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Huang L, Chen X, Yang X, Zhang Y, Liang Y, Qiu X. Elucidating epigenetic mechanisms governing odontogenic differentiation in dental pulp stem cells: an in-depth exploration. Front Cell Dev Biol 2024; 12:1394582. [PMID: 38863943 PMCID: PMC11165363 DOI: 10.3389/fcell.2024.1394582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
Epigenetics refers to the mechanisms such as DNA methylation and histone modification that influence gene expression without altering the DNA sequence. These epigenetic modifications can regulate gene transcription, splicing, and stability, thereby impacting cell differentiation, development, and disease occurrence. The formation of dentin is intrinsically linked to the odontogenic differentiation of dental pulp stem cells (DPSCs), which are recognized as the optimal cell source for dentin-pulp regeneration due to their varied odontogenic potential, strong proliferative and angiogenic characteristics, and ready accessibility Numerous studies have demonstrated the critical role of epigenetic regulation in DPSCs differentiation into specific cell types. This review thus provides a comprehensive review of the mechanisms by which epigenetic regulation controls the odontogenesis fate of DPSCs.
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Affiliation(s)
| | | | | | | | | | - Xiaoling Qiu
- Department of Endodontics, Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, Guangdong, China
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2
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Martella N, Pensabene D, Varone M, Colardo M, Petraroia M, Sergio W, La Rosa P, Moreno S, Segatto M. Bromodomain and Extra-Terminal Proteins in Brain Physiology and Pathology: BET-ing on Epigenetic Regulation. Biomedicines 2023; 11:biomedicines11030750. [PMID: 36979729 PMCID: PMC10045827 DOI: 10.3390/biomedicines11030750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/24/2023] [Accepted: 02/25/2023] [Indexed: 03/06/2023] Open
Abstract
BET proteins function as histone code readers of acetylated lysins that determine the positive regulation in transcription of genes involved in cell cycle progression, differentiation, inflammation, and many other pathways. In recent years, thanks to the development of BET inhibitors, interest in this protein family has risen for its relevance in brain development and function. For example, experimental evidence has shown that BET modulation affects neuronal activity and the expression of genes involved in learning and memory. In addition, BET inhibition strongly suppresses molecular pathways related to neuroinflammation. These observations suggest that BET modulation may play a critical role in the onset and during the development of diverse neurodegenerative and neuropsychiatric disorders, such as Alzheimer’s disease, fragile X syndrome, and Rett syndrome. In this review article, we summarize the most recent evidence regarding the involvement of BET proteins in brain physiology and pathology, as well as their pharmacological potential as targets for therapeutic purposes.
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Affiliation(s)
- Noemi Martella
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Daniele Pensabene
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
- Department of Science, University Roma Tre, Viale Marconi 446, 00146 Rome, Italy
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 64 via del Fosso di Fiorano, 00179 Rome, Italy
| | - Michela Varone
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Mayra Colardo
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Michele Petraroia
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - William Sergio
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
| | - Piergiorgio La Rosa
- Division of Neuroscience, Department of Psychology, Sapienza University of Rome, via dei Marsi 78, 00185 Rome, Italy
| | - Sandra Moreno
- Department of Science, University Roma Tre, Viale Marconi 446, 00146 Rome, Italy
- Laboratory of Neurodevelopment, Neurogenetics and Neuromolecular Biology, IRCCS Santa Lucia Foundation, 64 via del Fosso di Fiorano, 00179 Rome, Italy
| | - Marco Segatto
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, 86090 Pesche, Italy
- Correspondence:
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3
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Mishra LN, Thiriet C, Vasudevan D. Editorial: Chromatin structure and function. Front Genet 2023; 14:1140534. [PMID: 36824440 PMCID: PMC9941686 DOI: 10.3389/fgene.2023.1140534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 01/25/2023] [Indexed: 02/10/2023] Open
Affiliation(s)
- Laxmi Narayan Mishra
- Albert Einstein College of Medicine, Bronx, NY, United States,*Correspondence: Laxmi Narayan Mishra, ; Christophe Thiriet, , Dileep Vasudevan,
| | - Christophe Thiriet
- Université de Rennes 1, CNRS-UMR6290 Institut génétique et développement de Rennes (IGDR), Rennes, France,*Correspondence: Laxmi Narayan Mishra, ; Christophe Thiriet, , Dileep Vasudevan,
| | - Dileep Vasudevan
- DBT-Institute of Life Sciences, Bhubaneswar, India,*Correspondence: Laxmi Narayan Mishra, ; Christophe Thiriet, , Dileep Vasudevan,
