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Romero DVL, Balendran T, Hasang W, Rogerson SJ, Aitken EH, Achuthan AA. Epigenetic and transcriptional regulation of cytokine production by Plasmodium falciparum-exposed monocytes. Sci Rep 2024; 14:2949. [PMID: 38316918 PMCID: PMC10844200 DOI: 10.1038/s41598-024-53519-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/01/2024] [Indexed: 02/07/2024] Open
Abstract
Plasmodium falciparum infection causes the most severe form of malaria, where excessive production of proinflammatory cytokines can drive the pathogenesis of the disease. Monocytes play key roles in host defense against malaria through cytokine production and phagocytosis; however, they are also implicated in pathogenesis through excessive proinflammatory cytokine production. Understanding the underlying molecular mechanisms that contribute to inflammatory cytokine production in P. falciparum-exposed monocytes is key towards developing better treatments. Here, we provide molecular evidence that histone 3 lysine 4 (H3K4) methylation is key for inflammatory cytokine production in P. falciparum-exposed monocytes. In an established in vitro system that mimics blood stage infection, elevated proinflammatory TNF and IL-6 cytokine production is correlated with increased mono- and tri-methylated H3K4 levels. Significantly, we demonstrate through utilizing a pharmacological inhibitor of H3K4 methylation that TNF and IL-6 expression can be suppressed in P. falciparum-exposed monocytes. This elucidated epigenetic regulatory mechanism, controlling inflammatory cytokine production, potentially provides new therapeutic options for future malaria treatment.
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Affiliation(s)
- David V L Romero
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, 1F Royal Parade, Parkville, VIC, 3010, Australia
| | - Thivya Balendran
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, 1F Royal Parade, Parkville, VIC, 3010, Australia
| | - Wina Hasang
- Department of Infectious Diseases, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Stephen J Rogerson
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, 1F Royal Parade, Parkville, VIC, 3010, Australia
- Department of Infectious Diseases, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Elizabeth H Aitken
- Department of Infectious Diseases, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Adrian A Achuthan
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, 1F Royal Parade, Parkville, VIC, 3010, Australia.
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2
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Qin R, Wang P, Li L. Knockdown of JMJD3 ameliorates cigarette smoke extract-triggered bronchial epithelial cell injury via ACSL4-dependent ferroptosis. Toxicol In Vitro 2024; 94:105731. [PMID: 37967773 DOI: 10.1016/j.tiv.2023.105731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/17/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
Chronic obstructive pulmonary disease (COPD), a heterogeneity of chronic respiratory disease pattern, presents considerable prevalence and mortality. We aimed to explore the role and mechanisms of Jumonji domain-containing protein-3 (JMJD3) in COPD. The viability and JMJD3 expression in human bronchial epithelial cell line BEAS-2B were respectively assayed by CCK-8 assay and Western blot following stepwise exposure to increasing concentrations of cigarette smoke extract (CSE). After JMJD3 was silenced and acyl-CoA synthetase long-chain family member 4 (ACSL4) was overexpressed in CSE-treated BEAS-2B cells, cell viability, cytotoxicity, oxidative stress and total iron level were estimated using kits. ELISA estimated inflammatory levels. DCFH-DA probe and BODIPY 581/591 C11 probe were exposed to assess ROS production and lipid peroxidation. Western blot tested the expressions of ferroptosis-associated proteins. Besides, H3K27me3 and ACSL4 expressions were tested by Western blot and immunofluorescence staining. In CSE-induced BEAS-2B cells, JMJD3 expression was increased and deletion of JMJD3 improved cell viability, reduced LDH release, mitigated inflammation, oxidative stress and inhibited ferroptosis. Moreover, JMJD3 interference raised H3K27me3 expression whereas lessened ACSL4 expression in CSE-treated BEAS-2B cells. CSE exposure reduced the abundance of ACSL4 in H3K27me3 antibody. Further ACSL4 elevation reversed the impacts of JMJD3 silencing on the damage of CSE-induced BEAS-2B cells. Collectively, JMJD3 depletion might suppress ferroptosis mediated by ACSL4 to alleviate CSE-triggered inflammation and oxidative stress in BEAS-2B cells.
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Affiliation(s)
- Ruijun Qin
- Department of Respiratory and Critical Care Medicine, Taiyuan Central Hospital, Taiyuan, Shanxi 030009, China..
| | - Ping Wang
- Department of Respiratory and Critical Care Medicine, Taiyuan Central Hospital, Taiyuan, Shanxi 030009, China
| | - Lingzhi Li
- Department of Respiratory and Critical Care Medicine, Taiyuan Central Hospital, Taiyuan, Shanxi 030009, China
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3
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Rehman SU, Ullah N, Zhang Z, Zhen Y, Din AU, Cui H, Wang M. Recent insights into the functions and mechanisms of antisense RNA: emerging applications in cancer therapy and precision medicine. Front Chem 2024; 11:1335330. [PMID: 38274897 PMCID: PMC10809404 DOI: 10.3389/fchem.2023.1335330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
The antisense RNA molecule is a unique DNA transcript consisting of 19-23 nucleotides, characterized by its complementary nature to mRNA. These antisense RNAs play a crucial role in regulating gene expression at various stages, including replication, transcription, and translation. Additionally, artificial antisense RNAs have demonstrated their ability to effectively modulate gene expression in host cells. Consequently, there has been a substantial increase in research dedicated to investigating the roles of antisense RNAs. These molecules have been found to be influential in various cellular processes, such as X-chromosome inactivation and imprinted silencing in healthy cells. However, it is important to recognize that in cancer cells; aberrantly expressed antisense RNAs can trigger the epigenetic silencing of tumor suppressor genes. Moreover, the presence of deletion-induced aberrant antisense RNAs can lead to the development of diseases through epigenetic silencing. One area of drug development worth mentioning is antisense oligonucleotides (ASOs), and a prime example of an oncogenic trans-acting long noncoding RNA (lncRNA) is HOTAIR (HOX transcript antisense RNA). NATs (noncoding antisense transcripts) are dysregulated in many cancers, and researchers are just beginning to unravel their roles as crucial regulators of cancer's hallmarks, as well as their potential for cancer therapy. In this review, we summarize the emerging roles and mechanisms of antisense RNA and explore their application in cancer therapy.
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Affiliation(s)
- Shahab Ur Rehman
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Numan Ullah
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Zhenbin Zhang
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
| | - Yongkang Zhen
- College of Animals Nutrition Yangzhou University, Yangzhou, China
| | - Aziz-Ud Din
- Department of Human Genetics, Hazara University Mansehra, Mansehra, Pakistan
| | - Hengmi Cui
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
- Institute of Epigenetics and Epigenomics Yangzhou University, College of Animal Nutrition Yangzhou University, Yangzhou, China
| | - Mengzhi Wang
- College of Animals Science and Technology Yangzhou University, Yangzhou, China
- College of Animals Nutrition Yangzhou University, Yangzhou, China
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4
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Mori S, Oya S, Takahashi M, Takashima K, Inagaki S, Kakutani T. Cotranscriptional demethylation induces global loss of H3K4me2 from active genes in Arabidopsis. EMBO J 2023; 42:e113798. [PMID: 37849386 PMCID: PMC10690457 DOI: 10.15252/embj.2023113798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
Based on studies of animals and yeasts, methylation of histone H3 lysine 4 (H3K4me1/2/3, for mono-, di-, and tri-methylation, respectively) is regarded as the key epigenetic modification of transcriptionally active genes. In plants, however, H3K4me2 correlates negatively with transcription, and the regulatory mechanisms of this counterintuitive H3K4me2 distribution in plants remain largely unexplored. A previous genetic screen for factors regulating plant regeneration identified Arabidopsis LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 (LDL3), which is a major H3K4me2 demethylase. Here, we show that LDL3-mediated H3K4me2 demethylation depends on the transcription elongation factor Paf1C and phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII). In addition, LDL3 binds to phosphorylated RNAPII. These results suggest that LDL3 is recruited to transcribed genes by binding to elongating RNAPII and demethylates H3K4me2 cotranscriptionally. Importantly, the negative correlation between H3K4me2 and transcription is significantly attenuated in the ldl3 mutant, demonstrating the genome-wide impacts of the transcription-driven LDL3 pathway to control H3K4me2 in plants. Our findings implicate H3K4me2 demethylation in plants as chromatin records of transcriptional activity, which ensures robust gene control.
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Affiliation(s)
- Shusei Mori
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | - Satoyo Oya
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | | | | | - Soichi Inagaki
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
| | - Tetsuji Kakutani
- Department of Biological Sciences, Graduate School of ScienceThe University of TokyoTokyoJapan
- National Institute of GeneticsShizuokaJapan
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5
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Lupancu TJ, Lee KM, Eivazitork M, Hor C, Fleetwood AJ, Cook AD, Olshansky M, Turner SJ, de Steiger R, Lim K, Hamilton JA, Achuthan AA. Epigenetic and transcriptional regulation of CCL17 production by glucocorticoids in arthritis. iScience 2023; 26:108079. [PMID: 37860753 PMCID: PMC10583050 DOI: 10.1016/j.isci.2023.108079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 08/17/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
Glucocorticoids (GCs) are potent anti-inflammatory agents and are broadly used in treating rheumatoid arthritis (RA) patients, albeit with adverse side effects associated with long-term usage. The negative consequences of GC therapy provide an impetus for research into gaining insights into the molecular mechanisms of GC action. We have previously reported that granulocyte-macrophage colony-stimulating factor (GM-CSF)-induced CCL17 has a non-redundant role in inflammatory arthritis. Here, we provide molecular evidence that GCs can suppress GM-CSF-mediated upregulation of IRF4 and CCL17 expression via downregulating JMJD3 expression and activity. In mouse models of inflammatory arthritis, GC treatment inhibited CCL17 expression and ameliorated arthritic pain-like behavior and disease. Significantly, GC treatment of RA patient peripheral blood mononuclear cells ex vivo resulted in decreased CCL17 production. This delineated pathway potentially provides new therapeutic options for the treatment of many inflammatory conditions, where GCs are used as an anti-inflammatory drug but without the associated adverse side effects.
