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Weinzapfel EN, Fedder-Semmes KN, Sun ZW, Keogh MC. Beyond the tail: the consequence of context in histone post-translational modification and chromatin research. Biochem J 2024; 481:219-244. [PMID: 38353483 PMCID: PMC10903488 DOI: 10.1042/bcj20230342] [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: 12/30/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
The role of histone post-translational modifications (PTMs) in chromatin structure and genome function has been the subject of intense debate for more than 60 years. Though complex, the discourse can be summarized in two distinct - and deceptively simple - questions: What is the function of histone PTMs? And how should they be studied? Decades of research show these queries are intricately linked and far from straightforward. Here we provide a historical perspective, highlighting how the arrival of new technologies shaped discovery and insight. Despite their limitations, the tools available at each period had a profound impact on chromatin research, and provided essential clues that advanced our understanding of histone PTM function. Finally, we discuss recent advances in the application of defined nucleosome substrates, the study of multivalent chromatin interactions, and new technologies driving the next era of histone PTM research.
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2
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Muenstermann C, Clemens KJ. Epigenetic mechanisms of nicotine dependence. Neurosci Biobehav Rev 2024; 156:105505. [PMID: 38070842 DOI: 10.1016/j.neubiorev.2023.105505] [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: 08/31/2023] [Revised: 11/09/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023]
Abstract
Smoking continues to be a leading cause of preventable disease and death worldwide. Nicotine dependence generates a lifelong propensity towards cravings and relapse, presenting an ongoing challenge for the development of treatments. Accumulating evidence supports a role for epigenetics in the development and maintenance of addiction to many drugs of abuse, however, the involvement of epigenetics in nicotine dependence is less clear. Here we review evidence that nicotine interacts with epigenetic mechanisms to enable the maintenance of nicotine-seeking across time. Research across species suggests that nicotine increases permissive histone acetylation, decreases repressive histone methylation, and modulates levels of DNA methylation and noncoding RNA expression throughout the brain. These changes are linked to the promoter regions of genes critical for learning and memory, reward processing and addiction. Pharmacological manipulation of enzymes that catalyze core epigenetic modifications regulate nicotine reward and associative learning, demonstrating a functional role of epigenetic modifications in nicotine dependence. These findings are consistent with nicotine promoting an overall permissive chromatin state at genes important for learning, memory and reward. By exploring these links through next-generation sequencing technologies, epigenetics provides a promising avenue for future interventions to treat nicotine dependence.
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Affiliation(s)
| | - Kelly J Clemens
- School of Psychology, University of New South Wales, Sydney, Australia.
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3
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Zhang X, Fawwal DV, Spangle JM, Corbett AH, Jones CY. Exploring the Molecular Underpinnings of Cancer-Causing Oncohistone Mutants Using Yeast as a Model. J Fungi (Basel) 2023; 9:1187. [PMID: 38132788 PMCID: PMC10744705 DOI: 10.3390/jof9121187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Understanding the molecular basis of cancer initiation and progression is critical in developing effective treatment strategies. Recently, mutations in genes encoding histone proteins that drive oncogenesis have been identified, converting these essential proteins into "oncohistones". Understanding how oncohistone mutants, which are commonly single missense mutations, subvert the normal function of histones to drive oncogenesis requires defining the functional consequences of such changes. Histones genes are present in multiple copies in the human genome with 15 genes encoding histone H3 isoforms, the histone for which the majority of oncohistone variants have been analyzed thus far. With so many wildtype histone proteins being expressed simultaneously within the oncohistone, it can be difficult to decipher the precise mechanistic consequences of the mutant protein. In contrast to humans, budding and fission yeast contain only two or three histone H3 genes, respectively. Furthermore, yeast histones share ~90% sequence identity with human H3 protein. Its genetic simplicity and evolutionary conservation make yeast an excellent model for characterizing oncohistones. The power of genetic approaches can also be exploited in yeast models to define cellular signaling pathways that could serve as actionable therapeutic targets. In this review, we focus on the value of yeast models to serve as a discovery tool that can provide mechanistic insights and inform subsequent translational studies in humans.
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Affiliation(s)
- Xinran Zhang
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
| | - Dorelle V. Fawwal
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Jennifer M. Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Anita H. Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Celina Y. Jones
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
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4
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Brickner JH. Inheritance of epigenetic transcriptional memory through read-write replication of a histone modification. Ann N Y Acad Sci 2023; 1526:50-58. [PMID: 37391188 DOI: 10.1111/nyas.15033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2023]
Abstract
Epigenetic transcriptional regulation frequently requires histone modifications. Some, but not all, of these modifications are able to template their own inheritance. Here, I discuss the molecular mechanisms by which histone modifications can be inherited and relate these ideas to new results about epigenetic transcriptional memory, a phenomenon that poises recently repressed genes for faster reactivation and has been observed in diverse organisms. Recently, we found that the histone H3 lysine 4 dimethylation that is associated with this phenomenon plays a critical role in sustaining memory and, when factors critical for the establishment of memory are inactivated, can be stably maintained through multiple mitoses. This chromatin-mediated inheritance mechanism may involve a physical interaction between an H3K4me2 reader, SET3C, and an H3K4me2 writer, Spp1- COMPASS. This is the first example of a chromatin-mediated inheritance of a mark that promotes transcription.
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Affiliation(s)
- Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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5
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Zalambani C, Rizzardi N, Marziali G, Foschi C, Morselli S, Djusse ME, Naldi M, Fato R, Calonghi N, Marangoni A. Role of D(-)-Lactic Acid in Prevention of Chlamydia trachomatis Infection in an In Vitro Model of HeLa Cells. Pathogens 2023; 12:883. [PMID: 37513730 PMCID: PMC10383594 DOI: 10.3390/pathogens12070883] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
A vaginal microbiota dominated by certain Lactobacillus species may have a protective effect against Chlamydia trachomatis infection. One of the key antimicrobial compounds produced is lactic acid, which is believed to play a central role in host defense. Lactobacillus strains producing the D(-)-lactic acid isomer are known to exert stronger protection. However, the molecular mechanisms underlying this antimicrobial action are not well understood. The aim of this study was to investigate the role of D(-)-lactic acid isomer in the prevention of C. trachomatis infection in an in vitro HeLa cell model. We selected two strains of lactobacilli belonging to different species: a vaginal isolate of Lactobacillus crispatus that releases both D(-) and L(+) isomers and a strain of Lactobacillus reuteri that produces only the L(+) isomer. Initially, we demonstrated that L. crispatus was significantly more effective than L. reuteri in reducing C. trachomatis infectivity. A different pattern of histone acetylation and lactylation was observed when HeLa cells were pretreated for 24 h with supernatants of Lactobacillus crispatus or L. reuteri, resulting in different transcription of genes such as CCND1, CDKN1A, ITAG5 and HER-1. Similarly, distinct transcription patterns were found in HeLa cells treated with 10 mM D(-)- or L(+)-lactic acid isomers. Our findings suggest that D(-) lactic acid significantly affects two non-exclusive mechanisms involved in C. trachomatis infection: regulation of the cell cycle and expression of EGFR and α5β1-integrin.
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Affiliation(s)
- Chiara Zalambani
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Nicola Rizzardi
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Giacomo Marziali
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Claudio Foschi
- Microbiology, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
- Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Sara Morselli
- Microbiology, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Marielle Ezekielle Djusse
- Microbiology, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Marina Naldi
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Romana Fato
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Natalia Calonghi
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Antonella Marangoni
- Microbiology, Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
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Wang TK, Xu S, Fan Y, Wu J, Wang Z, Chen Y, Zhang Y. The Synergistic Effect of Proanthocyanidin and HDAC Inhibitor Inhibit Breast Cancer Cell Growth and Promote Apoptosis. Int J Mol Sci 2023; 24:10476. [PMID: 37445654 DOI: 10.3390/ijms241310476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 07/15/2023] Open
Abstract
Histone deacetylase inhibitor (HDACi) is a drug mainly used to treat hematological tumors and breast cancer, but its inhibitory effect on breast cancer falls short of expectations. Grape seed proanthocyanidin extract (GSPE) with abundant proanthocyanidins (PAs) has been explored for its inhibition of HDAC activity in vitro and in vivo. To enhance HDACi's effectiveness, we investigated the potential of PA to synergistically enhance HDACi chidamide (Chi), and determined the underlying mechanism. We evaluated the half-inhibitory concentration (IC50) of PA and Chi using the cell counting kit 8 (CCK8), and analyzed drugs' synergistic effect with fixed-ratio combination using the software Compusyn. Breast cancer cell's phenotypes, including short-term and long-term proliferation, migration, invasion, apoptosis, and reactive oxygen species (ROS) levels, were assessed via CCK8, clone-formation assay, wound-healing test, Transwell Matrigel invasion assay, and flow-cytometry. Protein-protein interaction analysis (PPI) and KEGG pathway analysis were used to determine the underlying mechanism of synergy. PA + Chi synergistically inhibited cell growth in T47D and MDA-MB-231 breast cancer cell lines. Short-term and long-term proliferation were significantly inhibited, while cell apoptosis was promoted. Ten signaling pathways were identified to account for the synergistic effect after RNA sequencing. Their synergism may be closely related to the steroid biosynthesis and extracellular matrix (ECM) receptor interaction pathways. PA + Chi can synergistically inhibit breast cancer cell growth and proliferation, and promote apoptosis. These effects may be related to steroid biosynthesis or the ECM receptor pathway.
