosiou
- Institute of Applied Biosciences, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
| | - Sotiris I Patsios
- Laboratory of Natural Resources and Renewable Energies, Chemical Process and Energy Resources Institute, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
| | - Antiopi Tsoureki
- Institute of Applied Biosciences, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
| | - Aggeliki Andreadelli
- Institute of Applied Biosciences, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
| | - Elisavet Papa
- Institute of Applied Biosciences, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Amalia Aggeli
- Department of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anastasios J Karabelas
- Laboratory of Natural Resources and Renewable Energies, Chemical Process and Energy Resources Institute, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece
| | - Antonios M Makris
- Institute of Applied Biosciences, Centre for Research and Technology - Hellas, Thermi, Thessaloniki, Greece.
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8
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Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon M, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ. Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.533220. [PMID: 36993485 PMCID: PMC10055266 DOI: 10.1101/2023.03.17.533220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The intricate regulation of chromatin plays a key role in controlling genome architecture and accessibility. Histone lysine methyltransferases regulate chromatin by catalyzing the methylation of specific histone residues but are also hypothesized to have equally important non-catalytic roles. SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation, and is dysregulated in several cancers. Many of these processes were linked to its catalytic activity. However, deletion and inhibition of SUV420H1 have shown distinct phenotypes suggesting the enzyme likely has uncharacterized non-catalytic activities. To characterize the catalytic and non-catalytic mechanisms SUV420H1 uses to modify chromatin, we determined cryo- EM structures of SUV420H1 complexes with nucleosomes containing histone H2A or its variant H2A.Z. Our structural, biochemical, biophysical, and cellular analyses reveal how both SUV420H1 recognizes its substrate and H2A.Z stimulates its activity, and show that SUV420H1 binding to nucleosomes causes a dramatic detachment of nucleosomal DNA from histone octamer. We hypothesize that this detachment increases DNA accessibility to large macromolecular complexes, a prerequisite for DNA replication and repair. We also show that SUV420H1 can promote chromatin condensates, another non-catalytic role that we speculate is needed for its heterochromatin functions. Together, our studies uncover and characterize the catalytic and non-catalytic mechanisms of SUV420H1, a key histone methyltransferase that plays an essential role in genomic stability.
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Affiliation(s)
- Stephen Abini-Agbomson
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Kristjan Gretarsson
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Rochelle M. Shih
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Laura Hsieh
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Tracy Lou
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Pablo De Ioannes
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Rachel Lee
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Miao Wang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
| | - Matthew Simon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Geeta Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Shixin Liu
- Laboratory of Nanoscale Biophysics and Biochemistry, The Rockefeller University, New York, NY, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
| | - Karim-Jean Armache
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Lead contact
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9
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He F, Yu Q, Wang M, Wang R, Gong X, Ge F, Yu X, Li S. SESAME-catalyzed H3T11 phosphorylation inhibits Dot1-catalyzed H3K79me3 to regulate autophagy and telomere silencing. Nat Commun 2022; 13:7526. [PMID: 36473858 PMCID: PMC9726891 DOI: 10.1038/s41467-022-35182-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
The glycolytic enzyme, pyruvate kinase Pyk1 maintains telomere heterochromatin by phosphorylating histone H3T11 (H3pT11), which promotes SIR (silent information regulator) complex binding at telomeres and prevents autophagy-mediated Sir2 degradation. However, the exact mechanism of action for H3pT11 is poorly understood. Here, we report that H3pT11 directly inhibits Dot1-catalyzed H3K79 tri-methylation (H3K79me3) and uncover how this histone crosstalk regulates autophagy and telomere silencing. Mechanistically, Pyk1-catalyzed H3pT11 directly reduces the binding of Dot1 to chromatin and inhibits Dot1-catalyzed H3K79me3, which leads to transcriptional repression of autophagy genes and reduced autophagy. Despite the antagonism between H3pT11 and H3K79me3, they work together to promote the binding of SIR complex at telomeres to maintain telomere silencing. Furthermore, we identify Reb1 as a telomere-associated factor that recruits Pyk1-containing SESAME (Serine-responsive SAM-containing Metabolic Enzyme) complex to telomere regions to phosphorylate H3T11 and prevent the invasion of H3K79me3 from euchromatin into heterochromatin to maintain telomere silencing. Together, these results uncover a histone crosstalk and provide insights into dynamic regulation of silent heterochromatin and autophagy in response to cell metabolism.