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Affiliation(s)
- Tanya J. Lupancu
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Kevin M.C. Lee
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Mahtab Eivazitork
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Cecil Hor
- Department of Medicine, Western Health, The University of Melbourne, St Albans, VIC 3021, Australia
| | - Andrew J. Fleetwood
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
- Haematopoiesis and Leukocyte Biology, Baker IDI Heart and Diabetes Institute, Melbourne, VIC 3004, Australia
| | - Andrew D. Cook
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Moshe Olshansky
- Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Stephen J. Turner
- Department of Microbiology, Monash University, Clayton, VIC 3800, Australia
| | - Richard de Steiger
- Department of Surgery, Epworth HealthCare, The University of Melbourne, Richmond, VIC 3121, Australia
| | - Keith Lim
- Department of Medicine, Western Health, The University of Melbourne, St Albans, VIC 3021, Australia
| | - John A. Hamilton
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Adrian A. Achuthan
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
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6
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Johnson D, Letchumanan V, Thum CC, Thurairajasingam S, Lee LH. A Microbial-Based Approach to Mental Health: The Potential of Probiotics in the Treatment of Depression. Nutrients 2023; 15:nu15061382. [PMID: 36986112 PMCID: PMC10053794 DOI: 10.3390/nu15061382] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
Probiotics are currently the subject of intensive research pursuits and also represent a multi-billion-dollar global industry given their vast potential to improve human health. In addition, mental health represents a key domain of healthcare, which currently has limited, adverse-effect prone treatment options, and probiotics may hold the potential to be a novel, customizable treatment for depression. Clinical depression is a common, potentially debilitating condition that may be amenable to a precision psychiatry-based approach utilizing probiotics. Although our understanding has not yet reached a sufficient level, this could be a therapeutic approach that can be tailored for specific individuals with their own unique set of characteristics and health issues. Scientifically, the use of probiotics as a treatment for depression has a valid basis rooted in the microbiota-gut-brain axis (MGBA) mechanisms, which play a role in the pathophysiology of depression. In theory, probiotics appear to be ideal as adjunct therapeutics for major depressive disorder (MDD) and as stand-alone therapeutics for mild MDD and may potentially revolutionize the treatment of depressive disorders. Although there is a wide range of probiotics and an almost limitless range of therapeutic combinations, this review aims to narrow the focus to the most widely commercialized and studied strains, namely Lactobacillus and Bifidobacterium, and to bring together the arguments for their usage in patients with major depressive disorder (MDD). Clinicians, scientists, and industrialists are critical stakeholders in exploring this groundbreaking concept.
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Affiliation(s)
- Dinyadarshini Johnson
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia
| | - Vengadesh Letchumanan
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia
- Pathogen Resistome Virulome and Diagnostic Research Group (PathRiD), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia
| | - Chern Choong Thum
- Department of Psychiatry, Hospital Sultan Abdul Aziz Shah, Persiaran Mardi-UPM, Serdang 43400, Malaysia
| | - Sivakumar Thurairajasingam
- Clinical School Johor Bahru, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Johor Bahru 80100, Malaysia
- Correspondence: (S.T.); or (L.-H.L.)
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia
- Pathogen Resistome Virulome and Diagnostic Research Group (PathRiD), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia
- Correspondence: (S.T.); or (L.-H.L.)
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7
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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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8
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Chou KY, Lee JY, Kim KB, Kim E, Lee HS, Ryu HY. Histone modification in Saccharomyces cerevisiae: A review of the current status. Comput Struct Biotechnol J 2023; 21:1843-1850. [PMID: 36915383 PMCID: PMC10006725 DOI: 10.1016/j.csbj.2023.02.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a well-characterized and popular model system for investigating histone modifications and the inheritance of chromatin states. The data obtained from this model organism have provided essential and critical information for understanding the complexity of epigenetic interactions and regulation in eukaryotes. Recent advances in biotechnology have facilitated the detection and quantitation of protein post-translational modification (PTM), including acetylation, methylation, phosphorylation, ubiquitylation, sumoylation, and acylation, and led to the identification of several novel modification sites in histones. Determining the cellular function of these new histone markers is essential for understanding epigenetic mechanisms and their impact on various biological processes. In this review, we describe recent advances and current views on histone modifications and their effects on chromatin dynamics in S. cerevisiae.
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Key Words
- AdoMet, S-adenosylmethionine
- CAF-1, chromatin assembly factor-1
- CTD, C-terminal domain
- DSB, double-strand break
- E Glu, glutamic acid
- HAT, histone acetyltransferase
- HDAC, histone deacetylase
- Histone acetylation
- Histone acylation
- Histone methylation
- Histone phosphorylation
- Histone sumoylation
- Histone ubiquitylation
- JMJC, Jumonji C
- K Lys, lysine
- PTM, post-translational modification
- R Arg, arginine
- S, serine
- SAGA, Spt-Ada-Gcn5 acetyltransferase
- STUbL, SUMO-targeted ubiquitin ligase
- SUMO, small ubiquitin-like modifier
- T, threonine
- Y, tyrosine
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Affiliation(s)
- Kwon Young Chou
- School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jun-Yeong Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kee-Beom Kim
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Eunjeong Kim
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyun-Shik Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hong-Yeoul Ryu
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
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Li C, Li N, Zhang Z, Song Y, Li J, Wang Z, Bo H, Zhang Y. The specific mitochondrial unfolded protein response in fast- and slow-twitch muscles of high-fat diet-induced insulin-resistant rats. Front Endocrinol (Lausanne) 2023; 14:1127524. [PMID: 37008907 PMCID: PMC10061072 DOI: 10.3389/fendo.2023.1127524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
INTRODUCTION Skeletal muscle insulin resistance (IR) plays an important role in the pathogenesis of type 2 diabetes mellitus. Skeletal muscle is a heterogeneous tissue composed of different muscle fiber types that contribute distinctly to IR development. Glucose transport shows more protection in slow-twitch muscles than in fast-twitch muscles during IR development, while the mechanisms involved remain unclear. Therefore, we investigated the role of the mitochondrial unfolded protein response (UPRmt) in the distinct resistance of two types of muscle in IR. METHODS Male Wistar rats were divided into high-fat diet (HFD) feeding and control groups. We measured glucose transport, mitochondrial respiration, UPRmt and histone methylation modification of UPRmt-related proteins to examine the UPRmt in the slow fiber-enriched soleus (Sol) and fast fiber-enriched tibialis anterior (TA) under HFD conditions. RESULTS Our results indicate that 18 weeks of HFD can cause systemic IR, while the disturbance of Glut4-dependent glucose transport only occurred in fast-twitch muscle. The expression levels of UPRmt markers, including ATF5, HSP60 and ClpP, and the UPRmt-related mitokine MOTS-c were significantly higher in slow-twitch muscle than in fast-twitch muscle under HFD conditions. Mitochondrial respiratory function is maintained only in slow-twitch muscle. Additionally, in the Sol, histone methylation at the ATF5 promoter region was significantly higher than that in the TA after HFD feeding. CONCLUSION The expression of proteins involved in glucose transport in slow-twitch muscle remains almost unaltered after HFD intervention, whereas a significant decline of these proteins was observed in fast-twitch muscle. Specific activation of the UPRmt in slow-twitch muscle, accompanied by higher mitochondrial respiratory function and MOTS-c expression, may contribute to the higher resistance to HFD in slow-twitch muscle. Notably, the different histone modifications of UPRmt regulators may underlie the specific activation of the UPRmt in different muscle types. However, future work applying genetic or pharmacological approaches should further uncover the relationship between the UPRmt and insulin resistance.
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Affiliation(s)
- Can Li
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, School of Exercise and Health, Tianjin University of Sport, Tianjin, China
| | - Nan Li
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, School of Exercise and Health, Tianjin University of Sport, Tianjin, China
| | - Ziyi Zhang
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, School of Exercise and Health, Tianjin University of Sport, Tianjin, China
| | - Yu Song
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, School of Exercise and Health, Tianjin University of Sport, Tianjin, China
| | - Jialin Li
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, School of Exercise and Health, Tianjin University of Sport, Tianjin, China
| | - Zhe Wang
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, School of Exercise and Health, Tianjin University of Sport, Tianjin, China
| | - Hai Bo
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, School of Exercise and Health, Tianjin University of Sport, Tianjin, China
- Department of Military Training Medicines, Logistics University of Chinese People’s Armed Police Force, Tianjin, China
- *Correspondence: Hai Bo, ; Yong Zhang,
| | - Yong Zhang
- Tianjin Key Laboratory of Exercise Physiology and Sports Medicine, School of Exercise and Health, Tianjin University of Sport, Tianjin, China
- *Correspondence: Hai Bo, ; Yong Zhang,
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10
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Gong C, Xu D, Sun D, Kang J, Wang W, Xu JR, Zhang X. FgSnt1 of the Set3 HDAC complex plays a key role in mediating the regulation of histone acetylation by the cAMP-PKA pathway in Fusarium graminearum. PLoS Genet 2022; 18:e1010510. [PMID: 36477146 PMCID: PMC9728937 DOI: 10.1371/journal.pgen.1010510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
The cAMP-PKA pathway is critical for regulating growth, differentiation, and pathogenesis in fungal pathogens. In Fusarium graminearum, mutants deleted of PKR regulatory-subunit of PKA had severe defects but often produced spontaneous suppressors. In this study eleven pkr suppressors were found to have mutations in FgSNT1, a component of the Set3C histone deacetylase (HDAC) complex, that result in the truncation of its C-terminal region. Targeted deletion of the C-terminal 98 aa (CT98) in FgSNT1 suppressed the defects of pkr in growth and H4 acetylation. CT98 truncation also increased the interaction of FgSnt1 with Hdf1, a major HDAC in the Set3 complex. The pkr mutant had no detectable expression of the Cpk1 catalytic subunit and PKA activities, which was not suppressed by mutations in FgSNT1. Cpk1 directly interacted with the N-terminal region of FgSnt1 and phosphorylated it at S443, a conserved PKA-phosphorylation site. CT98 of FgSnt1 carrying the S443D mutation interacted with its own N-terminal region. Expression of FgSNT1S443D rescued the defects of pkr in growth and H4 acetylation. Therefore, phosphorylation at S443 and suppressor mutations may relieve self-inhibitory binding of FgSnt1 and increase its interaction with Hdf1 and H4 acetylation, indicating a key role of FgSnt1 in crosstalk between cAMP signaling and Set3 complex.
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Affiliation(s)
- Chen Gong
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Daiying Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
| | - Daiyuan Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jiangang Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Wei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jin-Rong Xu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail: (J-RX); (XZ)
| | - Xue Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- * E-mail: (J-RX); (XZ)
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11
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Biochemical Characterization of the TINTIN Module of the NuA4 Complex Reveals Allosteric Regulation of Nucleosome Interaction. Mol Cell Biol 2022; 42:e0017022. [PMID: 36190236 PMCID: PMC9670870 DOI: 10.1128/mcb.00170-22] [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: 12/25/2022] Open
Abstract
Trimer Independent of NuA4 involved in Transcription Interactions with Nucleosomes (TINTIN) is an integral module of the essential yeast lysine acetyltransferase complex NuA4 that plays key roles in transcription regulation and DNA repair. Composed of Eaf3, Eaf5, and Eaf7, TINTIN mediates targeting of NuA4 to chromatin through the chromodomain-containing subunit Eaf3 that is shared with the Rpd3S histone deacetylase complex. How Eaf3 mediates chromatin interaction in the context of TINTIN and how is it different from what has been observed in Rpd3S is unclear. Here, we reconstituted recombinant TINTIN and its subassemblies and characterized their biochemical and structural properties. Our coimmunoprecipitation, AlphaFold2 modeling, and hydrogen deuterium exchange mass spectrometry (HDX-MS) analyses revealed that the Eaf3 MRG domain contacts Eaf7 and this binding induces conformational changes throughout Eaf3. Nucleosome-binding assays showed that Eaf3 and TINTIN interact non-specifically with the DNA on nucleosomes. Furthermore, integration into TINTIN enhances the affinity of Eaf3 toward nucleosomes and this improvement is a result of allosteric activation of the Eaf3 chromodomain. Negative stain electron microscopy (EM) analysis revealed that TINTIN binds to the edge of nucleosomes with increased specificity in the presence of H3K36me3. Collectively, our work provides insights into the dynamics of TINTIN and the mechanism by which its interactions with chromatin are regulated.