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4
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Chen Y, Wang X, Wu Z, Jia S, Wan M. Epigenetic regulation of dental-derived stem cells and their application in pulp and periodontal regeneration. PeerJ 2023; 11:e14550. [PMID: 36620748 PMCID: PMC9817962 DOI: 10.7717/peerj.14550] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/20/2022] [Indexed: 01/05/2023] Open
Abstract
Dental-derived stem cells have excellent proliferation ability and multi-directional differentiation potential, making them an important research target in tissue engineering. An increasing number of dental-derived stem cells have been discovered recently, including dental pulp stem cells (DPSCs), stem cells from exfoliated deciduous teeth (SHEDs), stem cells from apical papilla (SCAPs), dental follicle precursor cells (DFPCs), and periodontal ligament stem cells (PDLSCs). These stem cells have significant application prospects in tissue regeneration because they are found in an abundance of sources, and they have good biocompatibility and are highly effective. The biological functions of dental-derived stem cells are regulated in many ways. Epigenetic regulation means changing the expression level and function of a gene without changing its sequence. Epigenetic regulation is involved in many biological processes, such as embryonic development, bone homeostasis, and the fate of stem cells. Existing studies have shown that dental-derived stem cells are also regulated by epigenetic modifications. Pulp and periodontal regeneration refers to the practice of replacing damaged pulp and periodontal tissue and restoring the tissue structure and function under normal physiological conditions. This treatment has better therapeutic effects than traditional treatments. This article reviews the recent research on the mechanism of epigenetic regulation of dental-derived stem cells, and the core issues surrounding the practical application and future use of pulp and periodontal regeneration.
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Affiliation(s)
- Yuyang Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China School of Stomatology, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Xiayi Wang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China School of Stomatology, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Zhuoxuan Wu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China School of Stomatology, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Shiyu Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China School of Stomatology, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Mian Wan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China School of Stomatology, Sichuan University, Chengdu, Sichuan, People’s Republic of China,State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, People’s Republic of China
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5
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Bisserier M, Brojakowska A, Saffran N, Rai AK, Lee B, Coleman M, Sebastian A, Evans A, Mills PJ, Addya S, Arakelyan A, Garikipati VNS, Hadri L, Goukassian DA. Astronauts Plasma-Derived Exosomes Induced Aberrant EZH2-Mediated H3K27me3 Epigenetic Regulation of the Vitamin D Receptor. Front Cardiovasc Med 2022; 9:855181. [PMID: 35783863 PMCID: PMC9243458 DOI: 10.3389/fcvm.2022.855181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
There are unique stressors in the spaceflight environment. Exposure to such stressors may be associated with adverse effects on astronauts' health, including increased cancer and cardiovascular disease risks. Small extracellular vesicles (sEVs, i.e., exosomes) play a vital role in intercellular communication and regulate various biological processes contributing to their role in disease pathogenesis. To assess whether spaceflight alters sEVs transcriptome profile, sEVs were isolated from the blood plasma of 3 astronauts at two different time points: 10 days before launch (L-10) and 3 days after return (R+3) from the Shuttle mission. AC16 cells (human cardiomyocyte cell line) were treated with L-10 and R+3 astronauts-derived exosomes for 24 h. Total RNA was isolated and analyzed for gene expression profiling using Affymetrix microarrays. Enrichment analysis was performed using Enrichr. Transcription factor (TF) enrichment analysis using the ENCODE/ChEA Consensus TF database identified gene sets related to the polycomb repressive complex 2 (PRC2) and Vitamin D receptor (VDR) in AC16 cells treated with R+3 compared to cells treated with L-10 astronauts-derived exosomes. Further analysis of the histone modifications using datasets from the Roadmap Epigenomics Project confirmed enrichment in gene sets related to the H3K27me3 repressive mark. Interestingly, analysis of previously published H3K27me3–chromatin immunoprecipitation sequencing (ChIP-Seq) ENCODE datasets showed enrichment of H3K27me3 in the VDR promoter. Collectively, our results suggest that astronaut-derived sEVs may epigenetically repress the expression of the VDR in human adult cardiomyocytes by promoting the activation of the PRC2 complex and H3K27me3 levels.