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Affiliation(s)
- Tsz Ki Wang
- Department of Breast Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
- Laboratory of Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
| | - Shaoting Xu
- Department of Breast Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
- Laboratory of Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
| | - Yuanjian Fan
- Department of Breast Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
- Laboratory of Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
| | - Jing Wu
- Department of Breast Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
- Laboratory of Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
| | - Zilin Wang
- Department of Breast Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
- Laboratory of Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
| | - Yue Chen
- Laboratory of Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
- Department of Thyroid Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
| | - Yunjian Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Sun-Yat Sen University, Guangzhou 510080, China
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7
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Deshpande N, Bryk M. Diverse and dynamic forms of gene regulation by the S. cerevisiae histone methyltransferase Set1. Curr Genet 2023; 69:91-114. [PMID: 37000206 DOI: 10.1007/s00294-023-01265-3] [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: 03/11/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 04/01/2023]
Abstract
Gene transcription is an essential and highly regulated process. In eukaryotic cells, the structural organization of nucleosomes with DNA wrapped around histone proteins impedes transcription. Chromatin remodelers, transcription factors, co-activators, and histone-modifying enzymes work together to make DNA accessible to RNA polymerase. Histone lysine methylation can positively or negatively regulate gene transcription. Methylation of histone 3 lysine 4 by SET-domain-containing proteins is evolutionarily conserved from yeast to humans. In higher eukaryotes, mutations in SET-domain proteins are associated with defects in the development and segmentation of embryos, skeletal and muscle development, and diseases, including several leukemias. Since histone methyltransferases are evolutionarily conserved, the mechanisms of gene regulation mediated by these enzymes are also conserved. Budding yeast Saccharomyces cerevisiae is an excellent model system to study the impact of histone 3 lysine 4 (H3K4) methylation on eukaryotic gene regulation. Unlike larger eukaryotes, yeast cells have only one enzyme that catalyzes H3K4 methylation, Set1. In this review, we summarize current knowledge about the impact of Set1-catalyzed H3K4 methylation on gene transcription in S. cerevisiae. We describe the COMPASS complex, factors that influence H3K4 methylation, and the roles of Set1 in gene silencing at telomeres and heterochromatin, as well as repression and activation at euchromatic loci. We also discuss proteins that "read" H3K4 methyl marks to regulate transcription and summarize alternate functions for Set1 beyond H3K4 methylation.
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Affiliation(s)
- Neha Deshpande
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Mary Bryk
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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8
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Luo G, Liu B, Fu T, Liu Y, Li B, Li N, Geng Q. The Role of Histone Deacetylases in Acute Lung Injury-Friend or Foe. Int J Mol Sci 2023; 24:ijms24097876. [PMID: 37175583 PMCID: PMC10178380 DOI: 10.3390/ijms24097876] [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: 03/07/2023] [Revised: 04/04/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023] Open
Abstract
Acute lung injury (ALI), caused by intrapulmonary or extrapulmonary factors such as pneumonia, shock, and sepsis, eventually disrupts the alveolar-capillary barrier, resulting in diffuse pulmonary oedema and microatasis, manifested by refractory hypoxemia, and respiratory distress. Not only is ALI highly lethal, but even if a patient survives, there are also multiple sequelae. Currently, there is no better treatment than supportive care, and we urgently need to find new targets to improve ALI. Histone deacetylases (HDACs) are epigenetically important enzymes that, together with histone acetylases (HATs), regulate the acetylation levels of histones and non-histones. While HDAC inhibitors (HDACis) play a therapeutic role in cancer, inflammatory, and neurodegenerative diseases, there is also a large body of evidence suggesting the potential of HDACs as therapeutic targets in ALI. This review explores the unique mechanisms of HDACs in different cell types of ALI, including macrophages, pulmonary vascular endothelial cells (VECs), alveolar epithelial cells (AECs), and neutrophils.
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Affiliation(s)
- Guoqing Luo
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Bohao Liu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Tinglv Fu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yi Liu
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Boyang Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ning Li
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Qing Geng
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
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Nazri JM, Oikonomopoulou K, de Araujo ED, Kraskouskaya D, Gunning PT, Chandran V. Histone deacetylase inhibitors as a potential new treatment for psoriatic disease and other inflammatory conditions. Crit Rev Clin Lab Sci 2023; 60:300-320. [PMID: 36846924 DOI: 10.1080/10408363.2023.2177251] [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: 03/01/2023]
Abstract
Collectively known as psoriatic disease, psoriasis and psoriatic arthritis (PsA) are immune-mediated inflammatory diseases in which patients present with cutaneous and musculoskeletal inflammation. Affecting roughly 2-3% of the world's total population, there remains unmet therapeutic needs in both psoriasis and PsA despite the availability of current immunomodulatory treatments. As a result, patients with psoriatic disease often experience reduced quality of life. Recently, a class of small molecules, commonly investigated as anti-cancer agents, called histone deacetylase (HDAC) inhibitors, have been proposed as a new promising anti-inflammatory treatment for immune- and inflammatory-related diseases. In inflammatory diseases, current evidence is derived from studies on diseases like rheumatoid arthritis (RA) and systematic lupus erythematosus (SLE), and while there are some reports studying psoriasis, data on PsA patients are not yet available. In this review, we provide a brief overview of psoriatic disease, psoriasis, and PsA, as well as HDACs, and discuss the rationale behind the potential use of HDAC inhibitors in the management of persistent inflammation to suggest its possible use in psoriatic disease.
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Affiliation(s)
- Jehan Mohammad Nazri
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | | | - Elvin D de Araujo
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, Canada
| | - Dziyana Kraskouskaya
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, Canada
| | - Patrick T Gunning
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada
| | - Vinod Chandran
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Schroeder Arthritis Institute, University Health Network, Toronto, Canada.,Department of Medicine, University of Toronto, Toronto, Canada.,Institute of Medical Science, University of Toronto, Toronto, Canada.,Department of Medicine, Memorial University, St. John's, Canada
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10
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PIWI-Interacting RNA (piRNA) and Epigenetic Editing in Environmental Health Sciences. Curr Environ Health Rep 2022; 9:650-660. [PMID: 35917009 DOI: 10.1007/s40572-022-00372-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW: The epigenome modulates gene expression in response to environmental stimuli. Modifications to the epigenome are potentially reversible, making them a promising therapeutic approach to mitigate environmental exposure effects on human health. This review details currently available genome and epigenome editing technologies and highlights ncRNA, including piRNA, as potential tools for targeted epigenome editing. RECENT FINDINGS: Zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR) associated nuclease (CRISPR/Cas) research has significantly advanced genome editing technology, with broad promise in genetic research and targeted therapies. Initial epigenome-directed therapies relied on global modification and suffered from limited specificity. Adapted from current genome editing tools, zinc finger protein (ZFP), TALE, and CRISPR/nuclease-deactivated Cas (dCas) systems now confer locus-specific epigenome editing, with promising applicability in the field of environmental health sciences. However, high incidence of off-target effects and time taken for screening limit their use. FUTURE DEVELOPMENT: ncRNA serve as a versatile biomarker with well-characterized regulatory mechanisms that can easily be adapted to edit the epigenome. For instance, the transposon silencing mechanism of germline PIWI-interacting RNAs (piRNA) could be engineered to specifically methylate a given gene, overcoming pitfalls of current global modifiers. Future developments in epigenome editing technologies will inform risk assessment through mechanistic investigation and serve as potential modes of intervention to mitigate environmentally induced adverse health outcomes later in life.
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11
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Wang Q, Xiong F, Wu G, Liu W, Chen J, Wang B, Chen Y. Gene body methylation in cancer: molecular mechanisms and clinical applications. Clin Epigenetics 2022; 14:154. [PMID: 36443876 PMCID: PMC9706891 DOI: 10.1186/s13148-022-01382-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
DNA methylation is an important epigenetic mechanism that regulates gene expression. To date, most DNA methylation studies have focussed on CpG islands in the gene promoter region, and the mechanism of methylation and the regulation of gene expression after methylation have been clearly elucidated. However, genome-wide methylation studies have shown that DNA methylation is widespread not only in promoters but also in gene bodies. Gene body methylation is widely involved in the expression regulation of many genes and is closely related to the occurrence and progression of malignant tumours. This review focusses on the formation of gene body methylation patterns, its regulation of transcription, and its relationship with tumours, providing clues to explore the mechanism of gene body methylation in regulating gene transcription and its significance and application in the field of oncology.
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Affiliation(s)
- Qi Wang
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Fei Xiong
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Guanhua Wu
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Wenzheng Liu
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Junsheng Chen
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Bing Wang
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Yongjun Chen
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
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12
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Svoboda LK, Perera BPU, Morgan RK, Polemi KM, Pan J, Dolinoy DC. Toxicoepigenetics and Environmental Health: Challenges and Opportunities. Chem Res Toxicol 2022; 35:1293-1311. [PMID: 35876266 PMCID: PMC9812000 DOI: 10.1021/acs.chemrestox.1c00445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The rapidly growing field of toxicoepigenetics seeks to understand how toxicant exposures interact with the epigenome to influence disease risk. Toxicoepigenetics is a promising field of environmental health research, as integrating epigenetics into the field of toxicology will enable a more thorough evaluation of toxicant-induced disease mechanisms as well as the elucidation of the role of the epigenome as a biomarker of exposure and disease and possible mediator of exposure effects. Likewise, toxicoepigenetics will enhance our knowledge of how environmental exposures, lifestyle factors, and diet interact to influence health. Ultimately, an understanding of how the environment impacts the epigenome to cause disease may inform risk assessment, permit noninvasive biomonitoring, and provide potential opportunities for therapeutic intervention. However, the translation of research from this exciting field into benefits for human and animal health presents several challenges and opportunities. Here, we describe four significant areas in which we see opportunity to transform the field and improve human health by reducing the disease burden caused by environmental exposures. These include (1) research into the mechanistic role for epigenetic change in environment-induced disease, (2) understanding key factors influencing vulnerability to the adverse effects of environmental exposures, (3) identifying appropriate biomarkers of environmental exposures and their associated diseases, and (4) determining whether the adverse effects of environment on the epigenome and human health are reversible through pharmacologic, dietary, or behavioral interventions. We then highlight several initiatives currently underway to address these challenges.