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Affiliation(s)
- Fei He
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062 China
| | - Qi Yu
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062 China
| | - Min Wang
- grid.9227.e0000000119573309Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 China
| | - Rongsha Wang
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062 China
| | - Xuanyunjing Gong
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062 China
| | - Feng Ge
- grid.9227.e0000000119573309Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072 China
| | - Xilan Yu
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062 China
| | - Shanshan Li
- grid.34418.3a0000 0001 0727 9022State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei 430062 China
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10
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Cheng Y, Chen Y, Wang G, Liu P, Xie G, Jing H, Chen H, Fan Y, Wang M, Zhou J. Protein Methylation in Diabetic Kidney Disease. Front Med (Lausanne) 2022; 9:736006. [PMID: 35647002 PMCID: PMC9133329 DOI: 10.3389/fmed.2022.736006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic kidney disease (CKD) is defined by persistent urine aberrations, structural abnormalities, or impaired excretory renal function. Diabetes is the leading cause of CKD. Their common pathological manifestation is renal fibrosis. Approximately half of all patients with type 2 diabetes and one-third with type 1 diabetes will develop CKD. However, renal fibrosis mechanisms are still poorly understood, especially post-transcriptional and epigenetic regulation. And an unmet need remains for innovative treatment strategies for preventing, arresting, treating, and reversing diabetic kidney disease (DKD). People believe that protein methylation, including histone and non-histone, is an essential type of post-translational modification (PTM). However, prevalent reviews mainly focus on the causes such as DNA methylation. This review will take insights into the protein part. Furthermore, by emphasizing the close relationship between protein methylation and DKD, we will summarize the clinical research status and foresee the application prospect of protein methyltransferase (PMT) inhibitors in DKD treatment. In a nutshell, our review will contribute to a more profound understanding of DKD’s molecular mechanism and inspire people to dig into this field.
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Affiliation(s)
- Ye Cheng
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Yanna Chen
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Guodong Wang
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Pei Liu
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Guiling Xie
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Huan Jing
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Hongtao Chen
- Department of Anesthesiology, The Eighth People’s Hospital of Guangzhou, Guangzhou, China
| | - Youlin Fan
- Department of Anesthesiology, Guangzhou Panyu Central Hospital of Panyu District, Guangzhou, China
| | - Min Wang
- Department of Anesthesiology, The Gaoming People’s Hospital, Foshan, China
| | - Jun Zhou
- Department of Anesthesiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- *Correspondence: Jun Zhou,
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11
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Selvam K, Plummer DA, Mao P, Wyrick JJ. Set2 histone methyltransferase regulates transcription coupled-nucleotide excision repair in yeast. PLoS Genet 2022; 18:e1010085. [PMID: 35263330 PMCID: PMC8936446 DOI: 10.1371/journal.pgen.1010085] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 03/21/2022] [Accepted: 02/08/2022] [Indexed: 12/17/2022] Open
Abstract
Helix-distorting DNA lesions, including ultraviolet (UV) light-induced damage, are repaired by the global genomic-nucleotide excision repair (GG-NER) and transcription coupled-nucleotide excision repair (TC-NER) pathways. Previous studies have shown that histone post-translational modifications (PTMs) such as histone acetylation and methylation can promote GG-NER in chromatin. Whether histone PTMs also regulate the repair of DNA lesions by the TC-NER pathway in transcribed DNA is unknown. Here, we report that histone H3 K36 methylation (H3K36me) by the Set2 histone methyltransferase in yeast regulates TC-NER. Mutations in Set2 or H3K36 result in UV sensitivity that is epistatic with Rad26, the primary TC-NER factor in yeast, and cause a defect in the repair of UV damage across the yeast genome. We further show that mutations in Set2 or H3K36 in a GG-NER deficient strain (i.e., rad16Δ) partially rescue its UV sensitivity. Our data indicate that deletion of SET2 rescues UV sensitivity in a GG-NER deficient strain by activating cryptic antisense transcription, so that the non-transcribed strand (NTS) of yeast genes is repaired by TC-NER. These findings indicate that Set2 methylation of H3K36 establishes transcriptional asymmetry in repair by promoting canonical TC-NER of the transcribed strand (TS) and suppressing cryptic TC-NER of the NTS.