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Affiliation(s)
- Malik Bisserier
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY, United States
| | - Agnieszka Brojakowska
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY, United States
| | - Nathaniel Saffran
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY, United States
| | - Amit Kumar Rai
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Brooke Lee
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Matthew Coleman
- Lawrence Livermore National Laboratory, Livermore, CA, United States
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA, United States
| | - Aimy Sebastian
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Angela Evans
- Lawrence Livermore National Laboratory, Livermore, CA, United States
- Department of Radiation Oncology, University of California, Davis, Sacramento, CA, United States
| | - Paul J. Mills
- Center of Excellence for Research and Training in Integrative Health, University of California, San Diego, La Jolla, CA, United States
| | - Sankar Addya
- Kimmel Cancer Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Arsen Arakelyan
- Bioinformatics Group, Institute of Molecular Biology, National Academy of Sciences of the Republic of Armenia (NAS RA), Yerevan, Armenia
- Department of Bioengineering, Bioinformatics, and Molecular Biology, Russian-Armenian University, Yerevan, Armenia
| | - Venkata Naga Srikanth Garikipati
- Department of Emergency Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart Lung and Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Lahouaria Hadri
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY, United States
- Lahouaria Hadri
| | - David A. Goukassian
- Icahn School of Medicine at Mount Sinai, Cardiovascular Research Institute, New York, NY, United States
- *Correspondence: David A. Goukassian
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6
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Li Y, Zhao X, Sun M, Pei D, Li A. Deciphering the Epigenetic Code of Stem Cells Derived From Dental Tissues. FRONTIERS IN DENTAL MEDICINE 2022. [DOI: 10.3389/fdmed.2021.807046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Stem cells derived from dental tissues (DSCs) exhibit multipotent regenerative potential in pioneering tissue engineering regimens. The multipotency of DSCs is critically regulated by an intricate range of factors, of which the epigenetic influence is considered vital. To gain a better understanding of how epigenetic alterations are involved in the DSC fate determination, the present review overviews the current knowledge relating to DSC epigenetic modifications, paying special attention to the landscape of epigenetic modifying agents as well as the related signaling pathways in DSC regulation. In addition, insights into the future opportunities of epigenetic targeted therapies mediated by DSCs are discussed to hold promise for the novel therapeutic interventions in future translational medicine.
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7
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Barman S, Roy A, Bardhan I, Kandasamy T, Shivani S, Sudhamalla B. Insights into the Molecular Mechanisms of Histone Code Recognition by the BRPF3 Bromodomain. Chem Asian J 2021; 16:3404-3412. [PMID: 34448544 DOI: 10.1002/asia.202100793] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/24/2021] [Indexed: 01/16/2023]
Abstract
Bromodomains are evolutionarily conserved reader modules that recognize acetylated lysine residues on the histone tails to facilitate gene transcription. The bromodomain and PHD finger containing protein 3 (BRPF3) is a scaffolding protein that forms a tetrameric complex with HBO1 histone acetyltransferase (HAT) and two other subunits, which is known to regulate the HAT activity and substrate specificity. However, its molecular mechanism, histone ligands, and biological functions remain unknown. Herein, we identify mono- (H4K5ac) and di- (H4K5acK12ac) acetylated histone peptides as novel interacting partners of the BRPF3 bromodomain. Consistent with this, pull-down assays on purified histones from human cells confirm the interaction of BRPF3 bromodomain with acetylated histone H4. Further, MD simulation studies highlight the binding mode of acetyllysine (Kac) and the stability of bromodomain-histone peptide complexes. Collectively, our findings provide a key insight into how histone targets of the BRPF3 bromodomain direct the recruitment of HBO1 complex to chromatin for downstream transcriptional regulation.