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Affiliation(s)
- Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bambarendage P U Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Rachel K Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Katelyn M Polemi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Junru Pan
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
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13
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Anderson EM, Taniguchi M. Epigenetic Effects of Addictive Drugs in the Nucleus Accumbens. Front Mol Neurosci 2022; 15:828055. [PMID: 35813068 PMCID: PMC9260254 DOI: 10.3389/fnmol.2022.828055] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/30/2022] [Indexed: 12/28/2022] Open
Abstract
Substance use induces long-lasting behavioral changes and drug craving. Increasing evidence suggests that epigenetic gene regulation contributes to the development and expression of these long-lasting behavioral alterations. Here we systematically review extensive evidence from rodent models of drug-induced changes in epigenetic regulation and epigenetic regulator proteins. We focus on histone acetylation and histone methylation in a brain region important for drug-related behaviors: the nucleus accumbens. We also discuss how experimentally altering these epigenetic regulators via systemically administered compounds or nucleus accumbens-specific manipulations demonstrate the importance of these proteins in the behavioral effects of drugs and suggest potential therapeutic value to treat people with substance use disorder. Finally, we discuss limitations and future directions for the field of epigenetic studies in the behavioral effects of addictive drugs and suggest how to use these insights to develop efficacious treatments.
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14
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Elucidation of binding preferences of YEATS domains to site-specific acetylated nucleosome core particles. J Biol Chem 2022; 298:102164. [PMID: 35732209 PMCID: PMC9293779 DOI: 10.1016/j.jbc.2022.102164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 01/02/2023] Open
Abstract
Acetylated lysine residues (Kac) in histones are recognized by epigenetic reader proteins, such as Yaf9, ENL, AF9, Taf14, and Sas5 (YEATS) domain-containing proteins. Human YEATS domains bind to the acetylated N-terminal tail of histone H3; however, their Kac-binding preferences at the level of the nucleosome are unknown. Through genetic code reprogramming, here, we established a nucleosome core particle (NCP) array containing histones that were acetylated at specific residues and used it to compare the Kac-binding preferences of human YEATS domains. We found that AF9-YEATS showed basal binding to the unmodified NCP and that it bound stronger to the NCP containing a single acetylation at one of K4, K9, K14, or K27 of H3, or to histone H4 multi-acetylated between K5 and K16. Crystal structures of AF9-YEATS in complex with an H4 peptide diacetylated either at K5/K8 or K8/K12 revealed that the aromatic cage of the YEATS domain recognized the acetylated K8 residue. Interestingly, E57 and D103 of AF9, both located outside of the aromatic cage, were shown to interact with acetylated K5 and K12 of H4, respectively, consistent with the increase in AF9-YEATS binding to the H4K8-acetylated NCP upon additional acetylation at K5 or K12. Finally, we show that a mutation of E57 to alanine in AF9-YEATS reduced the binding affinity for H4 multiacetylated NCPs containing H4K5ac. Our data suggest that the Kac-binding affinity of AF9-YEATS increases additively with the number of Kac in the histone tail.
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15
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Abstract
Reducing sugars can covalently react with proteins to generate a heterogeneous and complex group of compounds called advanced glycation end products (AGEs). AGEs are generally considered as pathogenic molecules, mediating a pro-inflammatory response and contributing to the development of a number of human diseases. However, the intrinsic function of AGEs remains to be elucidated. We now provide multiple lines of evidence showing that AGEs can specifically bind histone localized on the cell surface as an AGE-binding protein, regulate the function of histone as a plasminogen receptor, and result in the regulation of monocytes/macrophage recruitment to the site of inflammation. Our finding of histone as a cell-surface receptor for AGEs suggests that, beside our common concept of AGEs as danger-associated molecular patterns mediating a pro-inflammatory response, they may also be involved in the homeostatic response via binding to histone. Advanced glycation end products (AGEs) are believed to be pathogenic molecules that mediate pro-inflammatory responses. Here the authors identify histone as a cell-surface receptor for AGEs and show that AGEs may also be involved in the homeostatic response via binding to histone.
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16
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Jonas F, Yaakov G, Barkai N. Rtt109 promotes nucleosome replacement ahead of the replication fork. Genome Res 2022; 32:1089-1098. [PMID: 35609993 DOI: 10.1101/gr.276674.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/05/2022] [Indexed: 11/25/2022]
Abstract
DNA replication perturbs chromatin by triggering the eviction, replacement, and incorporation of nucleosomes. How this dynamic is orchestrated in time and space is poorly understood. Here, we apply a genetically encoded sensor for histone exchange to follow the time-resolved histone H3 exchange profile in budding yeast cells undergoing slow synchronous replication in nucleotide-limiting conditions. We find that new histones are incorporated not only behind, but also ahead of the replication fork. We provide evidence that Rtt109, the S-phase-induced acetyltransferase, stabilizes nucleosomes behind the fork but promotes H3 replacement ahead of the fork. Increased replacement ahead of the fork is independent of the primary Rtt109 acetylation target H3K56 and rather results from Vps75-dependent Rtt109 activity toward the H3 N terminus. Our results suggest that, at least under nucleotide-limiting conditions, selective incorporation of differentially modified H3s behind and ahead of the replication fork results in opposing effects on histone exchange, likely reflecting the distinct challenges for genome stability at these different regions.
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Affiliation(s)
- Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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17
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Kim HJ, Lee J, Chung MY, Park SH, Park JH, Choi HK, Hwang JT. Tamarixetin Abrogates Adipogenesis Through Inhibiting p300/CBP-Associated Factor Acetyltransferase Activity in 3T3-L1 Preadipocyte Cells. J Med Food 2022; 25:272-280. [PMID: 35320012 DOI: 10.1089/jmf.2021.k.0126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Tamarixetin (TX) is an O-methylated flavonoid naturally derived from quercetin. TX has bioactive properties; however, whether it shows antilipogenic activity remains unknown. Therefore, in the present study, we aimed to determine the antilipogenic effects of TX using 3T3-L1 adipocytes. The 3T3-L1 adipocytes were cultured in a differentiation medium with or without TX. Lipid accumulation was diminished and the mRNA expression of lipogenesis-related genes was decreased following TX treatment. We found that TX exhibited antilipogenic effects by inhibiting the expression of p300/CBP-associated factor (pCAF), a histone acetyltransferase, as confirmed by pCAF knockdown. Furthermore, TX inhibited both pCAF expression and its activity, thereby reducing the total acetylation level of nonhistone and histone proteins. Finally, TX decreased the expression of CCAAT/enhancer-binding protein alpha and beta (CEBPα and CEBPβ), and peroxisome proliferator-activated receptor γ along with pCAF expression during adipogenesis of 3T3-L1 cells in a time-dependent manner. Collectively, our findings suggest that TX is a potent antilipogenic agent derived from natural products and may be used as a pCAF inhibitor.
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Affiliation(s)
- Hyo-Jin Kim
- Korea Food Research Institute, Jeollabuk-do, Korea.,Department of Food Biotechnology, Korea University of Science & Technology, Daejeon, Korea
| | - Jangho Lee
- Korea Food Research Institute, Jeollabuk-do, Korea
| | - Min-Yu Chung
- Korea Food Research Institute, Jeollabuk-do, Korea
| | | | - Jae Ho Park
- Korea Food Research Institute, Jeollabuk-do, Korea
| | | | - Jin-Taek Hwang
- Korea Food Research Institute, Jeollabuk-do, Korea.,Department of Food Biotechnology, Korea University of Science & Technology, Daejeon, Korea
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18
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Moritz L, Hammoud SS. The Art of Packaging the Sperm Genome: Molecular and Structural Basis of the Histone-To-Protamine Exchange. Front Endocrinol (Lausanne) 2022; 13:895502. [PMID: 35813619 PMCID: PMC9258737 DOI: 10.3389/fendo.2022.895502] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/02/2022] [Indexed: 01/18/2023] Open
Abstract
Male fertility throughout life hinges on the successful production of motile sperm, a developmental process that involves three coordinated transitions: mitosis, meiosis, and spermiogenesis. Germ cells undergo both mitosis and meiosis to generate haploid round spermatids, in which histones bound to the male genome are replaced with small nuclear proteins known as protamines. During this transformation, the chromatin undergoes extensive remodeling to become highly compacted in the sperm head. Despite its central role in spermiogenesis and fertility, we lack a comprehensive understanding of the molecular mechanisms underlying the remodeling process, including which remodelers/chaperones are involved, and whether intermediate chromatin proteins function as discrete steps, or unite simultaneously to drive successful exchange. Furthermore, it remains largely unknown whether more nuanced interactions instructed by protamine post-translational modifications affect chromatin dynamics or gene expression in the early embryo. Here, we bring together past and more recent work to explore these topics and suggest future studies that will elevate our understanding of the molecular basis of the histone-to-protamine exchange and the underlying etiology of idiopathic male infertility.
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Affiliation(s)
- Lindsay Moritz
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Lindsay Moritz, ; Saher Sue Hammoud,
| | - Saher Sue Hammoud
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, United States
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, United States
- Department of Urology, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Lindsay Moritz, ; Saher Sue Hammoud,
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19
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Mondal P, Tiwary N, Sengupta A, Dhang S, Roy S, Das C. Epigenetic Reprogramming of the Glucose Metabolic Pathways by the Chromatin Effectors During Cancer. Subcell Biochem 2022; 100:269-336. [PMID: 36301498 DOI: 10.1007/978-3-031-07634-3_9] [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] [Indexed: 06/16/2023]
Abstract
Glucose metabolism plays a vital role in regulating cellular homeostasis as it acts as the central axis for energy metabolism, alteration in which may lead to serious consequences like metabolic disorders to life-threatening diseases like cancer. Malignant cells, on the other hand, help in tumor progression through abrupt cell proliferation by adapting to the changed metabolic milieu. Metabolic intermediates also vary from normal cells to cancerous ones to help the tumor manifestation. However, metabolic reprogramming is an important phenomenon of cells through which they try to maintain the balance between normal and carcinogenic outcomes. In this process, transcription factors and chromatin modifiers play an essential role to modify the chromatin landscape of important genes related directly or indirectly to metabolism. Our chapter surmises the importance of glucose metabolism and the role of metabolic intermediates in the cell. Also, we summarize the influence of histone effectors in reprogramming the cancer cell metabolism. An interesting aspect of this chapter includes the detailed methods to detect the aberrant metabolic flux, which can be instrumental for the therapeutic regimen of cancer.