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12
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Jagtap S, Pirayre A, Bidard F, Duval L, Malliaros FD. BRANEnet: embedding multilayer networks for omics data integration. BMC Bioinformatics 2022; 23:429. [PMID: 36245002 PMCID: PMC9575224 DOI: 10.1186/s12859-022-04955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 08/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background Gene expression is regulated at different molecular levels, including chromatin accessibility, transcription, RNA maturation, and transport. These regulatory mechanisms have strong connections with cellular metabolism. In order to study the cellular system and its functioning, omics data at each molecular level can be generated and efficiently integrated. Here, we propose BRANEnet, a novel multi-omics integration framework for multilayer heterogeneous networks. BRANEnet is an expressive, scalable, and versatile method to learn node embeddings, leveraging random walk information within a matrix factorization framework. Our goal is to efficiently integrate multi-omics data to study different regulatory aspects of multilayered processes that occur in organisms. We evaluate our framework using multi-omics data of Saccharomyces cerevisiae, a well-studied yeast model organism. Results We test BRANEnet on transcriptomics (RNA-seq) and targeted metabolomics (NMR) data for wild-type yeast strain during a heat-shock time course of 0, 20, and 120 min. Our framework learns features for differentially expressed bio-molecules showing heat stress response. We demonstrate the applicability of the learned features for targeted omics inference tasks: transcription factor (TF)-target prediction, integrated omics network (ION) inference, and module identification. The performance of BRANEnet is compared to existing network integration methods. Our model outperforms baseline methods by achieving high prediction scores for a variety of downstream tasks. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04955-w.
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Affiliation(s)
- Surabhi Jagtap
- Université Paris-Saclay, CentraleSupélec, Inria, 3 Rue Joliot Curie, 91190, Gif-Sur-Yvette, France.,IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Aurélie Pirayre
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Frédérique Bidard
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Laurent Duval
- IFP Energies nouvelles, 1 et 4 avenue de Bois-Préau, 92852, Rueil-Malmaison, France
| | - Fragkiskos D Malliaros
- Université Paris-Saclay, CentraleSupélec, Inria, 3 Rue Joliot Curie, 91190, Gif-Sur-Yvette, France.
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13
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HIV-1 Preintegration Complex Preferentially Integrates the Viral DNA into Nucleosomes Containing Trimethylated Histone 3-Lysine 36 Modification and Flanking Linker DNA. J Virol 2022; 96:e0101122. [PMID: 36094316 PMCID: PMC9517705 DOI: 10.1128/jvi.01011-22] [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: 01/11/2023] Open
Abstract
HIV-1 DNA is preferentially integrated into chromosomal hot spots by the preintegration complex (PIC). To understand the mechanism, we measured the DNA integration activity of PICs-extracted from infected cells-and intasomes, biochemically assembled PIC substructures using a number of relevant target substrates. We observed that PIC-mediated integration into human chromatin is preferred compared to genomic DNA. Surprisingly, nucleosomes lacking histone modifications were not preferred integration compared to the analogous naked DNA. Nucleosomes containing the trimethylated histone 3 lysine 36 (H3K36me3), an epigenetic mark linked to active transcription, significantly stimulated integration, but the levels remained lower than the naked DNA. Notably, H3K36me3-modified nucleosomes with linker DNA optimally supported integration mediated by the PIC but not by the intasome. Interestingly, optimal intasome-mediated integration required the cellular cofactor LEDGF. Unexpectedly, LEDGF minimally affected PIC-mediated integration into naked DNA but blocked integration into nucleosomes. The block for the PIC-mediated integration was significantly relieved by H3K36me3 modification. Mapping the integration sites in the preferred substrates revealed that specific features of the nucleosome-bound DNA are preferred for integration, whereas integration into naked DNA was random. Finally, biochemical and genetic studies demonstrate that DNA condensation by the H1 protein dramatically reduces integration, providing further evidence that features inherent to the open chromatin are preferred for HIV-1 integration. Collectively, these results identify the optimal target substrate for HIV-1 integration, report a mechanistic link between H3K36me3 and integration preference, and importantly, reveal distinct mechanisms utilized by the PIC for integration compared to the intasomes. IMPORTANCE HIV-1 infection is dependent on integration of the viral DNA into the host chromosomes. The preintegration complex (PIC) containing the viral DNA, the virally encoded integrase (IN) enzyme, and other viral/host factors carries out HIV-1 integration. HIV-1 integration is not dependent on the target DNA sequence, and yet the viral DNA is selectively inserted into specific "hot spots" of human chromosomes. A growing body of literature indicates that structural features of the human chromatin are important for integration targeting. However, the mechanisms that guide the PIC and enable insertion of the PIC-associated viral DNA into specific hot spots of the human chromosomes are not fully understood. In this study, we describe a biochemical mechanism for the preference of the HIV-1 DNA integration into open chromatin. Furthermore, our study defines a direct role for the histone epigenetic mark H3K36me3 in HIV-1 integration preference and identify an optimal substrate for HIV-1 PIC-mediated viral DNA integration.
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14
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Ma Z, Wang Y, Quan Y, Wang Z, Liu Y, Ding Z. Maternal obesity alters methylation level of cytosine in CpG island for epigenetic inheritance in fetal umbilical cord blood. Hum Genomics 2022; 16:34. [PMID: 36045397 PMCID: PMC9429776 DOI: 10.1186/s40246-022-00410-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Over the past few decades, global maternal obesity prevalence has rapidly increased. This condition may induce long-lasting pathophysiological effects on either fetal or infant health that could be attributable to unknown unique changes in the umbilical blood composition. METHODS A total of 34 overweight/obese and 32 normal-weight pregnant women were recruited. Fifteen umbilical blood samples including 8 overweight/obese subjects and 7 normal weight women were sequenced using Targeted Bisulfite Sequencing technology to detect the average methylation level of cytosine and identify the differentially methylated region (DMR). GO and KEGG analyses were then employed to perform pathway enrichment analysis of DMR-related genes and promoters. Moreover, the mRNA levels of methylation-related genes histone deacetylases (HDACs) and DNA methyltransferases (DNMTs) were characterized in the samples obtained from these two groups. RESULTS Average methylated cytosine levels in both the CpG islands (CGI) and promoter significantly decreased in overweight/obese groups. A total of 1669 DMRs exhibited differences in their DNA methylation status between the overweight/obese and control groups. GO and KEGG analyses revealed that DMR-related genes and promoters were enriched in the metabolism, cancer and cardiomyopathy signaling pathways. Furthermore, the HDACs and DNMTs mRNA levels trended to decline in overweight/obese groups. CONCLUSIONS Decreased methylated cytosine levels in overweight/obese women induce the gene expression activity at a higher level than in the control group. DMRs between these two groups in the fetal blood may contribute to the changes in gene transcription that underlie the increased risk of metabolic disorders, cancers and cardiomyopathy in their offspring.
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Affiliation(s)
- Zhuoyao Ma
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China
| | - Yingjin Wang
- Department of Obstetrics and Gynecology, Shanghai Eighth People's Hospital, Shanghai, 200235, China
| | - Yanmei Quan
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China
| | - Zhijie Wang
- Department of Obstetrics and Gynecology, Shanghai Eighth People's Hospital, Shanghai, 200235, China.
| | - Yue Liu
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China.
| | - Zhide Ding
- Department of Histology, Embryology, Genetics and Developmental Biology, Shanghai Key Laboratory for Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, No.280, Chongqing Road (South), Shanghai, 200025, China.
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15
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Epigenetic Alterations in Sports-Related Injuries. Genes (Basel) 2022; 13:genes13081471. [PMID: 36011382 PMCID: PMC9408207 DOI: 10.3390/genes13081471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
It is a well-known fact that physical activity benefits people of all age groups. However, highly intensive training, maladaptation, improper equipment, and lack of sufficient rest lead to contusions and sports-related injuries. From the perspectives of sports professionals and those performing regular–amateur sports activities, it is important to maintain proper levels of training, without encountering frequent injuries. The bodily responses to physical stress and intensive physical activity are detected on many levels. Epigenetic modifications, including DNA methylation, histone protein methylation, acetylation, and miRNA expression occur in response to environmental changes and play fundamental roles in the regulation of cellular activities. In the current review, we summarise the available knowledge on epigenetic alterations present in tissues and organs (e.g., muscles, the brain, tendons, and bones) as a consequence of sports-related injuries. Epigenetic mechanism observations have the potential to become useful tools in sports medicine, as predictors of approaching pathophysiological alterations and injury biomarkers that have already taken place.
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16
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The role of NSD1, NSD2, and NSD3 histone methyltransferases in solid tumors. Cell Mol Life Sci 2022; 79:285. [PMID: 35532818 PMCID: PMC9520630 DOI: 10.1007/s00018-022-04321-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/03/2022]
Abstract
NSD1, NSD2, and NSD3 constitute the nuclear receptor-binding SET Domain (NSD) family of histone 3 lysine 36 (H3K36) methyltransferases. These structurally similar enzymes mono- and di-methylate H3K36, which contribute to the maintenance of chromatin integrity and regulate the expression of genes that control cell division, apoptosis, DNA repair, and epithelial-mesenchymal transition (EMT). Aberrant expression or mutation of members of the NSD family is associated with developmental defects and the occurrence of some types of cancer. In this review, we discuss the effect of alterations in NSDs on cancer patient's prognosis and response to treatment. We summarize the current understanding of the biological functions of NSD proteins, focusing on their activities and the role in the formation and progression in solid tumors biology, as well as how it depends on tumor etiologies. This review also discusses ongoing efforts to develop NSD inhibitors as a promising new class of cancer therapeutic agents.