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Affiliation(s)
- Soumen Barman
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
| | - Anirban Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
| | - Ishita Bardhan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
| | - Thirukumaran Kandasamy
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
| | - Shivani Shivani
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
| | - Babu Sudhamalla
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, 741246, Nadia, West Bengal, India
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8
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Zhang J, Cavallaro M, Hebenstreit D. Timing RNA polymerase pausing with TV-PRO-seq. CELL REPORTS METHODS 2021; 1:None. [PMID: 34723238 PMCID: PMC8547241 DOI: 10.1016/j.crmeth.2021.100083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/03/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022]
Abstract
Transcription of many genes in metazoans is subject to polymerase pausing, which is the transient stop of transcriptionally engaged polymerases. This is known to mainly occur in promoter-proximal regions but it is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been lacking. We present here the time-variant precision nuclear run-on and sequencing (TV-PRO-seq) assay, an extension of the standard PRO-seq that allows us to estimate genome-wide pausing times at single-base resolution. Its application to human cells demonstrates that, proximal to promoters, polymerases pause more frequently but for shorter times than in other genomic regions. Comparison with single-cell gene expression data reveals that the polymerase pausing times are longer in highly expressed genes, while transcriptionally noisier genes have higher pausing frequencies and slightly longer pausing times. Analyses of histone modifications suggest that the marker H3K36me3 is related to the polymerase pausing.
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Affiliation(s)
- Jie Zhang
- School of Life Sciences, Gibbet Hill Campus, the University of Warwick, CV4 7AL Coventry, UK
| | - Massimo Cavallaro
- School of Life Sciences, Gibbet Hill Campus, the University of Warwick, CV4 7AL Coventry, UK
- Mathematics Institute and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, the University of Warwick, CV4 7AL Coventry, UK
| | - Daniel Hebenstreit
- School of Life Sciences, Gibbet Hill Campus, the University of Warwick, CV4 7AL Coventry, UK
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9
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Xiong Y, Zhang M, Li Y. Recent Advances in the Development of CBP/p300 Bromodomain Inhibitors. Curr Med Chem 2020; 27:5583-5598. [DOI: 10.2174/0929867326666190731141055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022]
Abstract
CBP and p300 are two closely related Histone Acetyltransferases (HATs) that interact
with numerous transcription factors and act to increase the expression of their target genes. Both
proteins contain a bromodomain flanking the HAT catalytic domain that is important in binding of
CBP/p300 to chromatin, which offers an opportunity to develop protein-protein interaction inhibitors.
Since their discovery in 2006, CBP/p300 bromodomains have attracted much interest as promising
new epigenetic targets for diverse human diseases, including inflammation, cancer, autoimmune
disorders, and cardiovascular disease. Herein, we present a comprehensive review of the
structure, function, and inhibitors of CBP/p300 bromodomains developed in the last several years,
which is expected to be beneficial to relevant studies.