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Affiliation(s)
- Payel Mondal
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
- Homi Bhaba National Institute, Mumbai, India
| | - Niharika Tiwary
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Amrita Sengupta
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Sinjini Dhang
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Siddhartha Roy
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India.
- Homi Bhaba National Institute, Mumbai, India.
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20
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Nikolenko JV, Vdovina YA, Fefelova EI, Glukhova AA, Nabirochkina EN, Kopytova DV. The SAGA Deubiquitinilation (DUB) Module Participates in Pol III-Dependent Transcription. Mol Biol 2021. [DOI: 10.1134/s0026893321020278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Moriel-Carretero M. The Many Faces of Lipids in Genome Stability (and How to Unmask Them). Int J Mol Sci 2021; 22:12930. [PMID: 34884734 PMCID: PMC8657548 DOI: 10.3390/ijms222312930] [Citation(s) in RCA: 4] [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: 09/29/2021] [Revised: 11/12/2021] [Accepted: 11/26/2021] [Indexed: 12/15/2022] Open
Abstract
Deep efforts have been devoted to studying the fundamental mechanisms ruling genome integrity preservation. A strong focus relies on our comprehension of nucleic acid and protein interactions. Comparatively, our exploration of whether lipids contribute to genome homeostasis and, if they do, how, is severely underdeveloped. This disequilibrium may be understood in historical terms, but also relates to the difficulty of applying classical lipid-related techniques to a territory such as a nucleus. The limited research in this domain translates into scarce and rarely gathered information, which with time further discourages new initiatives. In this review, the ways lipids have been demonstrated to, or very likely do, impact nuclear transactions, in general, and genome homeostasis, in particular, are explored. Moreover, a succinct yet exhaustive battery of available techniques is proposed to tackle the study of this topic while keeping in mind the feasibility and habits of "nucleus-centered" researchers.
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Affiliation(s)
- María Moriel-Carretero
- Centre de Recherche en Biologie Cellulaire de Montpellier (CRBM), Université de Montpellier, Centre National de la Recherche Scientifique, CEDEX 5, 34293 Montpellier, France
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22
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Lysine acetylation regulates the interaction between proteins and membranes. Nat Commun 2021; 12:6466. [PMID: 34753925 PMCID: PMC8578602 DOI: 10.1038/s41467-021-26657-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/30/2021] [Indexed: 11/23/2022] Open
Abstract
Lysine acetylation regulates the function of soluble proteins in vivo, yet it remains largely unexplored whether lysine acetylation regulates membrane protein function. Here, we use bioinformatics, biophysical analysis of recombinant proteins, live-cell fluorescent imaging and genetic manipulation of Drosophila to explore lysine acetylation in peripheral membrane proteins. Analysis of 50 peripheral membrane proteins harboring BAR, PX, C2, or EHD membrane-binding domains reveals that lysine acetylation predominates in membrane-interaction regions. Acetylation and acetylation-mimicking mutations in three test proteins, amphiphysin, EHD2, and synaptotagmin1, strongly reduce membrane binding affinity, attenuate membrane remodeling in vitro and alter subcellular localization. This effect is likely due to the loss of positive charge, which weakens interactions with negatively charged membranes. In Drosophila, acetylation-mimicking mutations of amphiphysin cause severe disruption of T-tubule organization and yield a flightless phenotype. Our data provide mechanistic insights into how lysine acetylation regulates membrane protein function, potentially impacting a plethora of membrane-related processes. Lysine acetylation regulates the function of soluble proteins in vivo, yet it remains largely unexplored whether lysine acetylation regulates the function of membrane proteins. Here, the authors map lysine acetylation predominantly in membrane-interaction regions in peripheral membrane proteins and show with three candidate proteins how lysine acetylation is a regulator of membrane protein function.
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23
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Hansen JC, Maeshima K, Hendzel MJ. The solid and liquid states of chromatin. Epigenetics Chromatin 2021; 14:50. [PMID: 34717733 PMCID: PMC8557566 DOI: 10.1186/s13072-021-00424-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022] Open
Abstract
The review begins with a concise description of the principles of phase separation. This is followed by a comprehensive section on phase separation of chromatin, in which we recount the 60 years history of chromatin aggregation studies, discuss the evidence that chromatin aggregation intrinsically is a physiologically relevant liquid-solid phase separation (LSPS) process driven by chromatin self-interaction, and highlight the recent findings that under specific solution conditions chromatin can undergo liquid-liquid phase separation (LLPS) rather than LSPS. In the next section of the review, we discuss how certain chromatin-associated proteins undergo LLPS in vitro and in vivo. Some chromatin-binding proteins undergo LLPS in purified form in near-physiological ionic strength buffers while others will do so only in the presence of DNA, nucleosomes, or chromatin. The final section of the review evaluates the solid and liquid states of chromatin in the nucleus. While chromatin behaves as an immobile solid on the mesoscale, nucleosomes are mobile on the nanoscale. We discuss how this dual nature of chromatin, which fits well the concept of viscoelasticity, contributes to genome structure, emphasizing the dominant role of chromatin self-interaction.
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Affiliation(s)
- Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, 411-8540, Japan.
| | - Michael J Hendzel
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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24
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Roopa, Priya B, Bhalla V, Kumar M, Kumar N. Fluorescent molecular probe-based activity and inhibition monitoring of histone deacetylases. Chem Commun (Camb) 2021; 57:11153-11164. [PMID: 34613324 DOI: 10.1039/d1cc04034k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Extensive studies in recent decades have revealed that gene expression regulation is not limited to genetic mutations but also to processes that do not alter the genetic sequence. Post-translational histone modification is one of these processes in addition to DNA or RNA modifications. Histone modifications are essential in controlling histone functions and play a vital role in cellular gene expression. The reversible histone acetylation, regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), is an example of such modifications. HDACs are involved in the deacetylation of histones and lead to the termination of gene expression. Although this cellular process is essential, upregulation of HDACs is found in numerous cancers. Therefore, research related to the activity and inhibition monitoring of HDACs is necessary to gain profound knowledge of these enzymes and evaluate the success of the therapeutic approach. In this perspective, methodology derived from fluorescent molecular probes is one of the preferable methods. Herein, we describe fluorescent probes developed to target HDACs by considering their activity and inhibition characteristics.
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Affiliation(s)
- Roopa
- Department of Chemical Sciences, IKG-Punjab Technical University, Kapurthala 144603, Punjab, India.
| | - Bhanu Priya
- Department of Chemical Sciences, IKG-Punjab Technical University, Kapurthala 144603, Punjab, India.
| | - Vandana Bhalla
- Department of Chemistry, UGC Center of Advanced Study-II, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Manoj Kumar
- Department of Chemistry, UGC Center of Advanced Study-II, Guru Nanak Dev University, Amritsar-143005, Punjab, India
| | - Naresh Kumar
- Department of Chemistry, SRM University, Delhi-NCR, Sonepat-131029, Haryana, India.
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25
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Shirra MK, Kocik RA, Ellison MA, Arndt KM. Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2021; 11:6360461. [PMID: 34499735 PMCID: PMC8527469 DOI: 10.1093/g3journal/jkab298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/17/2021] [Indexed: 11/13/2022]
Abstract
Maintenance of chromatin structure under the disruptive force of transcription requires cooperation among numerous regulatory factors. Histone post-translational modifications can regulate nucleosome stability and influence the disassembly and reassembly of nucleosomes during transcription elongation. The Paf1 transcription elongation complex, Paf1C, is required for several transcription-coupled histone modifications, including the mono-ubiquitylation of H2B. In Saccharomyces cerevisiae, amino acid substitutions in the Rtf1 subunit of Paf1C greatly diminish H2B ubiquitylation and cause transcription to initiate at a cryptic promoter within the coding region of the FLO8 gene, an indicator of chromatin disruption. In a genetic screen to identify factors that functionally interact with Paf1C, we identified mutations in HDA3, a gene encoding a subunit of the Hda1C histone deacetylase (HDAC), as suppressors of an rtf1 mutation. Absence of Hda1C also suppresses the cryptic initiation phenotype of other mutants defective in H2B ubiquitylation. The genetic interactions between Hda1C and the H2B ubiquitylation pathway appear specific: loss of Hda1C does not suppress the cryptic initiation phenotypes of other chromatin mutants and absence of other HDACs does not suppress the absence of H2B ubiquitylation. Providing further support for an appropriate balance of histone acetylation in regulating cryptic initiation, absence of the Sas3 histone acetyltransferase elevates cryptic initiation in rtf1 mutants. Our data suggest that the H2B ubiquitylation pathway and Hda1C coordinately regulate chromatin structure during transcription elongation and point to a potential role for a HDAC in supporting chromatin accessibility.
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Affiliation(s)
- Margaret K Shirra
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Rachel A Kocik
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Mitchell A Ellison
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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26
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Weidemüller P, Kholmatov M, Petsalaki E, Zaugg JB. Transcription factors: Bridge between cell signaling and gene regulation. Proteomics 2021; 21:e2000034. [PMID: 34314098 DOI: 10.1002/pmic.202000034] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/05/2021] [Accepted: 07/16/2021] [Indexed: 01/17/2023]
Abstract
Transcription factors (TFs) are key regulators of intrinsic cellular processes, such as differentiation and development, and of the cellular response to external perturbation through signaling pathways. In this review we focus on the role of TFs as a link between signaling pathways and gene regulation. Cell signaling tends to result in the modulation of a set of TFs that then lead to changes in the cell's transcriptional program. We highlight the molecular layers at which TF activity can be measured and the associated technical and conceptual challenges. These layers include post-translational modifications (PTMs) of the TF, regulation of TF binding to DNA through chromatin accessibility and epigenetics, and expression of target genes. We highlight that a large number of TFs are understudied in both signaling and gene regulation studies, and that our knowledge about known TF targets has a strong literature bias. We argue that TFs serve as a perfect bridge between the fields of gene regulation and signaling, and that separating these fields hinders our understanding of cell functions. Multi-omics approaches that measure multiple dimensions of TF activity are ideally suited to study the interplay of cell signaling and gene regulation using TFs as the anchor to link the two fields.