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Affiliation(s)
- Kathiresan Selvam
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Dalton A. Plummer
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
| | - Peng Mao
- Department of Internal Medicine, Program in Cellular and Molecular Oncology, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico, United States of America
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States of America
- Center for Reproductive Biology, Washington State University, Pullman, Washington, United States of America
- * E-mail:
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12
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13
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Malcom CA, Ratri A, Piasecka-Srader J, Borosha S, Chakravarthi VP, Alvarez NS, Vivian JL, Fields TA, Karim Rumi M, Fields PE. Primitive Erythropoiesis in the Mouse is Independent of DOT1L Methyltransferase Activity. Front Cell Dev Biol 2022; 9:813503. [PMID: 35111761 PMCID: PMC8802720 DOI: 10.3389/fcell.2021.813503] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/07/2021] [Indexed: 12/27/2022] Open
Abstract
DOT1-like (DOT1L) histone methyltransferase is essential for mammalian erythropoiesis. Loss of DOT1L in knockout (Dot1l-KO) mouse embryos resulted in lethal anemia at midgestational age. The only recognized molecular function of DOT1L is its methylation of histone H3 lysine 79 (H3K79). We generated a Dot1l methyltransferase mutant (Dot1l-MM) mouse model to determine the role of DOT1L methyltransferase activity in early embryonic hematopoiesis. Dot1l-MM embryos failed to survive beyond embryonic day 13.5 (E13.5), similarly to Dot1l-KO mice. However, when examined at E10.5, Dot1l-MM embryos did not exhibit overt anemia like the Dot1l-KO. Vascularity and the presence of red blood cells in the Dot1l-MM yolk sacs as well as in the AGM region of Dot1l-MM embryos appeared to be similar to that of wildtype. In ex vivo cultures of yolk sac cells, Dot1l-MM primitive erythroblasts formed colonies comparable to those of the wildtype. Although ex vivo cultures of Dot1l-MM definitive erythroblasts formed relatively smaller colonies, inhibition of DOT1L methyltransferase activity in vivo by administration of EPZ-5676 minimally affected the erythropoiesis. Our results indicate that early embryonic erythropoiesis in mammals requires a DOT1L function that is independent of its intrinsic methyltransferase activity.
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14
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Bonitto K, Sarathy K, Atai K, Mitra M, Coller HA. Is There a Histone Code for Cellular Quiescence? Front Cell Dev Biol 2021; 9:739780. [PMID: 34778253 PMCID: PMC8586460 DOI: 10.3389/fcell.2021.739780] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022] Open
Abstract
Many of the cells in our bodies are quiescent, that is, temporarily not dividing. Under certain physiological conditions such as during tissue repair and maintenance, quiescent cells receive the appropriate stimulus and are induced to enter the cell cycle. The ability of cells to successfully transition into and out of a quiescent state is crucial for many biological processes including wound healing, stem cell maintenance, and immunological responses. Across species and tissues, transcriptional, epigenetic, and chromosomal changes associated with the transition between proliferation and quiescence have been analyzed, and some consistent changes associated with quiescence have been identified. Histone modifications have been shown to play a role in chromatin packing and accessibility, nucleosome mobility, gene expression, and chromosome arrangement. In this review, we critically evaluate the role of different histone marks in these processes during quiescence entry and exit. We consider different model systems for quiescence, each of the most frequently monitored candidate histone marks, and the role of their writers, erasers and readers. We highlight data that support these marks contributing to the changes observed with quiescence. We specifically ask whether there is a quiescence histone “code,” a mechanism whereby the language encoded by specific combinations of histone marks is read and relayed downstream to modulate cell state and function. We conclude by highlighting emerging technologies that can be applied to gain greater insight into the role of a histone code for quiescence.