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Affiliation(s)
- Ying Xiong
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Mingming Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yingxia Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
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10
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Zhang J, Chen P, Zhu P, Zheng P, Wang T, Wang L, Xu C, Zhou J, Zhang H. Development of small-molecule BRD4 degraders based on pyrrolopyridone derivative. Bioorg Chem 2020; 99:103817. [DOI: 10.1016/j.bioorg.2020.103817] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/30/2022]
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Abstract
Bromodomain-containing proteins are often part of chromatin-modifying complexes, and their activity can lead to altered expression of genes that drive cancer, inflammation and neurological disorders in humans. Bromodomain-PHD finger protein 1 (BRPF1) is part of the MOZ (monocytic leukemic zinc-finger protein) HAT (histone acetyltransferase) complex, which is associated with chromosomal translocations known to contribute to the development of acute myeloid leukemia (AML). BRPF1 contains a unique combination of chromatin reader domains including two plant homeodomain (PHD) fingers separated by a zinc knuckle (PZP domain), a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. BRPF1 is known to recruit the MOZ HAT complex to chromatin by recognizing acetylated lysine residues on the N-terminal histone tail region through its bromodomain. However, histone proteins can contain several acetylation modifications on their N-terminus, and it is unknown how additional marks influence bromodomain recruitment to chromatin. Here, we identify the BRPF1 bromodomain as a selective reader of di-acetyllysine modifications on histone H4. We used ITC assays to characterize the binding of di-acetylated histone ligands to the BRPF1 bromodomain and found that the domain binds preferentially to histone peptides H4K5acK8ac and H4K5acK12ac. Analytical ultracentrifugation (AUC) experiments revealed that the monomeric state of the BRPF1 bromodomain coordinates di-acetylated histone ligands. NMR chemical shift perturbation studies, along with binding and mutational analyses, revealed non-canonical regions of the bromodomain-binding pocket that are important for histone tail recognition. Together, our findings provide critical information on how the combinatorial action of post-translational modifications can modulate BRPF1 bromodomain binding and specificity.
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12
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Lazarchuk P, Hernandez-Villanueva J, Pavlova MN, Federation A, MacCoss M, Sidorova JM. Mutual Balance of Histone Deacetylases 1 and 2 and the Acetyl Reader ATAD2 Regulates the Level of Acetylation of Histone H4 on Nascent Chromatin of Human Cells. Mol Cell Biol 2020; 40:e00421-19. [PMID: 32015101 PMCID: PMC7156220 DOI: 10.1128/mcb.00421-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 09/25/2019] [Accepted: 01/21/2020] [Indexed: 01/04/2023] Open
Abstract
Newly synthesized histone H4 that is incorporated into chromatin during DNA replication is acetylated on lysines 5 and 12. Histone deacetylase 1 (HDAC1) and HDAC2 are responsible for reducing H4 acetylation as chromatin matures. Using CRISPR-Cas9-generated hdac1- or hdac2-null fibroblasts, we determined that HDAC1 and HDAC2 do not fully compensate for each other in removing de novo acetyls on H4 in vivo Proteomics of nascent chromatin and proximity ligation assays with newly replicated DNA revealed the binding of ATAD2, a bromodomain-containing posttranslational modification (PTM) reader that recognizes acetylated H4. ATAD2 is a transcription facilitator overexpressed in several cancers and in the simian virus 40 (SV40)-transformed human fibroblast model cell line used in this study. The recruitment of ATAD2 to nascent chromatin was increased in hdac2 cells over the wild type, and ATAD2 depletion reduced the levels of nascent chromatin-associated, acetylated H4 in wild-type and hdac2 cells. We propose that overexpressed ATAD2 shifts the balance of H4 acetylation by protecting this mark from removal and that HDAC2 but not HDAC1 can effectively compete with ATAD2 for the target acetyls. ATAD2 depletion also reduced global RNA synthesis and nascent DNA-associated RNA. A moderate dependence on ATAD2 for replication fork progression was noted only for hdac2 cells overexpressing the protein.