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Affiliation(s)
- Paula Weidemüller
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Maksim Kholmatov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg, 69117, Germany
| | - Evangelia Petsalaki
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, Heidelberg, 69117, Germany
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27
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Molecular Modeling for a Comparative Analysis of Interactions Between 2LTRZFP and 2-LTR-Circle Junctions. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10175-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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Frenkel N, Jonas F, Carmi M, Yaakov G, Barkai N. Rtt109 slows replication speed by histone N-terminal acetylation. Genome Res 2021; 31:426-435. [PMID: 33563717 PMCID: PMC7919450 DOI: 10.1101/gr.266510.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/28/2020] [Indexed: 01/17/2023]
Abstract
The wrapping of DNA around histone octamers challenges processes that use DNA as their template. In vitro, DNA replication through chromatin depends on histone modifiers, raising the possibility that cells modify histones to optimize fork progression. Rtt109 is an acetyl transferase that acetylates histone H3 before its DNA incorporation on the K56 and N-terminal residues. We previously reported that, in budding yeast, a wave of histone H3 K9 acetylation progresses ∼3–5 kb ahead of the replication fork. Whether this wave contributes to replication dynamics remained unknown. Here, we show that the replication fork velocity increases following deletion of RTT109, the gene encoding the enzyme required for the prereplication H3 acetylation wave. By using histone H3 mutants, we find that Rtt109-dependent N-terminal acetylation regulates fork velocity, whereas K56 acetylation contributes to replication dynamics only when N-terminal acetylation is compromised. We propose that acetylation of newly synthesized histones slows replication by promoting replacement of nucleosomes evicted by the incoming fork, thereby protecting genome integrity.
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Affiliation(s)
- Nelly Frenkel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miri Carmi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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29
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Ghoneim M, Fuchs HA, Musselman CA. Histone Tail Conformations: A Fuzzy Affair with DNA. Trends Biochem Sci 2021; 46:564-578. [PMID: 33551235 DOI: 10.1016/j.tibs.2020.12.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022]
Abstract
The core histone tails are critical in chromatin structure and signaling. Studies over the past several decades have provided a wealth of information on the histone tails and their interaction with chromatin factors. However, the conformation of the histone tails in a chromatin relevant context has remained elusive. Only recently has enough evidence emerged to start to build a structural model of the tails in the context of nucleosomes and nucleosome arrays. Here, we review these studies and propose that the histone tails adopt a high-affinity fuzzy complex with DNA, characterized by robust but dynamic association. Furthermore, we discuss how these DNA-bound conformational ensembles promote distinct chromatin structure and signaling, and that their fuzzy nature is important in transitioning between functional states.
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Affiliation(s)
- Mohamed Ghoneim
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Harrison A Fuchs
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Catherine A Musselman
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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Targeting Chromatin Complexes in Myeloid Malignancies and Beyond: From Basic Mechanisms to Clinical Innovation. Cells 2020; 9:cells9122721. [PMID: 33371192 PMCID: PMC7767226 DOI: 10.3390/cells9122721] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/13/2020] [Accepted: 12/20/2020] [Indexed: 12/12/2022] Open
Abstract
The aberrant function of chromatin regulatory networks (epigenetics) is a hallmark of cancer promoting oncogenic gene expression. A growing body of evidence suggests that the disruption of specific chromatin-associated protein complexes has therapeutic potential in malignant conditions, particularly those that are driven by aberrant chromatin modifiers. Of note, a number of enzymatic inhibitors that block the catalytic function of histone modifying enzymes have been established and entered clinical trials. Unfortunately, many of these molecules do not have potent single-agent activity. One potential explanation for this phenomenon is the fact that those drugs do not profoundly disrupt the integrity of the aberrant network of multiprotein complexes on chromatin. Recent advances in drug development have led to the establishment of novel inhibitors of protein–protein interactions as well as targeted protein degraders that may provide inroads to longstanding effort to physically disrupt oncogenic multiprotein complexes on chromatin. In this review, we summarize some of the current concepts on the role epigenetic modifiers in malignant chromatin states with a specific focus on myeloid malignancies and recent advances in early-phase clinical trials.
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Strickfaden H, Tolsma TO, Sharma A, Underhill DA, Hansen JC, Hendzel MJ. Condensed Chromatin Behaves like a Solid on the Mesoscale In Vitro and in Living Cells. Cell 2020; 183:1772-1784.e13. [PMID: 33326747 DOI: 10.1016/j.cell.2020.11.027] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/16/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022]
Abstract
The association of nuclear DNA with histones to form chromatin is essential for temporal and spatial control of eukaryotic genomes. In this study, we examined the physical state of condensed chromatin in vitro and in vivo. Our in vitro studies demonstrate that self-association of nucleosomal arrays under a wide range of solution conditions produces supramolecular condensates in which the chromatin is physically constrained and solid-like. By measuring DNA mobility in living cells, we show that condensed chromatin also exhibits solid-like behavior in vivo. Representative heterochromatin proteins, however, display liquid-like behavior and coalesce around the solid chromatin scaffold. Importantly, euchromatin and heterochromatin show solid-like behavior even under conditions that produce limited interactions between chromatin fibers. Our results reveal that condensed chromatin exists in a solid-like state whose properties resist external forces and create an elastic gel and provides a scaffold that supports liquid-liquid phase separation of chromatin binding proteins.
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Affiliation(s)
- Hilmar Strickfaden
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Thomas O Tolsma
- Department of Biochemistry and Molecular Biology, College of Natural Sciences, Colorado State University, Fort Collins, CO, USA
| | - Ajit Sharma
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - D Alan Underhill
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada; Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, College of Natural Sciences, Colorado State University, Fort Collins, CO, USA.
| | - Michael J Hendzel
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada; Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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Kunadis E, Lakiotaki E, Korkolopoulou P, Piperi C. Targeting post-translational histone modifying enzymes in glioblastoma. Pharmacol Ther 2020; 220:107721. [PMID: 33144118 DOI: 10.1016/j.pharmthera.2020.107721] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/08/2020] [Accepted: 10/27/2020] [Indexed: 12/30/2022]
Abstract
Glioblastoma (GBM) is the most common primary brain tumor in adults, and the most lethal form of glioma, characterized by variable histopathology, aggressiveness and poor clinical outcome and prognosis. GBMs constitute a challenge for oncologists because of their molecular heterogeneity, extensive invasion, and tendency to relapse. Glioma cells demonstrate a variety of deregulated genomic pathways and extensive interplay with epigenetic alterations. Epigenetic modifications have emerged as essential players in GBM research, with biomarker potential for tumor classification and prognosis and for drug targeting. Histone posttranslational modifications (PTMs) are crucial regulators of chromatin architecture and gene expression, playing a pivotal role in malignant transformation, tumor development and progression. Alteration in the expression of genes coding for lysine and arginine methyltransferases (G9a, SUV39H1 and SETDB1) and acetyltransferases and deacetylases (KAT6A, SIRT2, SIRT7, HDAC4, 6, 9) contribute to GBM pathogenesis. In addition, proteins of the sumoylation pathway are upregulated in GBM cell lines, including E1 (SAE1), E2 (Ubc9) components, and a SUMO-specific protease (SENP1). Preclinical and clinical studies are currently in progress targeting epigenetic enzymes in gliomas, including a new generation of histone deacetylase (HDAC), protein arginine methyltransferase (PRMT) and bromodomain (BRD) inhibitors. Herein, we provide an update on recent advances in glioma epigenetic research, focusing on the role of histone modifications and the use of epigenetic therapy as a valid treatment option for glioblastoma.
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Affiliation(s)
- Elena Kunadis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
| | - Eleftheria Lakiotaki
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
| | - Penelope Korkolopoulou
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 Mikras Asias Street, 11527 Athens, Greece.
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Burns AM, Gräff J. Cognitive epigenetic priming: leveraging histone acetylation for memory amelioration. Curr Opin Neurobiol 2020; 67:75-84. [PMID: 33120188 DOI: 10.1016/j.conb.2020.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022]
Abstract
Multiple studies have found that increasing histone acetylation by means of histone deacetylase inhibitor (HDACi) treatment can ameliorate memory and rescue cognitive impairments, but their mode of action is not fully understood. In particular, it is unclear how HDACis, applied systemically and devoid of genomic target selectivity, would specifically improve memory-related molecular processes. One theory for such specificity is called cognitive epigenetic priming (CEP), according to which HDACis promote memory by facilitating the expression of neuroplasticity-related genes that have been stimulated by learning itself. In this review, we summarize the experimental evidence in support of CEP, describe newly discovered off-target effects of HDACis and highlight similarities between drug-induced and naturally occurring CEP. Understanding the underlying mechanisms of CEP is important in light of the preclinical premise of HDACis as cognitive enhancers.
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Affiliation(s)
- Allison M Burns
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Johannes Gräff
- Laboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale Lausanne (EPFL), 1015, Lausanne, Switzerland.