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17
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Lee BB, Woo H, Lee MK, Youn S, Lee S, Roe JS, Lee SY, Kim T. Core promoter activity contributes to chromatin-based regulation of internal cryptic promoters. Nucleic Acids Res 2021; 49:8097-8109. [PMID: 34320189 PMCID: PMC8373055 DOI: 10.1093/nar/gkab639] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 07/01/2021] [Accepted: 07/16/2021] [Indexed: 12/11/2022] Open
Abstract
During RNA polymerase II (RNA Pol II) transcription, the chromatin structure undergoes dynamic changes, including opening and closing of the nucleosome to enhance transcription elongation and fidelity. These changes are mediated by transcription elongation factors, including Spt6, the FACT complex, and the Set2-Rpd3S HDAC pathway. These factors not only contribute to RNA Pol II elongation, reset the repressive chromatin structures after RNA Pol II has passed, thereby inhibiting aberrant transcription initiation from the internal cryptic promoters within gene bodies. Notably, the internal cryptic promoters of infrequently transcribed genes are sensitive to such chromatin-based regulation but those of hyperactive genes are not. To determine why, the weak core promoters of genes that generate cryptic transcripts in cells lacking transcription elongation factors (e.g. STE11) were replaced with those from more active genes. Interestingly, as core promoter activity increased, activation of internal cryptic promoter dropped. This associated with loss of active histone modifications at the internal cryptic promoter. Moreover, environmental changes and transcription elongation factor mutations that downregulated the core promoters of highly active genes concomitantly increased their cryptic transcription. We therefore propose that the chromatin-based regulation of internal cryptic promoters is mediated by core promoter strength as well as transcription elongation factors.
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Affiliation(s)
- Bo Bae Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Hyeonju Woo
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Min Kyung Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - SeoJung Youn
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Sumin Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Jae-Seok Roe
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Soo Young Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - TaeSoo Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
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18
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Devenish LP, Mhlanga MM, Negishi Y. Immune Regulation in Time and Space: The Role of Local- and Long-Range Genomic Interactions in Regulating Immune Responses. Front Immunol 2021; 12:662565. [PMID: 34046034 PMCID: PMC8144502 DOI: 10.3389/fimmu.2021.662565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 12/27/2022] Open
Abstract
Mammals face and overcome an onslaught of endogenous and exogenous challenges in order to survive. Typical immune cells and barrier cells, such as epithelia, must respond rapidly and effectively to encountered pathogens and aberrant cells to prevent invasion and eliminate pathogenic species before they become overgrown and cause harm. On the other hand, inappropriate initiation and failed termination of immune cell effector function in the absence of pathogens or aberrant tissue gives rise to a number of chronic, auto-immune, and neoplastic diseases. Therefore, the fine control of immune effector functions to provide for a rapid, robust response to challenge is essential. Importantly, immune cells are heterogeneous due to various factors relating to cytokine exposure and cell-cell interaction. For instance, tissue-resident macrophages and T cells are phenotypically, transcriptionally, and functionally distinct from their circulating counterparts. Indeed, even the same cell types in the same environment show distinct transcription patterns at the single cell level due to cellular noise, despite being robust in concert. Additionally, immune cells must remain quiescent in a naive state to avoid autoimmunity or chronic inflammatory states but must respond robustly upon activation regardless of their microenvironment or cellular noise. In recent years, accruing evidence from next-generation sequencing, chromatin capture techniques, and high-resolution imaging has shown that local- and long-range genome architecture plays an important role in coordinating rapid and robust transcriptional responses. Here, we discuss the local- and long-range genome architecture of immune cells and the resultant changes upon pathogen or antigen exposure. Furthermore, we argue that genome structures contribute functionally to rapid and robust responses under noisy and distinct cellular environments and propose a model to explain this phenomenon.
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Affiliation(s)
- Liam P Devenish
- Division of Chemical, Systems, and Synthetic Biology, Department of Integrative Biomedical Sciences, Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Musa M Mhlanga
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Yutaka Negishi
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, Netherlands.,Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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19
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Connacher J, Josling GA, Orchard LM, Reader J, Llinás M, Birkholtz LM. H3K36 methylation reprograms gene expression to drive early gametocyte development in Plasmodium falciparum. Epigenetics Chromatin 2021; 14:19. [PMID: 33794978 PMCID: PMC8017609 DOI: 10.1186/s13072-021-00393-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Background The Plasmodium sexual gametocyte stages are the only transmissible form of the malaria parasite and are thus responsible for the continued transmission of the disease. Gametocytes undergo extensive functional and morphological changes from commitment to maturity, directed by an equally extensive control program. However, the processes that drive the differentiation and development of the gametocyte post-commitment, remain largely unexplored. A previous study reported enrichment of H3K36 di- and tri-methylated (H3K36me2&3) histones in early-stage gametocytes. Using chromatin immunoprecipitation followed by high-throughput sequencing, we identify a stage-specific association between these repressive histone modifications and transcriptional reprogramming that define a stage II gametocyte transition point. Results Here, we show that H3K36me2 and H3K36me3 from stage II gametocytes are associated with repression of genes involved in asexual proliferation and sexual commitment, indicating that H3K36me2&3-mediated repression of such genes is essential to the transition from early gametocyte differentiation to intermediate development. Importantly, we show that the gene encoding the transcription factor AP2-G as commitment master regulator is enriched with H3K36me2&3 and actively repressed in stage II gametocytes, providing the first evidence of ap2-g gene repression in post-commitment gametocytes. Lastly, we associate the enhanced potency of the pan-selective Jumonji inhibitor JIB-04 in gametocytes with the inhibition of histone demethylation including H3K36me2&3 and a disruption of normal transcriptional programs. Conclusions Taken together, our results provide the first description of an association between global gene expression reprogramming and histone post-translational modifications during P. falciparum early sexual development. The stage II gametocyte-specific abundance of H3K36me2&3 manifests predominantly as an independent regulatory mechanism targeted towards genes that are repressed post-commitment. H3K36me2&3-associated repression of genes is therefore involved in key transcriptional shifts that accompany the transition from early gametocyte differentiation to intermediate development. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00393-9.
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Affiliation(s)
- Jessica Connacher
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Gabrielle A Josling
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lindsey M Orchard
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA
| | - Janette Reader
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa
| | - Manuel Llinás
- Department of Biochemistry & Molecular Biology and the Huck Center for Malaria Research, Pennsylvania State University, University Park, PA, 16802, USA.,Department of Chemistry, Pennsylvania State University, University Park, PA, 16802, USA
| | - Lyn-Marié Birkholtz
- Department of Biochemistry, Genetics and Microbiology, Institute for Sustainable Malaria Control, University of Pretoria, Private Bag x20, Hatfield, 0028, South Africa.
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20
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Shaban K, Sauty SM, Yankulov K. Variation, Variegation and Heritable Gene Repression in S. cerevisiae. Front Genet 2021; 12:630506. [PMID: 33747046 PMCID: PMC7970126 DOI: 10.3389/fgene.2021.630506] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/08/2021] [Indexed: 11/13/2022] Open
Abstract
Phenotypic heterogeneity provides growth advantages for a population upon changes of the environment. In S. cerevisiae, such heterogeneity has been observed as "on/off" states in the expression of individual genes in individual cells. These variations can persist for a limited or extended number of mitotic divisions. Such traits are known to be mediated by heritable chromatin structures, by the mitotic transmission of transcription factors involved in gene regulatory circuits or by the cytoplasmic partition of prions or other unstructured proteins. The significance of such epigenetic diversity is obvious, however, we have limited insight into the mechanisms that generate it. In this review, we summarize the current knowledge of epigenetically maintained heterogeneity of gene expression and point out similarities and converging points between different mechanisms. We discuss how the sharing of limiting repression or activation factors can contribute to cell-to-cell variations in gene expression and to the coordination between short- and long- term epigenetic strategies. Finally, we discuss the implications of such variations and strategies in adaptation and aging.
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Affiliation(s)
- Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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21
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Arora I, Tollefsbol TO. Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications. Methods 2021; 187:92-103. [PMID: 32941995 PMCID: PMC7914156 DOI: 10.1016/j.ymeth.2020.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/20/2022] Open
Abstract
Epigenetics is mainly comprised of features that regulate genomic interactions thereby playing a crucial role in a vast array of biological processes. Epigenetic mechanisms such as DNA methylation and histone modifications influence gene expression by modulating the packaging of DNA in the nucleus. A plethora of studies have emphasized the importance of analyzing epigenetics data through genome-wide studies and high-throughput approaches, thereby providing key insights towards epigenetics-based diseases such as cancer. Recent advancements have been made towards translating epigenetics research into a high throughput approach such as genome-scale profiling. Amongst all, bioinformatics plays a pivotal role in achieving epigenetics-related computational studies. Despite significant advancements towards epigenomic profiling, it is challenging to understand how various epigenetic modifications such as chromatin modifications and DNA methylation regulate gene expression. Next-generation sequencing (NGS) provides accurate and parallel sequencing thereby allowing researchers to comprehend epigenomic profiling. In this review, we summarize different computational methods such as machine learning and other bioinformatics tools, publicly available databases and resources to identify key modifications associated with epigenetic machinery. Additionally, the review also focuses on understanding recent methodologies related to epigenome profiling using NGS methods ranging from library preparation, different sequencing platforms and analytical techniques to evaluate various epigenetic modifications such as DNA methylation and histone modifications. We also provide detailed information on bioinformatics tools and computational strategies responsible for analyzing large scale data in epigenetics.
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Affiliation(s)
- Itika Arora
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA; Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA; Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA.
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22
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Kim JH, Yoon CY, Jun Y, Lee BB, Lee JE, Ha SD, Woo H, Choi A, Lee S, Jeong W, Kim JH, Kim T. NuA3 HAT antagonizes the Rpd3S and Rpd3L HDACs to optimize mRNA and lncRNA expression dynamics. Nucleic Acids Res 2020; 48:10753-10767. [PMID: 33010166 PMCID: PMC7641726 DOI: 10.1093/nar/gkaa781] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/03/2020] [Accepted: 09/09/2020] [Indexed: 01/16/2023] Open
Abstract
In yeast, NuA3 histone acetyltransferase (NuA3 HAT) promotes acetylation of histone H3 lysine 14 (H3K14) and transcription of a subset of genes through interaction between the Yng1 plant homeodomain (PHD) finger and H3K4me3. Although NuA3 HAT has multiple chromatin binding modules with distinct specificities, their interdependence and combinatorial actions in chromatin binding and transcription remain unknown. Modified peptide pulldown assays reveal that the Yng1 N-terminal region is important for the integrity of NuA3 HAT by mediating the interaction between core subunits and two methyl-binding proteins, Yng1 and Pdp3. We further uncover that NuA3 HAT contributes to the regulation of mRNA and lncRNA expression dynamics by antagonizing the histone deacetylases (HDACs) Rpd3S and Rpd3L. The Yng1 N-terminal region, the Nto1 PHD finger and Pdp3 are important for optimal induction of mRNA and lncRNA transcription repressed by the Set2-Rpd3S HDAC pathway, whereas the Yng1 PHD finger–H3K4me3 interaction affects transcriptional repression memory regulated by Rpd3L HDAC. These findings suggest that NuA3 HAT uses distinct chromatin readers to compete with two Rpd3-containing HDACs to optimize mRNA and lncRNA expression dynamics.