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Affiliation(s)
- Pavlo Lazarchuk
- University of Washington, Department of Pathology, Seattle, Washington, USA
| | | | - Maria N Pavlova
- University of Washington, Department of Pathology, Seattle, Washington, USA
| | | | - Michael MacCoss
- University of Washington, Department of Genome Sciences, Seattle, Washington, USA
| | - Julia M Sidorova
- University of Washington, Department of Pathology, Seattle, Washington, USA
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13
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Abstract
Proteotoxic stress, that is, stress caused by protein misfolding and aggregation, triggers the rapid and global reprogramming of transcription at genes and enhancers. Genome-wide assays that track transcriptionally engaged RNA polymerase II (Pol II) at nucleotide resolution have provided key insights into the underlying molecular mechanisms that regulate transcriptional responses to stress. In addition, recent kinetic analyses of transcriptional control under heat stress have shown how cells 'prewire' and rapidly execute genome-wide changes in transcription while concurrently becoming poised for recovery. The regulation of Pol II at genes and enhancers in response to heat stress is coupled to chromatin modification and compartmentalization, as well as to co-transcriptional RNA processing. These mechanistic features seem to apply broadly to other coordinated genome-regulatory responses.
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14
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Lazarchuk P, Roy S, Schlacher K, Sidorova J. Detection and Quantitation of Acetylated Histones on Replicating DNA Using In Situ Proximity Ligation Assay and Click-It Chemistry. Methods Mol Biol 2019; 1983:29-45. [PMID: 31087291 PMCID: PMC10439737 DOI: 10.1007/978-1-4939-9434-2_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Histone acetylation plays important roles in the regulation of DNA transcription, repair, and replication. Here we detail a method for quantitative detection of specific histone modifications in the nascent chromatin at or behind replication forks in vivo in cultured cells. The method involves labeling DNA with EdU, using Click chemistry to biotinylate EdU moieties in DNA, and then using in situ proximity ligation assay (PLA) to selectively visualize co-localization of EdU with a modified histone of choice recognized by a modification-specific antibody. We focus on detection of acetylated histones H3 and H4 in the nascent chromatin of cultured human cells as a specific example of the method's application. Notably, the method is fully applicable to studies of histones or nonhistone proteins expected to be present on nascent DNA or at replication forks, and has been successfully used in model organisms and human tissue culture.
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Affiliation(s)
- Pavlo Lazarchuk
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Sunetra Roy
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katharina Schlacher
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Julia Sidorova
- Department of Pathology, University of Washington, Seattle, WA, USA.
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15
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Structural basis for activation of SAGA histone acetyltransferase Gcn5 by partner subunit Ada2. Proc Natl Acad Sci U S A 2018; 115:10010-10015. [PMID: 30224453 DOI: 10.1073/pnas.1805343115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Gcn5 histone acetyltransferase (HAT) subunit of the SAGA transcriptional coactivator complex catalyzes acetylation of histone H3 and H2B N-terminal tails, posttranslational modifications associated with gene activation. Binding of the SAGA subunit partner Ada2 to Gcn5 activates Gcn5's intrinsically weak HAT activity on histone proteins, but the mechanism for this activation by the Ada2 SANT domain has remained elusive. We have employed Fab antibody fragments as crystallization chaperones to determine crystal structures of a yeast Ada2/Gcn5 complex. Our structural and biochemical results indicate that the Ada2 SANT domain does not activate Gcn5's activity by directly affecting histone peptide binding as previously proposed. Instead, the Ada2 SANT domain enhances Gcn5 binding of the enzymatic cosubstrate acetyl-CoA. This finding suggests a mechanism for regulating chromatin modification enzyme activity: controlling binding of the modification cosubstrate instead of the histone substrate.
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16
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Liang YY, Zhang CM, Liu ZP. Evaluation of WO2017018805: 1,3,4-oxadiazole sulfamide derivatives as selective HDAC6 inhibitors. Expert Opin Ther Pat 2018; 28:647-651. [PMID: 30073889 DOI: 10.1080/13543776.2018.1508451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
INTRODUCTION There are great potential in the development of selective HDAC6 inhibitors for the treatment of infectious diseases, neoplasms, endocrine diseases, and other diseases associated with HDAC6 activity. Areas covered: The application claims 1,3,4-oxadiazole sulfamide derivatives as selective HDAC6 inhibitors for the treatment of infectious diseases, neoplasms, endocrine, nutritional, and metabolic diseases; mental and behavioral disorders; neurological diseases; diseases of the eye and adnexa; cardiovascular diseases; respiratory diseases; digestive diseases; diseases of the skin and subcutaneous tissue; disease of the musculoskeletal system and connective tissue; or congenital malformations, deformations and chromosomal abnormalities. Many of the exemplified compounds showed nanomole potency against HDAC6 and were more than 5000-fold selectivity for HDAC6 over HDAC1. Expert opinion: These 1,3,4-oxadiazole sulfamide derivatives have a unique zinc-binding group (ZBG) that provide good leads for the discovery of potent selective HDAC6 inhibitors for the treatment of a variety of diseases associated with HDAC6 activity.