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Affiliation(s)
- Kenya Bonitto
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kirthana Sarathy
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kaiser Atai
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Interdepartmental Doctoral Program, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Mithun Mitra
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Hilary A Coller
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, United States
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15
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Kwesi-Maliepaard EM, Jacobs H, van Leeuwen F. Signals for antigen-independent differentiation of memory CD8 + T cells. Cell Mol Life Sci 2021; 78:6395-6408. [PMID: 34398252 PMCID: PMC8558200 DOI: 10.1007/s00018-021-03912-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/23/2021] [Accepted: 08/03/2021] [Indexed: 12/18/2022]
Abstract
Conventional CD8+ memory T cells develop upon stimulation with foreign antigen and provide increased protection upon re-challenge. Over the past two decades, new subsets of CD8+ T cells have been identified that acquire memory features independently of antigen exposure. These antigen-inexperienced memory T cells (TAIM) are described under several names including innate memory, virtual memory, and memory phenotype. TAIM cells exhibit characteristics of conventional or true memory cells, including antigen-specific responses. In addition, they show responsiveness to innate stimuli and have been suggested to provide additional levels of protection toward infections and cancer. Here, we discuss the current understanding of TAIM cells, focusing on extrinsic and intrinsic molecular conditions that favor their development, their molecular definitions and immunological properties, as well as their transcriptional and epigenetic regulation.
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Affiliation(s)
| | - Heinz Jacobs
- Division of Tumor Biology and Immunology, Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX, Amsterdam, The Netherlands.
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, 1105AZ, Amsterdam, The Netherlands.
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16
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Valencia-Sánchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ. Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation. Science 2021; 371:371/6527/eabc6663. [PMID: 33479126 DOI: 10.1126/science.abc6663] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/27/2020] [Indexed: 12/30/2022]
Abstract
Dot1 (disruptor of telomeric silencing-1), the histone H3 lysine 79 (H3K79) methyltransferase, is conserved throughout evolution, and its deregulation is found in human leukemias. Here, we provide evidence that acetylation of histone H4 allosterically stimulates yeast Dot1 in a manner distinct from but coordinating with histone H2B ubiquitination (H2BUb). We further demonstrate that this stimulatory effect is specific to acetylation of lysine 16 (H4K16ac), a modification central to chromatin structure. We provide a mechanism of this histone cross-talk and show that H4K16ac and H2BUb play crucial roles in H3K79 di- and trimethylation in vitro and in vivo. These data reveal mechanisms that control H3K79 methylation and demonstrate how H4K16ac, H3K79me, and H2BUb function together to regulate gene transcription and gene silencing to ensure optimal maintenance and propagation of an epigenetic state.