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Rispal J, Escaffit F, Trouche D. Chromatin Dynamics in Intestinal Epithelial Homeostasis: A Paradigm of Cell Fate Determination versus Cell Plasticity. Stem Cell Rev Rep 2020; 16:1062-1080. [PMID: 33051755 PMCID: PMC7667136 DOI: 10.1007/s12015-020-10055-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2020] [Indexed: 12/12/2022]
Abstract
The rapid renewal of intestinal epithelium is mediated by a pool of stem cells, located at the bottom of crypts, giving rise to highly proliferative progenitor cells, which in turn differentiate during their migration along the villus. The equilibrium between renewal and differentiation is critical for establishment and maintenance of tissue homeostasis, and is regulated by signaling pathways (Wnt, Notch, Bmp…) and specific transcription factors (TCF4, CDX2…). Such regulation controls intestinal cell identities by modulating the cellular transcriptome. Recently, chromatin modification and dynamics have been identified as major actors linking signaling pathways and transcriptional regulation in the control of intestinal homeostasis. In this review, we synthesize the many facets of chromatin dynamics involved in controlling intestinal cell fate, such as stemness maintenance, progenitor identity, lineage choice and commitment, and terminal differentiation. In addition, we present recent data underlying the fundamental role of chromatin dynamics in intestinal cell plasticity. Indeed, this plasticity, which includes dedifferentiation processes or the response to environmental cues (like microbiota’s presence or food ingestion), is central for the organ’s physiology. Finally, we discuss the role of chromatin dynamics in the appearance and treatment of diseases caused by deficiencies in the aforementioned mechanisms, such as gastrointestinal cancer, inflammatory bowel disease or irritable bowel syndrome. Graphical abstract ![]()
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Affiliation(s)
- Jérémie Rispal
- LBCMCP, Centre of Integrative Biology (CBI), Université de Toulouse, CNRS, UPS, Toulouse, 31062, France
| | - Fabrice Escaffit
- LBCMCP, Centre of Integrative Biology (CBI), Université de Toulouse, CNRS, UPS, Toulouse, 31062, France.
| | - Didier Trouche
- LBCMCP, Centre of Integrative Biology (CBI), Université de Toulouse, CNRS, UPS, Toulouse, 31062, France
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Marrocco J, Einhorn NR, McEwen BS. Environmental epigenetics of sex differences in the brain. HANDBOOK OF CLINICAL NEUROLOGY 2020; 175:209-220. [PMID: 33008526 DOI: 10.1016/b978-0-444-64123-6.00015-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Experiences throughout the life course lead to unique phenotypes even among those with the same genotype. Genotype sets the substrate on which physiologic processes, which communicate with the brain, mediate the effects of life experiences via epigenetics. Epigenetics modify the expression of genes in the brain and body in response to circulating hormones and other mediators, which are activated to facilitate survival responses through a process called allostasis. Epigenetic signatures can even be inherited, resulting in transgenerational effects. This chapter addresses epigenetics in the context of sex differences, discussing the intersection between genetics and gonadal hormones and their effect in the brain at discrete developmental periods.
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Affiliation(s)
- Jordan Marrocco
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, Rockefeller University, New York, NY, United States.
| | - Nathan R Einhorn
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, Rockefeller University, New York, NY, United States
| | - Bruce S McEwen
- Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, Rockefeller University, New York, NY, United States
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Tafessu A, Banaszynski LA. Establishment and function of chromatin modification at enhancers. Open Biol 2020; 10:200255. [PMID: 33050790 PMCID: PMC7653351 DOI: 10.1098/rsob.200255] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/22/2020] [Indexed: 12/17/2022] Open
Abstract
How a single genome can give rise to distinct cell types remains a fundamental question in biology. Mammals are able to specify and maintain hundreds of cell fates by selectively activating unique subsets of their genome. This is achieved, in part, by enhancers-genetic elements that can increase transcription of both nearby and distal genes. Enhancers can be identified by their unique chromatin signature, including transcription factor binding and the enrichment of specific histone post-translational modifications, histone variants, and chromatin-associated cofactors. How each of these chromatin features contributes to enhancer function remains an area of intense study. In this review, we provide an overview of enhancer-associated chromatin states, and the proteins and enzymes involved in their establishment. We discuss recent insights into the effects of the enhancer chromatin state on ongoing transcription versus their role in the establishment of new transcription programmes, such as those that occur developmentally. Finally, we highlight the role of enhancer chromatin in new conceptual advances in gene regulation such as condensate formation.
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Affiliation(s)
| | - Laura A. Banaszynski
- UT Southwestern Medical Center, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Department of Obstetrics and Gynecology, Children's Research Institute, Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390-8511, USA
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Wang XW, Lv JL, Shi YR, Guo LY. Comparative Transcriptome Analysis Revealed Genes Regulated by Histone Acetylation and Genes Related to Sex Hormone Biosynthesis in Phytophthora infestans. Front Genet 2020; 11:508. [PMID: 32508886 PMCID: PMC7253629 DOI: 10.3389/fgene.2020.00508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
Late blight caused by Phytophthora infestans, is one of the most devastating diseases of potato, and was responsible for the death of millions of people during the Irish Potato Famine in the nineteenth century. Phytophthora infestans is a heterothallic oomycete that typically requires two compatible types (mating types), A1 and A2, to complete sexual reproduction (i.e., oospore production). Oospores have critical effects on disease epidemiology because they serve as the primary inoculum in subsequent growing seasons. The sexual reproduction of Phytophthora species is regulated by α hormones. In previous studies, we proved that transformants in which selected histone deacetylase (HDAC) genes are silenced exhibit abnormal hormone production. In the current study, we compared the transcriptomes of HDAC-silenced and wild-type strains to explore the genes regulated by HDAC and the genes involved in sex hormone biosynthesis in Phytophthora species. A total of 14,423 transcripts of unigenes were identified in the wild-type strain, the HDAC family-silenced transformant (HDST), and the HDAC7-silenced transformant (H7ST). After comparing the intergroup gene expression levels, 1,612 unigenes were identified as differentially expressed among these strains. The expression levels of 16 differentially expressed genes (DEGs) were validated by quantitative real-time PCR. The functional annotation of the DEGs by gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that HDACs affect the expression of genes related to metabolic and biosynthetic processes, RNA processing, translation, ribosome biogenesis, cellular structural constituents, RNA binding, and protein binding. Moreover, HDAC7 specifically influences the transcription of genes associated with transport, methylation, mitochondria, organelle inner membranes, receptors and transporters, and hydrolase activities. We also identified 18 candidate genes related to α hormones biosynthesis, including a gene encoding the NF-Y transcription factor (PITG_10861). The overexpression of PITG_10861 increased the production of hormone α2. The results of this study revealed P. infestans genes affected by histone acetylation. The data presented herein provide useful inputs for future research on the epigenetic mechanisms and mating behaviors of Phytophthora species.
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Affiliation(s)
- Xiao-Wen Wang
- Ministry of Agriculture (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jia-Lu Lv
- Ministry of Agriculture (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ya-Ru Shi
- Ministry of Agriculture (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Li-Yun Guo
- Ministry of Agriculture (MOA) Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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Bittarello AC, Vieira JCS, Braga CP, da Cunha Bataglioli I, de Oliveira G, Rocha LC, Zara LF, Buzalaf MAR, de Oliveira LCS, Adamec J, de Magalhães Padilha P. Metalloproteomic approach of mercury-binding proteins in liver and kidney tissues of Plagioscion squamosissimus (corvina) and Colossoma macropomum (tambaqui) from Amazon region: Possible identification of mercury contamination biomarkers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 711:134547. [PMID: 31812405 DOI: 10.1016/j.scitotenv.2019.134547] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Fish is an important source of protein, vitamins, and minerals. However, this food is also a major source of human exposure to toxic contaminants such as mercury. Thus, this paper aimed to evaluate mercury-binding proteins for possible application as biomarkers of mercury contamination in hepatic and renal tissues of Plagioscion squamosissimus (carnivorous fish) and Colossoma macropomum (omnivorous fish) from the Amazon region using metalloproteomic approach. The proteome of hepatic and renal tissues of fish species was separated by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and the mercury concentrations in protein spots were determined by graphite furnace atomic absorption spectrometry (GFAAS). Finally, the protein spots associated to mercury were characterized by electrospray ionization mass spectrometry (ESI-MS/MS). The activity of antioxidant enzymes (SOD, CAT, GPx, and GST) and lipid peroxidation (LPO) were also determined. The results showed that the highest concentrations of mercury were found in the carnivorous species (P. squamosissimus) and that the accumulation pattern of this metal was higher in hepatic tissues than in renal tissues for both species. A tendency was observed for greater enzymatic activity in the hepatic and renal tissues of P. squamosissimus, the species with the highest concentration of mercury. Only GPx activity in the kidney and GST in the liver were lower for the P. squamosissimus species, and this finding can be explained by the interaction of mercury with these enzymes. The data obtained by ESI-MS/MS allowed for the characterization of the protein spots associated to mercury, revealing proteins involved in energy metabolism, biomolecules transport, protein synthesis and degradation, cell differentiation, gene regulation, and the antioxidant system. The results obtained in the present study can contribute to understanding the physiological processes underlying mercury toxicity and have provided new perspectives on possible candidates for mercury contamination biomarkers in fish.
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Affiliation(s)
- Alis Correia Bittarello
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Botucatu, Brazil
| | - José Cavalcante Souza Vieira
- São Paulo State University (UNESP), Institute of Biosciences, Botucatu, Brazil; Institute of Chemistry (INQUI), Federal University of Mato Grosso do Sul, Campo Grande (UFMS), Brazil.
| | | | | | | | - Leone Campos Rocha
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Botucatu, Brazil
| | - Luiz Fabrício Zara
- University of Brasília (UNB), College of Planaltina, Distrito Federal, Brazil
| | | | | | - Jiri Adamec
- University of Nebraska (UNL), Lincoln, United States
| | - Pedro de Magalhães Padilha
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Botucatu, Brazil; São Paulo State University (UNESP), Institute of Biosciences, Botucatu, Brazil.