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Affiliation(s)
- Ji Hyun Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Chae Young Yoon
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Yukyung Jun
- Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul 03760, Korea
| | - Bo Bae Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Ji Eun Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - So Dam Ha
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Hyeonju Woo
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Ahyoung Choi
- Department of Bio-Information Science, Ewha Womans University, Seoul, 03760, Korea
| | - Sanghyuk Lee
- Ewha-JAX Cancer Immunotherapy Research Center, Ewha Womans University, Seoul 03760, Korea.,Department of Bio-Information Science, Ewha Womans University, Seoul, 03760, Korea
| | - Woojin Jeong
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Ji Hyung Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - TaeSoo Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
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23
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Lee MK, Kim T. Histone H4-Specific Deacetylation at Active Coding Regions by Hda1C. Mol Cells 2020; 43:841-847. [PMID: 32913143 PMCID: PMC7604025 DOI: 10.14348/molcells.2020.0141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/04/2020] [Accepted: 08/24/2020] [Indexed: 01/19/2023] Open
Abstract
Histone acetylation and deacetylation play central roles in the regulation of chromatin structure and transcription by RNA polymerase II (RNA Pol II). Although Hda1 histone deacetylase complex (Hda1C) is known to selectively deacetylate histone H3 and H2B to repress transcription, previous studies have suggested its potential roles in histone H4 deacetylation. Recently, we have shown that Hda1C has two distinct functions in histone deacetylation and transcription. Histone H4-specific deacetylation at highly transcribed genes negatively regulates RNA Pol II elongation and H3 deacetylation at inactive genes fine-tunes the kinetics of gene induction upon environmental changes. Here, we review the recent understandings of transcriptional regulation via histone deacetylation by Hda1C. In addition, we discuss the potential mechanisms for histone substrate switching by Hda1C, depending on transcriptional frequency and activity.
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Affiliation(s)
- Min Kyung Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - TaeSoo Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
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24
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Sauty SM, Shaban K, Yankulov K. Gene repression in S. cerevisiae-looking beyond Sir-dependent gene silencing. Curr Genet 2020; 67:3-17. [PMID: 33037902 DOI: 10.1007/s00294-020-01114-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/08/2020] [Accepted: 09/24/2020] [Indexed: 01/09/2023]
Abstract
Gene silencing by the SIR (Silent Information Region) family of proteins in S. cerevisiae has been extensively studied and has served as a founding paradigm for our general understanding of gene repression and its links to histone deacetylation and chromatin structure. In recent years, our understanding of other mechanisms of gene repression in S.cerevisiae was significantly advanced. In this review, we focus on such Sir-independent mechanisms of gene repression executed by various Histone Deacetylases (HDACs) and Histone Methyl Transferases (HMTs). We focus on the genes regulated by these enzymes and their known mechanisms of action. We describe the cooperation and redundancy between HDACs and HMTs, and their involvement in gene repression by non-coding RNAs or by their non-histone substrates. We also propose models of epigenetic transmission of the chromatin structures produced by these enzymes and discuss these in the context of gene repression phenomena in other organisms. These include the recycling of the epigenetic marks imposed by HMTs or the recycling of the complexes harboring HDACs.
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Affiliation(s)
- Safia Mahabub Sauty
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Kholoud Shaban
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada
| | - Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada.
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25
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Chen Z, Zehraoui E, Atanasoff-Kardjalieff AK, Strauss J, Studt L, Ponts N. Effect of H2A.Z deletion is rescued by compensatory mutations in Fusarium graminearum. PLoS Genet 2020; 16:e1009125. [PMID: 33091009 PMCID: PMC7608984 DOI: 10.1371/journal.pgen.1009125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 11/03/2020] [Accepted: 09/21/2020] [Indexed: 12/31/2022] Open
Abstract
Fusarium head blight is a destructive disease of grains resulting in reduced yields and contamination of grains with mycotoxins worldwide; Fusarium graminearum is its major causal agent. Chromatin structure changes play key roles in regulating mycotoxin biosynthesis in filamentous fungi. Using a split-marker approach in three F. graminearum strains INRA156, INRA349 and INRA812 (PH-1), we knocked out the gene encoding H2A.Z, a ubiquitous histone variant reported to be involved in a diverse range of biological processes in yeast, plants and animals, but rarely studied in filamentous fungi. All ΔH2A.Z mutants exhibit defects in development including radial growth, sporulation, germination and sexual reproduction, but with varying degrees of severity between them. Heterogeneity of osmotic and oxidative stress response as well as mycotoxin production was observed in ΔH2A.Z strains. Adding-back wild-type H2A.Z in INRA349ΔH2A.Z could not rescue the phenotypes. Whole genome sequencing revealed that, although H2A.Z has been removed from the genome and the deletion cassette is inserted at H2A.Z locus only, mutations occur at other loci in each mutant regardless of the genetic background. Genes affected by these mutations encode proteins involved in chromatin remodeling, such as the helicase Swr1p or an essential subunit of the histone deacetylase Rpd3S, and one protein of unknown function. These observations suggest that H2A.Z and the genes affected by such mutations are part or the same genetic interaction network. Our results underline the genetic plasticity of F. graminearum facing detrimental gene perturbation. These findings suggest that intergenic suppressions rescue deleterious phenotypes in ΔH2A.Z strains, and that H2A.Z may be essential in F. graminearum. This assumption is further supported by the fact that H2A.Z deletion failed in another Fusarium spp., i.e., the rice pathogen Fusarium fujikuroi.
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Affiliation(s)
| | | | - Anna K. Atanasoff-Kardjalieff
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Joseph Strauss
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
| | - Lena Studt
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Vienna, Austria
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26
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de Jonge WJ, Brok M, Lijnzaad P, Kemmeren P, Holstege FCP. Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function. Mol Syst Biol 2020; 16:e9885. [PMID: 33280256 PMCID: PMC7586999 DOI: 10.15252/msb.20209885] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/06/2020] [Accepted: 09/10/2020] [Indexed: 11/25/2022] Open
Abstract
Protein-DNA interactions are dynamic, and these dynamics are an important aspect of chromatin-associated processes such as transcription or replication. Due to a lack of methods to study on- and off-rates across entire genomes, protein-DNA interaction dynamics have not been studied extensively. Here, we determine in vivo off-rates for the Saccharomyces cerevisiae chromatin organizing factor Abf1, at 191 sites simultaneously across the yeast genome. Average Abf1 residence times span a wide range, varying between 4.2 and 33 min. Sites with different off-rates are associated with different functional characteristics. This includes their transcriptional dependency on Abf1, nucleosome positioning and the size of the nucleosome-free region, as well as the ability to roadblock RNA polymerase II for termination. The results show how off-rates contribute to transcription factor function and that DIVORSEQ (Determining In Vivo Off-Rates by SEQuencing) is a meaningful way of investigating protein-DNA binding dynamics genome-wide.
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Affiliation(s)
- Wim J de Jonge
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Mariël Brok
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Philip Lijnzaad
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric OncologyUtrechtThe Netherlands
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27
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Liang XH, Nichols JG, De Hoyos CL, Crooke ST. Some ASOs that bind in the coding region of mRNAs and induce RNase H1 cleavage can cause increases in the pre-mRNAs that may blunt total activity. Nucleic Acids Res 2020; 48:9840-9858. [PMID: 32870273 PMCID: PMC7515700 DOI: 10.1093/nar/gkaa715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/13/2020] [Accepted: 08/19/2020] [Indexed: 01/06/2023] Open
Abstract
Antisense oligonucleotide (ASO) drugs that trigger RNase H1 cleavage of target RNAs have been developed to treat various diseases. Basic pharmacological principles suggest that the development of tolerance is a common response to pharmacological interventions. In this manuscript, for the first time we report a molecular mechanism of tolerance that occurs with some ASOs. Two observations stimulated our interest: some RNA targets are difficult to reduce with RNase H1 activating ASOs and some ASOs display a shorter duration of activity than the prolonged target reduction typically observed. We found that certain ASOs targeting the coding region of some mRNAs that initially reduce target mRNAs can surprisingly increase the levels of the corresponding pre-mRNAs. The increase in pre-mRNA is delayed and due to enhanced transcription and likely also slower processing. This process requires that the ASOs bind in the coding region and reduce the target mRNA by RNase H1 while the mRNA resides in the ribosomes. The pre-mRNA increase is dependent on UPF3A and independent of the NMD pathway or the XRN1-CNOT pathway. The response is consistent in multiple cell lines and independent of the methods used to introduce ASOs into cells.
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Affiliation(s)
- Xue-hai Liang
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Joshua G Nichols
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Cheryl L De Hoyos
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Stanley T Crooke
- Core Antisense Research, Ionis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
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28
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Kaczmarek Michaels K, Mohd Mostafa S, Ruiz Capella J, Moore CL. Regulation of alternative polyadenylation in the yeast Saccharomyces cerevisiae by histone H3K4 and H3K36 methyltransferases. Nucleic Acids Res 2020; 48:5407-5425. [PMID: 32356874 PMCID: PMC7261179 DOI: 10.1093/nar/gkaa292] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 12/17/2022] Open
Abstract
Adjusting DNA structure via epigenetic modifications, and altering polyadenylation (pA) sites at which precursor mRNA is cleaved and polyadenylated, allows cells to quickly respond to environmental stress. Since polyadenylation occurs co-transcriptionally, and specific patterns of nucleosome positioning and chromatin modifications correlate with pA site usage, epigenetic factors potentially affect alternative polyadenylation (APA). We report that the histone H3K4 methyltransferase Set1, and the histone H3K36 methyltransferase Set2, control choice of pA site in Saccharomyces cerevisiae, a powerful model for studying evolutionarily conserved eukaryotic processes. Deletion of SET1 or SET2 causes an increase in serine-2 phosphorylation within the C-terminal domain of RNA polymerase II (RNAP II) and in the recruitment of the cleavage/polyadenylation complex, both of which could cause the observed switch in pA site usage. Chemical inhibition of TOR signaling, which causes nutritional stress, results in Set1- and Set2-dependent APA. In addition, Set1 and Set2 decrease efficiency of using single pA sites, and control nucleosome occupancy around pA sites. Overall, our study suggests that the methyltransferases Set1 and Set2 regulate APA induced by nutritional stress, affect the RNAP II C-terminal domain phosphorylation at Ser2, and control recruitment of the 3′ end processing machinery to the vicinity of pA sites.
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Affiliation(s)
- Katarzyna Kaczmarek Michaels
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA
| | - Salwa Mohd Mostafa
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.,Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
| | - Julia Ruiz Capella
- Department of Biotechnology, Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid 28223, Spain
| | - Claire L Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.,Tufts University Graduate School of Biomedical Sciences, Boston, MA 02111, USA
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29
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Tettey TT, Gao X, Shao W, Li H, Story BA, Chitsazan AD, Glaser RL, Goode ZH, Seidel CW, Conaway RC, Zeitlinger J, Blanchette M, Conaway JW. A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing. Cell Rep 2020; 27:3770-3779.e7. [PMID: 31242411 DOI: 10.1016/j.celrep.2019.05.099] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 04/22/2019] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
FACT (facilitates chromatin transcription) is an evolutionarily conserved histone chaperone that was initially identified as an activity capable of promoting RNA polymerase II (Pol II) transcription through nucleosomes in vitro. In this report, we describe a global analysis of FACT function in Pol II transcription in Drosophila. We present evidence that loss of FACT has a dramatic impact on Pol II elongation-coupled processes including histone H3 lysine 4 (H3K4) and H3K36 methylation, consistent with a role for FACT in coordinating histone modification and chromatin architecture during Pol II transcription. Importantly, we identify a role for FACT in the maintenance of promoter-proximal Pol II pausing, a key step in transcription activation in higher eukaryotes. These findings bring to light a broader role for FACT in the regulation of Pol II transcription.