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Affiliation(s)
- Marco Igor Valencia-Sánchez
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Pablo De Ioannes
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Miao Wang
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - David M Truong
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA
| | - Rachel Lee
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jef D Boeke
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
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17
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DOT1L-controlled cell-fate determination and transcription elongation are independent of H3K79 methylation. Proc Natl Acad Sci U S A 2020; 117:27365-27373. [PMID: 33077595 DOI: 10.1073/pnas.2001075117] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Actively transcribed genes in mammals are decorated by H3K79 methylation, which is correlated with transcription levels and is catalyzed by the histone methyltransferase DOT1L. DOT1L is required for mammalian development, and the inhibition of its catalytic activity has been extensively studied for cancer therapy; however, the mechanisms underlying DOT1L's functions in normal development and cancer pathogenesis remain elusive. To dissect the relationship between H3K79 methylation, cellular differentiation, and transcription regulation, we systematically examined the role of DOT1L and its catalytic activity in embryonic stem cells (ESCs). DOT1L is dispensable for ESC self-renewal but is required for establishing the proper expression signature of neural progenitor cells, while catalytic inactivation of DOT1L has a lesser effect. Furthermore, DOT1L loss, rather than its catalytic inactivation, causes defects in glial cell specification. Although DOT1L loss by itself has no major defect in transcription elongation, transcription elongation defects seen with the super elongation complex inhibitor KL-2 are exacerbated in DOT1L knockout cells, but not in catalytically dead DOT1L cells, revealing a role of DOT1L in promoting productive transcription elongation that is independent of H3K79 methylation. Taken together, our study reveals a catalytic-independent role of DOT1L in modulating cell-fate determination and in transcriptional elongation control.
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18
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Goodnight D, Rine J. S-phase-independent silencing establishment in Saccharomyces cerevisiae. eLife 2020; 9:58910. [PMID: 32687055 PMCID: PMC7398696 DOI: 10.7554/elife.58910] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/18/2020] [Indexed: 02/06/2023] Open
Abstract
The establishment of silent chromatin, a heterochromatin-like structure at HML and HMR in Saccharomyces cerevisiae, depends on progression through S phase of the cell cycle, but the molecular nature of this requirement has remained elusive despite intensive study. Using high-resolution chromatin immunoprecipitation and single-molecule RNA analysis, we found that silencing establishment proceeded via gradual repression of transcription in individual cells over several cell cycles, and that the cell-cycle-regulated step was downstream of Sir protein recruitment. In contrast to prior results, HML and HMR had identical cell-cycle requirements for silencing establishment, with no apparent contribution from a tRNA gene adjacent to HMR. We identified the cause of the S-phase requirement for silencing establishment: removal of transcription-favoring histone modifications deposited by Dot1, Sas2, and Rtt109. These results revealed that silencing establishment was absolutely dependent on the cell-cycle-regulated interplay between euchromatic and heterochromatic histone modifications.
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Affiliation(s)
- Davis Goodnight
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Jasper Rine
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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19
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Nunes VS, Moretti NS, da Silva MS, Elias MC, Janzen CJ, Schenkman S. Trimethylation of histone H3K76 by Dot1B enhances cell cycle progression after mitosis in Trypanosoma cruzi. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118694. [PMID: 32151656 DOI: 10.1016/j.bbamcr.2020.118694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 12/11/2022]
Abstract
Dot1 enzymes are histone methyltransferases that mono-, di- and trimethylate lysine 79 of histone H3 to affect several nuclear processes. The functions of these different methylation states are still largely unknown. Trypanosomes, which are flagellated protozoa that cause several parasitic diseases, have two Dot1 homologues. Dot1A catalyzes the mono- and dimethylation of lysine 76 during late G2 and mitosis, and Dot1B catalyzes trimethylation, which is a modification found in all stages of the cell cycle. Here, we generated Trypanosoma cruzi lines lacking Dot1B. Deletion of one allele resulted in parasites with increased levels of mono- and dimethylation and a reduction in H3K76me3. In the full knockout (DKO), no trimethylation was observed. Both the DKO and the single knockout (SKO) showed aberrant morphology and decreased growth due to cell cycle arrest after G2. This phenotype could be rescued by caffeine in the DKO, as caffeine is a checkpoint inhibitor of the cell cycle. The knockouts also phosphorylated γH2A without producing extensive DNA breaks, and Dot1B-depleted cells were more susceptible to general checkpoint kinase inhibitors, suggesting that a lack of H3K76 trimethylation prevents the initiation and/or completion of cytokinesis.