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You D, Richardson JR, Aleksunes LM. Epigenetic Regulation of Multidrug Resistance Protein 1 and Breast Cancer Resistance Protein Transporters by Histone Deacetylase Inhibition. Drug Metab Dispos 2020; 48:459-480. [PMID: 32193359 DOI: 10.1124/dmd.119.089953] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
Multidrug resistance protein 1 (MDR1, ABCB1, P-glycoprotein) and breast cancer resistance protein (BCRP, ABCG2) are key efflux transporters that mediate the extrusion of drugs and toxicants in cancer cells and healthy tissues, including the liver, kidneys, and the brain. Altering the expression and activity of MDR1 and BCRP influences the disposition, pharmacodynamics, and toxicity of chemicals, including a number of commonly prescribed medications. Histone acetylation is an epigenetic modification that can regulate gene expression by changing the accessibility of the genome to transcriptional regulators and transcriptional machinery. Recently, studies have suggested that pharmacological inhibition of histone deacetylases (HDACs) modulates the expression and function of MDR1 and BCRP transporters as a result of enhanced histone acetylation. This review addresses the ability of HDAC inhibitors to modulate the expression and the function of MDR1 and BCRP transporters and explores the molecular mechanisms by which HDAC inhibition regulates these transporters. While the majority of studies have focused on histone regulation of MDR1 and BCRP in drug-resistant and drug-sensitive cancer cells, emerging data point to similar responses in nonmalignant cells and tissues. Elucidating epigenetic mechanisms regulating MDR1 and BCRP is important to expand our understanding of the basic biology of these two key transporters and subsequent consequences on chemoresistance as well as tissue exposure and responses to drugs and toxicants. SIGNIFICANCE STATEMENT: Histone deacetylase inhibitors alter the expression of key efflux transporters multidrug resistance protein 1 and breast cancer resistance protein in healthy and malignant cells.
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Affiliation(s)
- Dahea You
- Joint Graduate Program in Toxicology, Rutgers, The State University of New Jersey, Piscataway, New Jersey (D.Y.); Department of Environmental Health Sciences, Robert Stempel School of Public Health and Social Work, Florida International University, Miami, Florida (J.R.R.); Environmental and Occupational Health Sciences Institute, Piscataway, New Jersey (J.R.R., L.M.A.); and Department of Pharmacology and Toxicology, Rutgers, The State University of New Jersey, Ernest Mario School of Pharmacy, Piscataway, New Jersey (L.M.A.)
| | - Jason R Richardson
- Joint Graduate Program in Toxicology, Rutgers, The State University of New Jersey, Piscataway, New Jersey (D.Y.); Department of Environmental Health Sciences, Robert Stempel School of Public Health and Social Work, Florida International University, Miami, Florida (J.R.R.); Environmental and Occupational Health Sciences Institute, Piscataway, New Jersey (J.R.R., L.M.A.); and Department of Pharmacology and Toxicology, Rutgers, The State University of New Jersey, Ernest Mario School of Pharmacy, Piscataway, New Jersey (L.M.A.)
| | - Lauren M Aleksunes
- Joint Graduate Program in Toxicology, Rutgers, The State University of New Jersey, Piscataway, New Jersey (D.Y.); Department of Environmental Health Sciences, Robert Stempel School of Public Health and Social Work, Florida International University, Miami, Florida (J.R.R.); Environmental and Occupational Health Sciences Institute, Piscataway, New Jersey (J.R.R., L.M.A.); and Department of Pharmacology and Toxicology, Rutgers, The State University of New Jersey, Ernest Mario School of Pharmacy, Piscataway, New Jersey (L.M.A.)
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Audugé N, Padilla-Parra S, Tramier M, Borghi N, Coppey-Moisan M. Chromatin condensation fluctuations rather than steady-state predict chromatin accessibility. Nucleic Acids Res 2020; 47:6184-6194. [PMID: 31081027 PMCID: PMC6614833 DOI: 10.1093/nar/gkz373] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/24/2019] [Accepted: 05/07/2019] [Indexed: 01/16/2023] Open
Abstract
Chromatin accessibility to protein factors is critical for genome activities. However, the dynamic properties of chromatin higher-order structures that regulate its accessibility are poorly understood. Here, we took advantage of the microenvironment sensitivity of the fluorescence lifetime of EGFP-H4 histone incorporated in chromatin to map in the nucleus of live cells the dynamics of chromatin condensation and its direct interaction with a tail acetylation recognition domain (the double bromodomain module of human TAFII250, dBD). We reveal chromatin condensation fluctuations supported by mechanisms fundamentally distinct from that of condensation. Fluctuations are spontaneous, yet their amplitudes are affected by their sub-nuclear localization and by distinct and competing mechanisms dependent on histone acetylation, ATP and both. Moreover, we show that accessibility of acetylated histone H4 to dBD is not restricted by chromatin condensation nor predicted by acetylation, rather, it is predicted by chromatin condensation fluctuations.
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Affiliation(s)
- Nicolas Audugé
- Institut Jacques Monod UMR 7592, Université de Paris - Centre National de la Recherche Scientifique, Paris, France
| | - Sergi Padilla-Parra
- Institut Jacques Monod UMR 7592, Université de Paris - Centre National de la Recherche Scientifique, Paris, France
| | - Marc Tramier
- Institut Jacques Monod UMR 7592, Université de Paris - Centre National de la Recherche Scientifique, Paris, France
| | - Nicolas Borghi
- Institut Jacques Monod UMR 7592, Université de Paris - Centre National de la Recherche Scientifique, Paris, France
| | - Maïté Coppey-Moisan
- Institut Jacques Monod UMR 7592, Université de Paris - Centre National de la Recherche Scientifique, Paris, France
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Park S, Kim GW, Kwon SH, Lee JS. Broad domains of histone H3 lysine 4 trimethylation in transcriptional regulation and disease. FEBS J 2020; 287:2891-2902. [PMID: 31967712 DOI: 10.1111/febs.15219] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/23/2019] [Accepted: 01/17/2020] [Indexed: 12/11/2022]
Abstract
Histone modifications affect transcription by changing the chromatin structure. In particular, histone H3 lysine 4 trimethylation (H3K4me3) is one of the most recognized epigenetic marks of active transcription. While many studies have provided evidence of the correlation between H3K4me3 and active transcription, details regarding the mechanism involved remain unclear. The first study on the broad H3K4me3 domain was reported in 2014; subsequently, the function of this domain has been studied in various cell types. In this review, we summarized the recent studies on the role of the broad H3K4me3 domain in transcription, development, memory formation, and several diseases, including cancer and autoimmune diseases. The broadest H3K4me3 domains are associated with increased transcriptional precision of cell-type-specific genes related to cell identity and other essential functions. The broad H3K4me3 domain regulates maternal zygotic activation in early mammalian development. In systemic autoimmune diseases, high expression of immune-responsive genes requires the presence of the broad H3K4me3 domain in the promoter-proximal regions. Transcriptional repression of tumor-suppressor genes is associated with the shortening of the broad H3K4me3 domains in cancer cells. Additionally, the broad H3K4me3 domain interacts with the super-enhancer to regulate cancer-associated genes. During memory formation, H3K4me3 breadth is regulated in the hippocampus CA1 neurons. Taken together, these findings indicate that H3K4me3 breadth is essential for the regulation of the transcriptional output across multiple cell types.
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Affiliation(s)
- Shinae Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Korea.,Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, Korea
| | - Go Woon Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea
| | - So Hee Kwon
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, Korea.,Department of Integrated OMICS for Biomedical Science, Yonsei University, Seoul, Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, Korea.,Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, Korea
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Zhang D, Meng YR, Zhang CY. Peptide-templated gold nanoparticle nanosensor for simultaneous detection of multiple posttranslational modification enzymes. Chem Commun (Camb) 2020; 56:213-216. [PMID: 31808495 DOI: 10.1039/c9cc09019c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We developed a peptide-templated gold nanoparticle (AuNP) nanosensor for simultaneous detection of multiple posttranslational modification (PTM) enzymes with a detection limit of 28 pM for histone deacetylase (HDAC) and 0.8 pM for protein tyrosine phosphatase 1B (PTP1B), and it can be further applied for the screening of PTM enzyme inhibitors and the measurement of PTM enzymes in cancer cells.
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Affiliation(s)
- Dandan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan 250014, China.
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Njeri CW, Ononye OE, Balakrishnan L. Quantification of In Vitro Protein Lysine Acetylation by Reversed Phase HPLC. Methods Mol Biol 2020; 1983:49-56. [PMID: 31087292 DOI: 10.1007/978-1-4939-9434-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Protein lysine acetylation is a reversible posttranslational modification that is catalyzed by a group of enzymes that are collectively referred to as lysine (K) acetyltransferases (KATs). These enzymes catalyze the transfer of the acetyl group from acetyl coenzyme A (Ac-CoA) to the ε-amino group of lysine amino acid. Protein lysine acetylation plays a critical role in the regulation of important cellular processes and it is therefore paramount that we understand the catalytic mechanisms of these enzymes. While there is a variety of methods that have been developed to analyze the enzymatic properties of KATs, majority of the proposed methods have considerable limitations. We describe here a reversed phase HPLC based method that monitors substrate consumption and product formation simultaneously. This method is highly reproducible and optimally suited for the determination of accurate kinetic parameters of KATs.
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Affiliation(s)
- Catherine W Njeri
- Department of Biology, School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Onyekachi E Ononye
- Department of Biology, School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Lata Balakrishnan
- Department of Biology, School of Science, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA.
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Guo XJ, Yang D, Zhang XY. Epigenetics recording varied environment and complex cell events represents the origin of cellular aging. J Zhejiang Univ Sci B 2020; 20:550-562. [PMID: 31168969 DOI: 10.1631/jzus.b1800507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Although a relationship between epigenetics and aging phenotypic changes has been established, a theoretical explanation of the intrinsic connection between the epigenetics and aging is lacking. In this essay, we propose that epigenetic recording of varied cell environment and complex history could be an origin of cellular aging. Through epigenetic modifications, the environment and historical events can induce the chromatin template into an activated or repressive accessible structure, thereby shaping the DNA template into a spectrum of chromatin states. The inner nature of diversity and conflicts born by the cell environment and its historical events are hence recorded into the chromatin template. This could result in a dissipated spectrum of the chromatin state and chaos in overall gene expression. An unavoidable degradation of epigenome entropy, similar to Shannon entropy, would be consequently induced. The resultant disorder in epigenome, characterized by corrosion of epigenome entropy as reflected in chromatin template, can be stably memorized and propagated through cell division. Furthermore, the hysteretic nature of epigenetics responding to the emerging environment could exacerbate the degradation of epigenome entropy. As well as stochastic errors, we propose that outside entropy (or chaos) derived from the varied environment and complex cell history, gradually input and imprinted into the chromatin via epigenetic modifications, would lead inevitably to cellular aging, the extent of which could be aggravated by hysteresis of epigenetics without error erasing and correction.