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Affiliation(s)
- Theophilus T Tettey
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; The Open University, Walton Hall, Milton Keynes, Buckinghamshire MK7 6AA, UK
| | - Xin Gao
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Wanqing Shao
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Hua Li
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Benjamin A Story
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Alex D Chitsazan
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Robert L Glaser
- Wadsworth Center, New York State Department of Health, PO Box 509, Albany, NY 12201, USA
| | - Zach H Goode
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Christopher W Seidel
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Marco Blanchette
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, 1000 E 50th St, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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30
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Demetriadou C, Koufaris C, Kirmizis A. Histone N-alpha terminal modifications: genome regulation at the tip of the tail. Epigenetics Chromatin 2020; 13:29. [PMID: 32680559 PMCID: PMC7367250 DOI: 10.1186/s13072-020-00352-w] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/09/2020] [Indexed: 01/07/2023] Open
Abstract
Histone proteins are decorated with numerous post-(PTMs) or co-(CTMs) translational modifications mainly on their unstructured tails, but also on their globular domain. For many decades research on histone modifications has been focused almost solely on the biological role of modifications occurring at the side-chain of internal amino acid residues. In contrast, modifications on the terminal N-alpha amino group of histones-despite being highly abundant and evolutionarily conserved-have been largely overlooked. This oversight has been due to the fact that these marks were being considered inert until recently, serving no regulatory functions. However, during the past few years accumulating evidence has drawn attention towards the importance of chemical marks added at the very N-terminal tip of histones and unveiled their role in key biological processes including aging and carcinogenesis. Further elucidation of the molecular mechanisms through which these modifications are regulated and by which they act to influence chromatin dynamics and DNA-based processes like transcription is expected to enlighten our understanding of their emerging role in controlling cellular physiology and contribution to human disease. In this review, we clarify the difference between N-alpha terminal (Nt) and internal (In) histone modifications; provide an overview of the different types of known histone Nt-marks and the associated histone N-terminal transferases (NTTs); and explore how they function to shape gene expression, chromatin architecture and cellular phenotypes.
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Affiliation(s)
- Christina Demetriadou
- Epigenetics Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Costas Koufaris
- Epigenetics Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus
| | - Antonis Kirmizis
- Epigenetics Laboratory, Department of Biological Sciences, University of Cyprus, 2109, Nicosia, Cyprus.
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31
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Tunable Transcriptional Interference at the Endogenous Alcohol Dehydrogenase Gene Locus in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2020; 10:1575-1583. [PMID: 32213532 PMCID: PMC7202008 DOI: 10.1534/g3.119.400937] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Neighboring sequences of a gene can influence its expression. In the phenomenon known as transcriptional interference, transcription at one region in the genome can repress transcription at a nearby region in cis. Transcriptional interference occurs at a number of eukaryotic loci, including the alcohol dehydrogenase (Adh) gene in Drosophila melanogaster. Adh is regulated by two promoters, which are distinct in their developmental timing of activation. It has been shown using transgene insertion that when the promoter distal from the Adh start codon is deleted, transcription from the proximal promoter becomes de-regulated. As a result, the Adh proximal promoter, which is normally active only during the early larval stages, becomes abnormally activated in adults. Whether this type of regulation occurs in the endogenous Adh context, however, remains unclear. Here, we employed the CRISPR/Cas9 system to edit the endogenous Adh locus and found that removal of the distal promoter also resulted in the untimely expression of the proximal promoter-driven mRNA isoform in adults, albeit at lower levels than previously reported. Importantly, transcription from the distal promoter was sufficient to repress proximal transcription in larvae, and the degree of this repression was dependent on the degree of distal promoter activity. Finally, upregulation of the distal Adh transcript led to the enrichment of histone 3 lysine 36 trimethylation over the Adh proximal promoter. We conclude that the endogenous Adh locus is developmentally regulated by transcriptional interference in a tunable manner.
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32
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Long noncoding RNA NEAT1 suppresses hepatocyte proliferation in fulminant hepatic failure through increased recruitment of EZH2 to the LATS2 promoter region and promotion of H3K27me3 methylation. Exp Mol Med 2020; 52:461-472. [PMID: 32157157 PMCID: PMC7156754 DOI: 10.1038/s12276-020-0387-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 12/17/2019] [Accepted: 12/27/2019] [Indexed: 01/06/2023] Open
Abstract
Fulminant hepatic failure (FHF) refers to the rapid development of severe acute liver injury with impaired synthetic function and encephalopathy in people with normal liver or well-compensated liver disease. This study aimed to investigate the function of long noncoding RNA (lncRNA) nuclear-enriched abundant transcript 1 (NEAT1) on the proliferation and apoptosis of hepatocytes in FHF. Our results revealed that lncRNA NEAT1 was upregulated in cell and animal models of FHF induced by D-galactosamine (D-GalN)/lipopolysaccharide (LPS). Overexpression of lncRNA NEAT1 resulted in elevated hepatocyte apoptosis and impaired large tumor-suppressor kinase 2 (LATS2) expression and proliferation. Functional analysis revealed that knockdown of lncRNA NEAT1 inhibited hepatocyte apoptosis and induced proliferation both in vitro and in vivo. RNA immunoprecipitation and chromatin immunoprecipitation assays demonstrated that lncRNA NEAT1 recruited enhancer of zeste homolog 2 (EZH2) to the LATS2 promoter and repressed LATS2 expression. Furthermore, ectopic expression of LATS2 increased proliferation and inhibited hepatocyte apoptosis by regulating the Hippo/Yes-associated protein (YAP) signaling pathway. Taken together, our findings indicate that lncRNA NEAT1 might serve as a novel target for FHF therapy due to its regulation of H3K27me3 methylation-dependent promotion of LATS2. A long noncoding RNA molecule, one that does not encode the synthesis of protein, is implicated in acute liver failure (AHF) and might offer a new target for drugs to treat the condition. AHF can be induced by various factors, including viruses, drugs, alcohol abuse, and inherited traits. Ke Cheng, Yujun Zhao and colleagues at Central South University in Changsha, China investigated the role of this RNA, called NEAT1, in cell and animal models of AHF. They identified increased production of NEAT1, which suppressed liver cell proliferation and promoted liver cell death. They also uncovered molecular details of the mechanisms underlying these effects, in which the RNA altered the production and regulatory modification of certain proteins. Further research should investigate the therapeutic possibilities of interfering with NEAT1 activity.
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33
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Nuño-Cabanes C, Ugidos M, Tarazona S, Martín-Expósito M, Ferrer A, Rodríguez-Navarro S, Conesa A. A multi-omics dataset of heat-shock response in the yeast RNA binding protein Mip6. Sci Data 2020; 7:69. [PMID: 32109230 PMCID: PMC7046740 DOI: 10.1038/s41597-020-0412-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/10/2020] [Indexed: 11/25/2022] Open
Abstract
Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12ac ChIP-seq data for wild-type and mip6Δ strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress. Raw data, processed data and preprocessing scripts are made available.
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Grants
- PROMETEO/2016/093 Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- PROMETEO/2016/093 Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- PROMETEO/2016/093 Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- PROMETEO/2016/093 Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- PROMETEO/2016/093 Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
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Affiliation(s)
- Carme Nuño-Cabanes
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC). Jaume Roig, 11, E-46010, Valencia, Spain
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Eduardo Primo-Yúfera, E-46012, Valencia, Spain
| | - Manuel Ugidos
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC). Jaume Roig, 11, E-46010, Valencia, Spain
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Eduardo Primo-Yúfera, E-46012, Valencia, Spain
| | - Sonia Tarazona
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València (UPV), Valencia, Spain
| | - Manuel Martín-Expósito
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC). Jaume Roig, 11, E-46010, Valencia, Spain
| | - Alberto Ferrer
- Department of Applied Statistics, Operations Research and Quality, Universitat Politècnica de València (UPV), Valencia, Spain
| | - Susana Rodríguez-Navarro
- Gene Expression and RNA Metabolism Laboratory, Instituto de Biomedicina de Valencia (CSIC). Jaume Roig, 11, E-46010, Valencia, Spain.
- Gene Expression and RNA Metabolism Laboratory, Centro de Investigación Príncipe Felipe, Eduardo Primo-Yúfera, E-46012, Valencia, Spain.
| | - Ana Conesa
- Microbiology and Cell Science Department, University of Florida, Gainesville, Florida, USA.
- Institute for Food and Agricultural Reserach, University of Florida, Gainesville, Florida, USA.
- Genetics Institute, University of Florida, Gainesville, Florida, USA.
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34
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Huff TC, Camarena V, Sant DW, Wilkes Z, Van Booven D, Aron AT, Muir RK, Renslo AR, Chang CJ, Monje PV, Wang G. Oscillatory cAMP signaling rapidly alters H3K4 methylation. Life Sci Alliance 2019; 3:3/1/e201900529. [PMID: 31882444 PMCID: PMC6935296 DOI: 10.26508/lsa.201900529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 01/02/2023] Open
Abstract
This work explores how GPCR-cAMP signaling dynamically influences histone methylation by altering intracellular labile Fe(II) levels and subsequently modulating histone demethylase activity. Epigenetic variation reflects the impact of a dynamic environment on chromatin. However, it remains elusive how environmental factors influence epigenetic events. Here, we show that G protein–coupled receptors (GPCRs) alter H3K4 methylation via oscillatory intracellular cAMP. Activation of Gs-coupled receptors caused a rapid decrease of H3K4me3 by elevating cAMP, whereas stimulation of Gi-coupled receptors increased H3K4me3 by diminishing cAMP. H3K4me3 gradually recovered towards baseline levels after the removal of GPCR ligands, indicating that H3K4me3 oscillates in tandem with GPCR activation. cAMP increased intracellular labile Fe(II), the cofactor for histone demethylases, through a non-canonical cAMP target—Rap guanine nucleotide exchange factor-2 (RapGEF2), which subsequently enhanced endosome acidification and Fe(II) release from the endosome via vacuolar H+-ATPase assembly. Removing Fe(III) from the media blocked intracellular Fe(II) elevation after stimulation of Gs-coupled receptors. Iron chelators and inhibition of KDM5 demethylases abolished cAMP-mediated H3K4me3 demethylation. Taken together, these results suggest a novel function of cAMP signaling in modulating histone demethylation through labile Fe(II).