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Affiliation(s)
- Yuan-Yuan Liang
- a Institute of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , PR China
| | - Cheng-Mei Zhang
- a Institute of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , PR China
| | - Zhao-Peng Liu
- a Institute of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , PR China
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17
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SAHA and cisplatin sensitize gastric cancer cells to doxorubicin by induction of DNA damage, apoptosis and perturbation of AMPK-mTOR signalling. Exp Cell Res 2018; 370:283-291. [PMID: 29959912 DOI: 10.1016/j.yexcr.2018.06.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 06/21/2018] [Accepted: 06/26/2018] [Indexed: 12/23/2022]
Abstract
Chemotherapy remains the most prescribed anti-cancer therapy, despite patients suffering severe side effects and frequently developing chemoresistance. These complications can be partially overcome by combining different chemotherapeutic agents that target multiple biological pathways. However, selecting efficacious drug combinations remains challenging. We previously used fission yeast Schizosaccharomycespombe as a surrogate model to predict drug combinations, and showed that suberoylanilide hydroxamic acid (SAHA) and cisplatin can sensitise gastric adenocarcinoma cells toward the cytotoxic effects of doxorubicin. Yet, how this combination undermines cell viability is unknown. Here, we show that SAHA and doxorubicin markedly enhance the cleavage of two apoptosis markers, caspase 3 and poly-ADP ribose polymerase (PARP-1), and increase the phosphorylation of γH2AX, a marker of DNA damage. Further, we found a prominent reduction in Ser485 phosphorylation of AMP-dependent protein kinase (AMPK), and reductions in its target mTOR and downstream ribosomal protein S6 phosphorylation. We show that SAHA contributes most of the effect, as confirmed using another histone deacetylase inhibitor, trichostatin A. Overall, our results show that the combination of SAHA and doxorubicin can induce apoptosis in gastric adenocarcinoma in a synthetically lethal manner, and that fission yeast offers an efficient tool for identifying potent drug combinations against human cancer cells.
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19
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Vihervaara A, Mahat DB, Guertin MJ, Chu T, Danko CG, Lis JT, Sistonen L. Transcriptional response to stress is pre-wired by promoter and enhancer architecture. Nat Commun 2017; 8:255. [PMID: 28811569 PMCID: PMC5557961 DOI: 10.1038/s41467-017-00151-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/05/2017] [Indexed: 12/29/2022] Open
Abstract
Programs of gene expression are executed by a battery of transcription factors that coordinate divergent transcription from a pair of tightly linked core initiation regions of promoters and enhancers. Here, to investigate how divergent transcription is reprogrammed upon stress, we measured nascent RNA synthesis at nucleotide-resolution, and profiled histone H4 acetylation in human cells. Our results globally show that the release of promoter-proximal paused RNA polymerase into elongation functions as a critical switch at which a gene’s response to stress is determined. Highly transcribed and highly inducible genes display strong transcriptional directionality and selective assembly of general transcription factors on the core sense promoter. Heat-induced transcription at enhancers, instead, correlates with prior binding of cell-type, sequence-specific transcription factors. Activated Heat Shock Factor 1 (HSF1) binds to transcription-primed promoters and enhancers, and CTCF-occupied, non-transcribed chromatin. These results reveal chromatin architectural features that orient transcription at divergent regulatory elements and prime transcriptional responses genome-wide. Heat Shock Factor 1 (HSF1) is a regulator of stress-induced transcription. Here, the authors investigate changes to transcription and chromatin organization upon stress and find that activated HSF1 binds to transcription-primed promoters and enhancers, and to CTCF occupied, untranscribed chromatin.