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Affiliation(s)
- Xue-Jun Guo
- State Key Laboratory of Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Dong Yang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Xiang-Yuan Zhang
- State Key Laboratory of Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
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45
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Khan SA, Rizwan K, Shahid S, Noamaan MA, Rasheed T, Amjad H. Synthesis, DFT, computational exploration of chemical reactivity, molecular docking studies of novel formazan metal complexes and their biological applications. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5444] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Shakeel Ahmad Khan
- Department of Chemistry, School of ScienceUniversity of Management and Technology Lahore 54770 Pakistan
- Center of Super Diamond and Advanced Films (COSDAF), Department of ChemistryCity University of Hong Kong 83 Tat Chee Avenue Kowloon China
| | - Komal Rizwan
- Department of ChemistryGovernment College Women University Faisalabad 38000 Pakistan
| | - Sammia Shahid
- Department of Chemistry, School of ScienceUniversity of Management and Technology Lahore 54770 Pakistan
| | - Mahmoud A. Noamaan
- Mathematics Department, Faculty of ScienceCairo University Giza 12613 Egypt
| | - Tahir Rasheed
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix CompositesShanghai Jiao Tong University Shanghai 200240 China
| | - Hira Amjad
- Department of Chemistry, School of ScienceUniversity of Management and Technology Lahore 54770 Pakistan
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46
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Choi MA, Park SY, Chae HY, Song Y, Sharma C, Seo YH. Design, synthesis and biological evaluation of a series of CNS penetrant HDAC inhibitors structurally derived from amyloid-β probes. Sci Rep 2019; 9:13187. [PMID: 31515509 PMCID: PMC6742641 DOI: 10.1038/s41598-019-49784-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022] Open
Abstract
To develop novel CNS penetrant HDAC inhibitors, a new series of HDAC inhibitors having benzoheterocycle were designed, synthesized, and biologically evaluated. Among the synthesized compounds, benzothiazole derivative 9b exhibited a remarkable anti-proliferative activity (GI50 = 2.01 μM) against SH-SY5Y cancer cell line in a dose and time-dependent manner, better than the reference drug SAHA (GI50 = 2.90 μM). Moreover, compound 9b effectively promoted the accumulation of acetylated Histone H3 and α-tubulin through inhibition of HDAC1 and HDAC6 enzymes, respectively. HDAC enzyme assay also confirmed that compound 9b efficiently inhibited HDAC1 and HDAC6 isoforms with IC50 values of 84.9 nM and 95.9 nM. Furthermore, compound 9b inhibited colony formation capacity of SH-SY5Y cells, which is considered a hallmark of cell carcinogenesis and metastatic potential. The theoretical prediction, in vitro PAMPA-BBB assay, and in vivo brain pharmacokinetic studies confirmed that compound 9b had much higher BBB permeability than SAHA. In silico docking study demonstrated that compound 9b fitted in the substrate binding pocket of HDAC1 and HDAC6. Taken together, compound 9b provided a novel scaffold for developing CNS penetrant HDAC inhibitors and therapeutic potential for CNS-related diseases.
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Affiliation(s)
- Myeong A Choi
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea
| | - Sun You Park
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea
| | - Hye Yun Chae
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea
| | - Yoojin Song
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea
| | | | - Young Ho Seo
- College of Pharmacy, Keimyung University, Daegu, 42601, South Korea.
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47
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Sheikh BN, Akhtar A. The many lives of KATs - detectors, integrators and modulators of the cellular environment. Nat Rev Genet 2019; 20:7-23. [PMID: 30390049 DOI: 10.1038/s41576-018-0072-4] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Research over the past three decades has firmly established lysine acetyltransferases (KATs) as central players in regulating transcription. Recent advances in genomic sequencing, metabolomics, animal models and mass spectrometry technologies have uncovered unexpected new roles for KATs at the nexus between the environment and transcriptional regulation. Thousands of reversible acetylation sites have been mapped in the proteome that respond dynamically to the cellular milieu and maintain major processes such as metabolism, autophagy and stress response. Concurrently, researchers are continuously uncovering how deregulation of KAT activity drives disease, including cancer and developmental syndromes characterized by severe intellectual disability. These novel findings are reshaping our view of KATs away from mere modulators of chromatin to detectors of the cellular environment and integrators of diverse signalling pathways with the ability to modify cellular phenotype.
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Affiliation(s)
- Bilal N Sheikh
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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48
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Sheikh BN, Guhathakurta S, Akhtar A. The non-specific lethal (NSL) complex at the crossroads of transcriptional control and cellular homeostasis. EMBO Rep 2019; 20:e47630. [PMID: 31267707 PMCID: PMC6607013 DOI: 10.15252/embr.201847630] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/10/2019] [Accepted: 03/19/2019] [Indexed: 12/14/2022] Open
Abstract
The functionality of chromatin is tightly regulated by post-translational modifications that modulate transcriptional output from target loci. Among the post-translational modifications of chromatin, reversible ε-lysine acetylation of histone proteins is prominent at transcriptionally active genes. Lysine acetylation is catalyzed by lysine acetyltransferases (KATs), which utilize the central cellular metabolite acetyl-CoA as their substrate. Among the KATs that mediate lysine acetylation, males absent on the first (MOF/KAT8) is particularly notable for its ability to acetylate histone 4 lysine 16 (H4K16ac), a modification that decompacts chromatin structure. MOF and its non-specific lethal (NSL) complex members have been shown to localize to gene promoters and enhancers in the nucleus, as well as to microtubules and mitochondria to regulate key cellular processes. Highlighting their importance, mutations or deregulation of NSL complex members has been reported in both human neurodevelopmental disorders and cancer. Based on insight gained from studies in human, mouse, and Drosophila model systems, this review discusses the role of NSL-mediated lysine acetylation in a myriad of cellular functions in both health and disease. Through these studies, the importance of the NSL complex in regulating core transcriptional and signaling networks required for normal development and cellular homeostasis is beginning to emerge.
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Affiliation(s)
- Bilal N Sheikh
- Max Planck Institute for Immunobiology and EpigeneticsFreiburg im BreisgauGermany
| | - Sukanya Guhathakurta
- Max Planck Institute for Immunobiology and EpigeneticsFreiburg im BreisgauGermany
- Faculty of BiologyAlbert Ludwig University of FreiburgFreiburgGermany
| | - Asifa Akhtar
- Max Planck Institute for Immunobiology and EpigeneticsFreiburg im BreisgauGermany
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49
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Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription. Essays Biochem 2019; 63:97-107. [PMID: 30940741 PMCID: PMC6484784 DOI: 10.1042/ebc20180061] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
Packaging the long and fragile genomes of eukaryotic species into nucleosomes is all well and good, but how do cells gain access to the DNA again after it has been bundled away? The solution, in every species from yeast to man, is to post-translationally modify histones, altering their chemical properties to either relax the chromatin, label it for remodelling or make it more compact still. Histones are subject to a myriad of modifications: acetylation, methylation, phosphorylation, ubiquitination etc. This review focuses on histone acylations, a diverse group of modifications which occur on the ε-amino group of Lysine residues and includes the well-characterised Lysine acetylation. Over the last 50 years, histone acetylation has been extensively characterised, with the discovery of histone acetyltransferases (HATs) and histone deacetylases (HDACs), and global mapping experiments, revealing an association of hyperacetylated histones with accessible, transcriptionally active chromatin. More recently, there has been an explosion in the number of unique short chain ‘acylations’ identified by MS, including: propionylation, butyrylation, crotonylation, succinylation, malonylation and 2-hydroxyisobutyrylation. These novel modifications add a range of chemical environments to histones, and similar to acetylation, appear to accumulate at transcriptional start sites and correlate with gene activity.
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50
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Elías-Villalobos A, Barrales RR, Ibeas JI. Chromatin modification factors in plant pathogenic fungi: Insights from Ustilago maydis. Fungal Genet Biol 2019; 129:52-64. [PMID: 30980908 DOI: 10.1016/j.fgb.2019.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 01/10/2023]
Abstract
Adaptation to the environment is a requirement for the survival of every organism. For pathogenic fungi this also implies coping with the different conditions that occur during the infection cycle. After detecting changes to external media, organisms must modify their gene expression patterns in order to accommodate the new circumstances. Control of gene expression is a complex process that involves the coordinated action of multiple regulatory elements. Chromatin modification is a well-known mechanism for controlling gene expression in response to environmental changes in all eukaryotes. In pathogenic fungi, chromatin modifications are known to play crucial roles in controlling host interactions and their virulence capacity, yet little is known about the specific genes they directly target and to which signals they respond. The smut fungus Ustilago maydis is an excellent model system in which multiple molecular and cellular approaches are available to study biotrophic interactions. Many target genes regulated during the infection process have been well studied, however, how they are controlled and specifically how chromatin modifications affect gene regulation in the context of infection is not well known in this organism. Here, we analyse the presence of chromatin modifying enzymes and complexes in U. maydis and discuss their putative roles in this plant pathogen in the context of findings from other organisms, including other plant pathogens such as Magnaporthe oryzae and Fusarium graminearum. We propose U. maydis as a remarkable organism with interesting chromatin features, which would allow finding new functions of chromatin modifications during plant pathogenesis.
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Affiliation(s)
- Alberto Elías-Villalobos
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR5237-Centre National de la Recherche Scientifique-Université de Montpellier, Montpellier, France.
| | - Ramón R Barrales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, de Sevilla-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain.
| | - José I Ibeas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, de Sevilla-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain
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