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Affiliation(s)
- Tyler C Huff
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Vladimir Camarena
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - David W Sant
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Zachary Wilkes
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Allegra T Aron
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Ryan K Muir
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - Christopher J Chang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Department of Chemistry, University of California, Berkeley, CA, USA.,Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Paula V Monje
- Department of Neurological Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gaofeng Wang
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA .,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
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35
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Greenstein RA, Barrales RR, Sanchez NA, Bisanz JE, Braun S, Al-Sady B. Set1/COMPASS repels heterochromatin invasion at euchromatic sites by disrupting Suv39/Clr4 activity and nucleosome stability. Genes Dev 2019; 34:99-117. [PMID: 31805521 PMCID: PMC6938669 DOI: 10.1101/gad.328468.119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/30/2019] [Indexed: 12/27/2022]
Abstract
In this study, Greenstein et al. set out to define the spatial encoding signals within euchromatin that act to limit heterochromatin spreading. Using molecular and cell-based assays in fission yeast, the authors report that heterochromatin repulsion is locally encoded by Set1/COMPASS on certain actively transcribed genes and that this protective role is most prominent at heterochromatin islands, small domains interspersed in euchromatin that regulate cell fate specifiers. Protection of euchromatin from invasion by gene-repressive heterochromatin is critical for cellular health and viability. In addition to constitutive loci such as pericentromeres and subtelomeres, heterochromatin can be found interspersed in gene-rich euchromatin, where it regulates gene expression pertinent to cell fate. While heterochromatin and euchromatin are globally poised for mutual antagonism, the mechanisms underlying precise spatial encoding of heterochromatin containment within euchromatic sites remain opaque. We investigated ectopic heterochromatin invasion by manipulating the fission yeast mating type locus boundary using a single-cell spreading reporter system. We found that heterochromatin repulsion is locally encoded by Set1/COMPASS on certain actively transcribed genes and that this protective role is most prominent at heterochromatin islands, small domains interspersed in euchromatin that regulate cell fate specifiers. Sensitivity to invasion by heterochromatin, surprisingly, is not dependent on Set1 altering overall gene expression levels. Rather, the gene-protective effect is strictly dependent on Set1's catalytic activity. H3K4 methylation, the Set1 product, antagonizes spreading in two ways: directly inhibiting catalysis by Suv39/Clr4 and locally disrupting nucleosome stability. Taken together, these results describe a mechanism for spatial encoding of euchromatic signals that repel heterochromatin invasion.
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Affiliation(s)
- R A Greenstein
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA.,TETRAD Graduate Program, University of California at San Francisco, San Francisco, California 94143, USA
| | - Ramon R Barrales
- Department of Physiological Chemistry, Biomedical Center (BMC), Ludwig Maximilians University of Munich, 82152 Martinsried, Germany.,International Max Planck Research School for Molecular and Cellular Life Sciences, 82152 Martinsried, Germany
| | - Nicholas A Sanchez
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA.,TETRAD Graduate Program, University of California at San Francisco, San Francisco, California 94143, USA
| | - Jordan E Bisanz
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA
| | - Sigurd Braun
- Department of Physiological Chemistry, Biomedical Center (BMC), Ludwig Maximilians University of Munich, 82152 Martinsried, Germany.,International Max Planck Research School for Molecular and Cellular Life Sciences, 82152 Martinsried, Germany
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California at San Francisco, San Francisco, California 94143, USA
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36
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Trinh DA, Shirakawa R, Kimura T, Sakata N, Goto K, Horiuchi H. Inhibitor of Growth 4 (ING4) is a positive regulator of rRNA synthesis. Sci Rep 2019; 9:17235. [PMID: 31754246 PMCID: PMC6872537 DOI: 10.1038/s41598-019-53767-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 08/30/2019] [Indexed: 01/29/2023] Open
Abstract
Ribosome biogenesis is essential for maintaining basic cellular activities although its mechanism is not fully understood. Inhibitor of growth 4 (ING4) is a member of ING family while its cellular functions remain controversial. Here, we identified several nucleolar proteins as novel ING4 interacting proteins. ING4 localized in the nucleus with strong accumulation in the nucleolus through its plant homeodomain, which is known to interact with histone trimethylated H3K4, commonly present in the promoter of active genes. ING4 deficient cells exhibited slower proliferation and the alteration in nucleolar structure with reduced rRNA transcription, which was rescued by exogenous expression of GFP-ING4 to the similar levels of wild type cells. In the ING4 deficient cells, histone H3K9 acetylation and the key rRNA transcription factor UBF at the promoter of rDNA were reduced, both of which were also recovered by exogenous GFP-ING4 expression. Thus, ING4 could positively regulate rRNA transcription through modulation of histone modifications at the rDNA promoter.
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Affiliation(s)
- Duc-Anh Trinh
- Department of Oral Cancer Therapeutics, Graduate School of Dentistry, Tohoku University, Sendai, Japan.,Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Ryutaro Shirakawa
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Tomohiro Kimura
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.,Research Center for Molecular Genetics, Institute for Promotion of Medical Science Research, Yamagata University Faculty of Medicine, Yamagata, Yamagata, Japan
| | - Natsumi Sakata
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Kota Goto
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hisanori Horiuchi
- Department of Oral Cancer Therapeutics, Graduate School of Dentistry, Tohoku University, Sendai, Japan. .,Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan.
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A mass spectrometry-based assay using metabolic labeling to rapidly monitor chromatin accessibility of modified histone proteins. Sci Rep 2019; 9:13613. [PMID: 31541121 PMCID: PMC6754405 DOI: 10.1038/s41598-019-49894-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/24/2019] [Indexed: 12/22/2022] Open
Abstract
Histone post-translational modifications (PTMs) contribute to chromatin accessibility due to their chemical properties and their ability to recruit enzymes responsible for DNA readout and chromatin remodeling. To date, more than 400 different histone PTMs and thousands of combinations of PTMs have been identified, the vast majority with still unknown biological function. Identification and quantification of histone PTMs has become routine in mass spectrometry (MS) but, since raising antibodies for each PTM in a study can be prohibitive, lots of potential is lost from MS datasets when uncharacterized PTMs are found to be significantly regulated. We developed an assay that uses metabolic labeling and MS to associate chromatin accessibility with histone PTMs and their combinations. The labeling is achieved by spiking in the cell media a 5x concentration of stable isotope labeled arginine and allow cells to grow for at least one cell cycle. We quantified the labeling incorporation of about 200 histone peptides with a proteomics workflow, and we confirmed that peptides carrying PTMs with extensively characterized roles in active transcription or gene silencing were in highly or poorly labeled forms, respectively. Data were further validated using next-generation sequencing to assess the transcription rate of chromatin regions modified with five selected PTMs. Furthermore, we quantified the labeling rate of peptides carrying co-existing PTMs, proving that this method is suitable for combinatorial PTMs. We focus on the abundant bivalent mark H3K27me3K36me2, showing that H3K27me3 dominantly represses histone swapping rate even in the presence of the more permissive PTM H3K36me2. Together, we envision this method will help to generate hypotheses regarding histone PTM functions and, potentially, elucidate the role of combinatorial histone codes.
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Transcription-dependent targeting of Hda1C to hyperactive genes mediates H4-specific deacetylation in yeast. Nat Commun 2019; 10:4270. [PMID: 31537788 PMCID: PMC6753149 DOI: 10.1038/s41467-019-12077-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 08/20/2019] [Indexed: 11/08/2022] Open
Abstract
In yeast, Hda1 histone deacetylase complex (Hda1C) preferentially deacetylates histones H3 and H2B, and functionally interacts with Tup1 to repress transcription. However, previous studies identified global increases in histone H4 acetylation in cells lacking Hda1, a component of Hda1C. Here, we find that Hda1C binds to hyperactive genes, likely via the interaction between the Arb2 domain of Hda1 and RNA polymerase II. Additionally, we report that Hda1C specifically deacetylates H4, but not H3, at hyperactive genes to partially inhibit elongation. This role is contrast to that of the Set2-Rpd3S pathway deacetylating histones at infrequently transcribed genes. We also find that Hda1C deacetylates H3 at inactive genes to delay the kinetics of gene induction. Therefore, in addition to fine-tuning of transcriptional response via H3-specific deacetylation, Hda1C may modulate elongation by specifically deacetylating H4 at highly transcribed regions.
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39
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Lee BB, Choi A, Kim JH, Jun Y, Woo H, Ha SD, Yoon CY, Hwang JT, Steinmetz L, Buratowski S, Lee S, Kim HY, Kim T. Rpd3L HDAC links H3K4me3 to transcriptional repression memory. Nucleic Acids Res 2019; 46:8261-8274. [PMID: 29982589 PMCID: PMC6144869 DOI: 10.1093/nar/gky573] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/14/2018] [Indexed: 11/13/2022] Open
Abstract
Transcriptional memory is critical for the faster reactivation of necessary genes upon environmental changes and requires that the genes were previously in an active state. However, whether transcriptional repression also displays ‘memory’ of the prior transcriptionally inactive state remains unknown. In this study, we show that transcriptional repression of ∼540 genes in yeast occurs much more rapidly if the genes have been previously repressed during carbon source shifts. This novel transcriptional response has been termed transcriptional repression memory (TREM). Interestingly, Rpd3L histone deacetylase (HDAC), targeted to active promoters induces TREM. Mutants for Rpd3L exhibit increased acetylation at active promoters and delay TREM significantly. Surprisingly, the interaction between H3K4me3 and Rpd3L via the Pho23 PHD finger is critical to promote histone deacetylation and TREM by Rpd3L. Therefore, we propose that an active mark, H3K4me3 enriched at active promoters, instructs Rpd3L HDAC to induce histone deacetylation and TREM.
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Affiliation(s)
- Bo Bae Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Ahyoung Choi
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Ji Hyun Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Yukyung Jun
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Hyeonju Woo
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - So Dam Ha
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Chae Young Yoon
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | | | - Lars Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, and Stanford Genome Technology Center and Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stephen Buratowski
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Sanghyuk Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Hye Young Kim
- Department of Biomedical Sciences and Medical Science, Seoul National University College of Medicine, Seoul 03080, Korea
| | - TaeSoo Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
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40
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Abstract
Cells must fine-tune their gene expression programs for optimal cellular activities in their natural growth conditions. Transcriptional memory, a unique transcriptional response, plays a pivotal role in faster reactivation of genes upon environmental changes, and is facilitated if genes were previously in an active state. Hyper-activation of gene expression by transcriptional memory is critical for cellular differentiation, development, and adaptation. TREM (Transcriptional REpression Memory), a distinct type of transcriptional memory, promoting hyper-repression of unnecessary genes, upon environmental changes has been recently reported. These two transcriptional responses may optimize specific gene expression patterns, in rapidly changing environments. Emerging evidence suggests that they are also critical for immune responses. In addition to memory B and T cells, innate immune cells are transcriptionally hyperactivated by restimulation, with the same or different pathogens known as trained immunity. In this review, we briefly summarize recent progress in chromatin-based regulation of transcriptional memory, and its potential role in immune responses. [BMB Reports 2019; 52(2): 127-132].