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Affiliation(s)
- Vinicius Santana Nunes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil; Centro de Ensino, Pesquisa e Inovação, Hospital Evangélico de Vila Velha, 29118-060 Vila Velha, ES, Brazil
| | - Nilmar Silvio Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil
| | | | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - Christian J Janzen
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil.
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20
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Salgado C, Kwesi-Maliepaard EM, Jochemsen AG, Visser M, Harland M, van Leeuwen F, van Doorn R, Gruis N. A novel germline variant in the DOT1L gene co-segregating in a Dutch family with a history of melanoma. Melanoma Res 2019; 29:582-589. [DOI: 10.1097/cmr.0000000000000640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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21
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Li R, Wei X, Jiang DS. Protein methylation functions as the posttranslational modification switch to regulate autophagy. Cell Mol Life Sci 2019; 76:3711-3722. [PMID: 31222372 PMCID: PMC11105718 DOI: 10.1007/s00018-019-03161-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 05/10/2019] [Accepted: 05/28/2019] [Indexed: 02/07/2023]
Abstract
Studies over the past decades have elucidated the critical role of autophagy in human health and diseases. Although the processes of autophagy in the cytoplasm have been well studied, the posttranscriptional and epigenetic regulation mechanisms of autophagy are still poorly understood. Protein methylation, including histone methylation and non-histone protein methylation, is the most important type of posttranscriptional and epigenetic modification. Recent studies have shown that protein methylation is associated with effects on autophagosome formation, autophagy-related protein expression, and signaling pathway activation, but the details are still unclear. Thus, it is important to summarize the current status and discuss the future directions of research on protein methylation in the context of autophagy.
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Affiliation(s)
- Rui Li
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave., Wuhan, 430030, China
| | - Xiang Wei
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave., Wuhan, 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China
- NHC Key Laboratory of Organ Transplantation, Ministry of Health, Wuhan, China
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Ding-Sheng Jiang
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Ave., Wuhan, 430030, China.
- Key Laboratory of Organ Transplantation, Ministry of Education, Wuhan, China.
- NHC Key Laboratory of Organ Transplantation, Ministry of Health, Wuhan, China.
- Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China.
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22
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Vlaming H, McLean CM, Korthout T, Alemdehy MF, Hendriks S, Lancini C, Palit S, Klarenbeek S, Kwesi‐Maliepaard EM, Molenaar TM, Hoekman L, Schmidlin TT, Altelaar AFM, van Welsem T, Dannenberg J, Jacobs H, van Leeuwen F. Conserved crosstalk between histone deacetylation and H3K79 methylation generates DOT1L-dose dependency in HDAC1-deficient thymic lymphoma. EMBO J 2019; 38:e101564. [PMID: 31304633 PMCID: PMC6627229 DOI: 10.15252/embj.2019101564] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/20/2019] [Accepted: 05/24/2019] [Indexed: 12/12/2022] Open
Abstract
DOT1L methylates histone H3K79 and is aberrantly regulated in MLL-rearranged leukemia. Inhibitors have been developed to target DOT1L activity in leukemia, but cellular mechanisms that regulate DOT1L are still poorly understood. We have identified the histone deacetylase Rpd3 as a negative regulator of budding yeast Dot1. At its target genes, the transcriptional repressor Rpd3 restricts H3K79 methylation, explaining the absence of H3K79me3 at a subset of genes in the yeast genome. Similar to the crosstalk in yeast, inactivation of the murine Rpd3 homolog HDAC1 in thymocytes led to an increase in H3K79 methylation. Thymic lymphomas that arise upon genetic deletion of Hdac1 retained the increased H3K79 methylation and were sensitive to reduced DOT1L dosage. Furthermore, cell lines derived from Hdac1Δ/Δ thymic lymphomas were sensitive to a DOT1L inhibitor, which induced apoptosis. In summary, we identified an evolutionarily conserved crosstalk between HDAC1 and DOT1L with impact in murine thymic lymphoma development.