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Affiliation(s)
- Min Young Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Ji Eun Lee
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
| | - Lark Kyun Kim
- Severance Biomedical Science Institute and BK21 PLUS Project to Medical Sciences, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 06230, Korea
| | - TaeSoo Kim
- Department of Life Science and the Research Center for Cellular Homeostasis, Ewha Womans University, Seoul 03760, Korea
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41
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Choudhury R, Singh S, Arumugam S, Roguev A, Stewart AF. The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation. Genes Dev 2019; 33:550-564. [PMID: 30842216 PMCID: PMC6499330 DOI: 10.1101/gad.322222.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/15/2019] [Indexed: 12/19/2022]
Abstract
In this study, Choudhury et al. report that yeast Set1C/COMPASS is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. This presents a new paradigm for the establishment of epigenetic detail, in which dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. Epigenetic modifications can maintain or alter the inherent symmetry of the nucleosome. However, the mechanisms that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.
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Affiliation(s)
- Rupam Choudhury
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Sukhdeep Singh
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Senthil Arumugam
- European Molecular Biology Laboratory Australia Node for Single Molecule Science, ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Assen Roguev
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94518, USA
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
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42
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Probiotic lactobacilli mediated changes in global epigenetic signatures of human intestinal epithelial cells during Escherichia coli challenge. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01451-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Mouche A, Archambeau J, Ricordel C, Chaillot L, Bigot N, Guillaudeux T, Grenon M, Pedeux R. ING3 is required for ATM signaling and DNA repair in response to DNA double strand breaks. Cell Death Differ 2019; 26:2344-2357. [PMID: 30804473 DOI: 10.1038/s41418-019-0305-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 01/16/2023] Open
Abstract
Inhibitor of Growth 3 (ING3) is a candidate tumor suppressor gene whose expression is lost in tumors such as hepatocellular carcinoma, head and neck squamous cell carcinoma and melanoma. In the present study, we show that ING3-depleted human cells and yeast cells deleted for its ortholog YNG2 are sensitive to DNA damage suggesting a conserved role in response to such stress. In human cells, ING3 is recruited to DNA double strand breaks and is required for ATM activation. Remarkably, in response to doxorubicin, ATM activation is dependent on ING3 but not on TIP60, whose recruitment to DNA breaks also depends on ING3. These events lead to ATM-mediated phosphorylation of NBS1 and the subsequent recruitment of RNF8, RNF168, 53BP1, and BRCA1, which are major mediators of the DNA damage response. Accordingly, upon genotoxic stress, DNA repair by non-homologous end joining (NHEJ) or homologous recombination (HR) were impaired in absence of ING3. Finally, immunoglobulin class switch recombination (CSR), a physiological mechanism requiring NHEJ repair, was impaired in the absence of ING3. Since deregulation of DNA double strand break repair is associated with genomic instability, we propose a novel function of ING3 as a caretaker tumor suppressor involved in the DNA damage signaling and repair.
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Affiliation(s)
- Audrey Mouche
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France.,INSERM U1236, MICMAC, Rennes, France
| | - Jérôme Archambeau
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France
| | - Charles Ricordel
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France
| | - Laura Chaillot
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France.,UMS Biosit, SFR Biologie-Santé, Rennes, France
| | - Nicolas Bigot
- Université de Rennes 1, Rennes, France.,INSERM U1236, MICMAC, Rennes, France.,Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Thierry Guillaudeux
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France.,Université de Rennes 1, Rennes, France.,UMS Biosit, SFR Biologie-Santé, Rennes, France
| | - Muriel Grenon
- Biochemistry, School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Rémy Pedeux
- INSERM U1242, Chemistry Oncogenesis Stress and Signaling, CLCC Eugène Marquis, Rennes, France. .,Université de Rennes 1, Rennes, France.
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Sah A, Sotnikov S, Kharitonova M, Schmuckermair C, Diepold RP, Landgraf R, Whittle N, Singewald N. Epigenetic Mechanisms Within the Cingulate Cortex Regulate Innate Anxiety-Like Behavior. Int J Neuropsychopharmacol 2019; 22:317-328. [PMID: 30668714 PMCID: PMC6441131 DOI: 10.1093/ijnp/pyz004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Pathological anxiety originates from a complex interplay of genetic predisposition and environmental factors, acting via epigenetic mechanisms. Epigenetic processes that can counteract detrimental genetic risk towards innate high anxiety are not well characterized. METHODS We used female mouse lines of selectively bred high (HAB)- vs low (LAB)-innate anxiety-related behavior and performed select environmental and pharmacological manipulations to alter anxiety levels as well as brain-specific manipulations and immunohistochemistry to investigate neuronal mechanisms associated with alterations in anxiety-related behavior. RESULTS Inborn hyperanxiety of high anxiety-like phenotypes was effectively reduced by environmental enrichment exposure. c-Fos mapping revealed that hyperanxiety in high anxiety-like phenotypes was associated with blunted challenge-induced neuronal activation in the cingulate-cortex, which was normalized by environmental enrichment. Relating this finding with epigenetic modifications, we found that high anxiety-like phenotypes (compared with low-innate anxiety phenotypes) showed reduced acetylation in the hypoactivated cingulate-cortex neurons following a mild emotional challenge, which again was normalized by environmental enrichment. Paralleling the findings using environmental enrichment, systemic administration of histone-deacetylase-inhibitor MS-275 elicited an anxiolytic-like effect, which was correlated with increased acetylated-histone-3 levels within cingulate-cortex. Finally, as a proof-of-principle, local MS-275 injection into cingulate-cortex rescued enhanced innate anxiety and increased acetylated-histone-3 within the cingulate-cortex, suggesting this epigenetic mark as a biomarker for treatment success. CONCLUSIONS Taken together, the present findings provide the first causal evidence that the attenuation of high innate anxiety-like behavior via environmental/pharmacological manipulations is epigenetically mediated via acetylation changes within the cingulate-cortex. Finally, histone-3 specific histone-deacetylase-inhibitor could be of therapeutic importance in anxiety disorders.
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Affiliation(s)
- Anupam Sah
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | | | - Maria Kharitonova
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Claudia Schmuckermair
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | | | | | - Nigel Whittle
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Nicolas Singewald
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria,Correspondence: Nicolas Singewald, PhD, Department of Pharmacology and Toxicology, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80–82/III, A-6020 Innsbruck, Austria ()
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45
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Soudet J, Gill JK, Stutz F. Noncoding transcription influences the replication initiation program through chromatin regulation. Genome Res 2018; 28:1882-1893. [PMID: 30401734 PMCID: PMC6280764 DOI: 10.1101/gr.239582.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/31/2018] [Indexed: 01/07/2023]
Abstract
In eukaryotic organisms, replication initiation follows a temporal program. Among the parameters that regulate this program in Saccharomyces cerevisiae, chromatin structure has been at the center of attention without considering the contribution of transcription. Here, we revisit the replication initiation program in the light of widespread genomic noncoding transcription. We find that noncoding RNA transcription termination in the vicinity of autonomously replicating sequences (ARSs) shields replication initiation from transcriptional readthrough. Consistently, high natural nascent transcription correlates with low ARS efficiency and late replication timing. High readthrough transcription is also linked to increased nucleosome occupancy and high levels of H3K36me3. Moreover, forcing ARS readthrough transcription promotes these chromatin features. Finally, replication initiation defects induced by increased transcriptional readthrough are partially rescued in the absence of H3K36 methylation. Altogether, these observations indicate that natural noncoding transcription into ARSs influences replication initiation through chromatin regulation.
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Affiliation(s)
- Julien Soudet
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| | - Jatinder Kaur Gill
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
| | - Françoise Stutz
- Department of Cell Biology, University of Geneva, 1211 Genève 4, Switzerland
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Palazzo AF, Lee ES. Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs. Front Genet 2018; 9:440. [PMID: 30386371 PMCID: PMC6199362 DOI: 10.3389/fgene.2018.00440] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/14/2018] [Indexed: 11/26/2022] Open
Abstract
Eukaryotes are divided into two major compartments: the nucleus where RNA is synthesized and processed, and the cytoplasm, where mRNA is translated into proteins. Although many different RNAs are made, only a subset is allowed access to the cytoplasm, primarily RNAs involved in protein synthesis (mRNA, tRNA, and rRNA). In contrast, nuclear retained transcripts are mostly long non-coding RNAs (lncRNAs) whose role in cell physiology has been a source of much investigation in the past few years. In addition, it is likely that many non-functional RNAs, which arise by spurious transcription and misprocessing of functional RNAs, are also retained in the nucleus and degraded. In this review, the main sequence features that dictate whether any particular mRNA or lncRNA is a substrate for retention in the nucleus, or export to the cytoplasm, are discussed. Although nuclear export is promoted by RNA-splicing due to the fact that the spliceosome can help recruit export factors to the mature RNA, nuclear export does not require splicing. Indeed, most stable unspliced transcripts are well exported and associate with these same export factors in a splicing-independent manner. In contrast, nuclear retention is promoted by specialized cis-elements found in certain RNAs. This new understanding of the determinants of nuclear retention and cytoplasmic export provides a deeper understanding of how information flow is regulated in eukaryotic cells. Ultimately these processes promote the evolution of complexity in eukaryotes by shaping the genomic content through constructive neutral evolution.
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Brown T, Howe FS, Murray SC, Wouters M, Lorenz P, Seward E, Rata S, Angel A, Mellor J. Antisense transcription-dependent chromatin signature modulates sense transcript dynamics. Mol Syst Biol 2018; 14:e8007. [PMID: 29440389 PMCID: PMC5810148 DOI: 10.15252/msb.20178007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 01/13/2018] [Accepted: 01/16/2018] [Indexed: 12/22/2022] Open
Abstract
Antisense transcription is widespread in genomes. Despite large differences in gene size and architecture, we find that yeast and human genes share a unique, antisense transcription-associated chromatin signature. We asked whether this signature is related to a biological function for antisense transcription. Using quantitative RNA-FISH, we observed changes in sense transcript distributions in nuclei and cytoplasm as antisense transcript levels were altered. To determine the mechanistic differences underlying these distributions, we developed a mathematical framework describing transcription from initiation to transcript degradation. At GAL1, high levels of antisense transcription alter sense transcription dynamics, reducing rates of transcript production and processing, while increasing transcript stability. This relationship with transcript stability is also observed as a genome-wide association. Establishing the antisense transcription-associated chromatin signature through disruption of the Set3C histone deacetylase activity is sufficient to similarly change these rates even in the absence of antisense transcription. Thus, antisense transcription alters sense transcription dynamics in a chromatin-dependent manner.
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Affiliation(s)
- Thomas Brown
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Struan C Murray
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Philipp Lorenz
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Emily Seward
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Scott Rata
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andrew Angel
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, Oxford, UK
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