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Affiliation(s)
- Hanneke Vlaming
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
- Present address:
Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMAUSA
| | - Chelsea M McLean
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tessy Korthout
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Mir Farshid Alemdehy
- Division of Tumor Biology & ImmunologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sjoerd Hendriks
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Cesare Lancini
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sander Palit
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Sjoerd Klarenbeek
- Experimental Animal PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | | | - Thom M Molenaar
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Liesbeth Hoekman
- Experimental Animal PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Thierry T Schmidlin
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular ResearchUtrecht Institute for Pharmaceutical SciencesUtrecht University and Netherlands Proteomics CentreUtrechtThe Netherlands
| | - AF Maarten Altelaar
- Biomolecular Mass Spectrometry and ProteomicsBijvoet Center for Biomolecular ResearchUtrecht Institute for Pharmaceutical SciencesUtrecht University and Netherlands Proteomics CentreUtrechtThe Netherlands
- Proteomics FacilityNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Tibor van Welsem
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Jan‐Hermen Dannenberg
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
- Present address:
Genmab B.V.Antibody SciencesUtrechtThe Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology & ImmunologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Fred van Leeuwen
- Division of Gene RegulationNetherlands Cancer InstituteAmsterdamThe Netherlands
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23
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Zhang Y, Tao H, Huang SY. Dynamics and Mechanisms in the Recruitment and Transference of Histone Chaperone CIA/ASF1. Int J Mol Sci 2019; 20:ijms20133325. [PMID: 31284555 PMCID: PMC6651421 DOI: 10.3390/ijms20133325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/21/2019] [Accepted: 06/28/2019] [Indexed: 12/14/2022] Open
Abstract
The recruitment and transference of proteins through protein-protein interactions is a general process involved in various biological functions in cells. Despite the importance of this general process, the dynamic mechanism of how proteins are recruited and transferred from one interacting partner to another remains unclear. In this study, we investigated the dynamic mechanisms of recruitment and translocation of histone chaperone CIA/ASF1 for nucleosome disassembly by exploring the conformational space and the free energy profile of unbound DBD(CCG1) and CIA/ASF1-bound DBD(CCG1) systems through extensive molecular dynamics simulations. It was found that there exists three metastable conformational states for DBD(CCG1), an unbound closed state, a CIA/ASF1-bound half-open state, and an open state. The free energy landscape shows that the closed state and the half-open state are separated by a high free energy barrier, while the half-open state and the open state are connected with a moderate free energy increase. The high free energy barrier between the closed and half-open states explains why DBD(CCG1) can recruit CIA/ASF1 and remain in the binding state during the transportation. In addition, the asymmetric binding of CIA/ASF1 on DBD(CCG1) allows DBD(CCG1) to adopt the open state by moving one of its two domains, such that the exposed domain of DBD(CCG1) is able to recognize the acetylated histone H4 tails. As such, CIA/ASF1 has a chance to translocate from DBD(CCG1) to histone, which is also facilitated by the moderate energy increase from the bound half-open state to the open state of DBD(CCG1). These findings suggest that the recruitment and transference of histone chaperone CIA/ASF1 is highly favored by its interaction with DBD(CCG1) via conformational selection and asymmetric binding, which may represent a general mechanism of similar biological processes.
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Affiliation(s)
- Yanjun Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Huanyu Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China.
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24
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van Welsem T, Korthout T, Ekkebus R, Morais D, Molenaar TM, van Harten K, Poramba-Liyanage DW, Sun SM, Lenstra TL, Srivas R, Ideker T, Holstege FCP, van Attikum H, El Oualid F, Ovaa H, Stulemeijer IJE, Vlaming H, van Leeuwen F. Dot1 promotes H2B ubiquitination by a methyltransferase-independent mechanism. Nucleic Acids Res 2019; 46:11251-11261. [PMID: 30203048 PMCID: PMC6265471 DOI: 10.1093/nar/gky801] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/27/2018] [Indexed: 12/16/2022] Open
Abstract
The histone methyltransferase Dot1 is conserved from yeast to human and methylates lysine 79 of histone H3 (H3K79) on the core of the nucleosome. H3K79 methylation by Dot1 affects gene expression and the response to DNA damage, and is enhanced by monoubiquitination of the C-terminus of histone H2B (H2Bub1). To gain more insight into the functions of Dot1, we generated genetic interaction maps of increased-dosage alleles of DOT1. We identified a functional relationship between increased Dot1 dosage and loss of the DUB module of the SAGA co-activator complex, which deubiquitinates H2Bub1 and thereby negatively regulates H3K79 methylation. Increased Dot1 dosage was found to promote H2Bub1 in a dose-dependent manner and this was exacerbated by the loss of SAGA-DUB activity, which also caused a negative genetic interaction. The stimulatory effect on H2B ubiquitination was mediated by the N-terminus of Dot1, independent of methyltransferase activity. Our findings show that Dot1 and H2Bub1 are subject to bi-directional crosstalk and that Dot1 possesses chromatin regulatory functions that are independent of its methyltransferase activity.
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Affiliation(s)
- Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Tessy Korthout
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Reggy Ekkebus
- Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Dominique Morais
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Thom M Molenaar
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Kirsten van Harten
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | | | - Su Ming Sun
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Tineke L Lenstra
- Molecular Cancer Research, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Rohith Srivas
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Frank C P Holstege
- Molecular Cancer Research, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | | | - Huib Ovaa
- Division of Cell Biology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Iris J E Stulemeijer
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Hanneke Vlaming
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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25
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Jang S, Kang C, Yang HS, Jung T, Hebert H, Chung KY, Kim SJ, Hohng S, Song JJ. Structural basis of recognition and destabilization of the histone H2B ubiquitinated nucleosome by the DOT1L histone H3 Lys79 methyltransferase. Genes Dev 2019; 33:620-625. [PMID: 30923167 PMCID: PMC6546062 DOI: 10.1101/gad.323790.118] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 03/08/2019] [Indexed: 01/01/2023]
Abstract
In this study, Jang et al. present cryo-EM structures of DOT1L complexes with unmodified or H2B ubiquitinated nucleosomes, showing that DOT1L recognizes H2B ubiquitin and the H2A/H2B acidic patch through a C-terminal hydrophobic helix and an arginine anchor in DOT1L, respectively. Their results establish the molecular basis of the cross-talk between H2B ubiquitination and H3 Lys79 methylation as well as nucleosome destabilization by DOT1L. DOT1L is a histone H3 Lys79 methyltransferase whose activity is stimulated by histone H2B Lys120 ubiquitination, suggesting cross-talk between histone H3 methylation and H2B ubiquitination. Here, we present cryo-EM structures of DOT1L complexes with unmodified or H2B ubiquitinated nucleosomes, showing that DOT1L recognizes H2B ubiquitin and the H2A/H2B acidic patch through a C-terminal hydrophobic helix and an arginine anchor in DOT1L, respectively. Furthermore, the structures combined with single-molecule FRET experiments show that H2B ubiquitination enhances a noncatalytic function of the DOT1L-destabilizing nucleosome. These results establish the molecular basis of the cross-talk between H2B ubiquitination and H3 Lys79 methylation as well as nucleosome destabilization by DOT1L.
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Affiliation(s)
- Seongmin Jang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Chanshin Kang
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
| | - Han-Sol Yang
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Taeyang Jung
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, S-141 52 Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, S-141 52 Huddinge, Sweden
| | - Hans Hebert
- School of Engineering Sciences in Chemistry, Biotechnology, and Health, Department of Biomedical Engineering and Health Systems, KTH Royal Institute of Technology, S-141 52 Huddinge, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, S-141 52 Huddinge, Sweden
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Korea
| | - Seung Joong Kim
- Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Sungchul Hohng
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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