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Affiliation(s)
- Anniina Vihervaara
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, 20520, Finland.,Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, 14853, USA
| | - Dig Bijay Mahat
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, 14853, USA
| | - Michael J Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, 22908, USA
| | - Tinyi Chu
- Department of Biomedical Sciences, The Baker Institute for Animal Health, Cornell University, Ithaca, New York, 14853, USA.,Graduate Field of Computational Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Charles G Danko
- Department of Biomedical Sciences, The Baker Institute for Animal Health, Cornell University, Ithaca, New York, 14853, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, 14853, USA.
| | - Lea Sistonen
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, 20520, Finland.
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20
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Ghezzi A, Li X, Lew LK, Wijesekera TP, Atkinson NS. Alcohol-Induced Neuroadaptation Is Orchestrated by the Histone Acetyltransferase CBP. Front Mol Neurosci 2017; 10:103. [PMID: 28442993 PMCID: PMC5387060 DOI: 10.3389/fnmol.2017.00103] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/24/2017] [Indexed: 12/19/2022] Open
Abstract
Homeostatic neural adaptations to alcohol underlie the production of alcohol tolerance and the associated symptoms of withdrawal. These adaptations have been shown to persist for relatively long periods of time and are believed to be of central importance in promoting the addictive state. In Drosophila, a single exposure to alcohol results in long-lasting alcohol tolerance and symptoms of withdrawal following alcohol clearance. These persistent adaptations involve mechanisms such as long-lasting changes in gene expression and perhaps epigenetic restructuring of chromosomal regions. Histone modifications have emerged as important modulators of gene expression and are thought to orchestrate and maintain the expression of multi-gene networks. Previously genes that contribute to tolerance were identified as those that show alcohol-induced changes in histone H4 acetylation following a single alcohol exposure. However, the molecular mediator of the acetylation process that orchestrates their expression remains unknown. Here we show that the Drosophila ortholog of mammalian CBP, nejire, is the histone acetyltransferase involved in regulatory changes producing tolerance—alcohol induces nejire expression, nejire mutations suppress tolerance, and transgenic nejire induction mimics tolerance in alcohol-naive animals. Moreover, we observed that a loss-of-function mutation in the alcohol tolerance gene slo epistatically suppresses the effects of CBP induction on alcohol resistance, linking nejire to a well-established alcohol tolerance gene network. We propose that CBP is a central regulator of the network of genes underlying an alcohol adaptation.
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Affiliation(s)
- Alfredo Ghezzi
- Department of Biology, University of Puerto Rico, Río Piedras CampusSan Juan, Puerto Rico
| | - Xiaolei Li
- Department of Neuroscience and Waggoner Center for Alcohol and Addiction Research, The University of Texas at AustinAustin, TX, USA
| | - Linda K Lew
- Department of Neuroscience and Waggoner Center for Alcohol and Addiction Research, The University of Texas at AustinAustin, TX, USA
| | - Thilini P Wijesekera
- Department of Neuroscience and Waggoner Center for Alcohol and Addiction Research, The University of Texas at AustinAustin, TX, USA
| | - Nigel S Atkinson
- Department of Neuroscience and Waggoner Center for Alcohol and Addiction Research, The University of Texas at AustinAustin, TX, USA
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Kejík Z, Kaplánek R, Havlík M, Bříza T, Jakubek M, Králová J, Mikula I, Martásek P, Král V. Optical probes and sensors as perspective tools in epigenetics. Bioorg Med Chem 2017; 25:2295-2306. [PMID: 28285925 DOI: 10.1016/j.bmc.2017.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/13/2016] [Accepted: 01/11/2017] [Indexed: 12/23/2022]
Abstract
Modifications of DNA cytosine bases and histone posttranslational modifications play key roles in the control of gene expression and specification of cell states. Such modifications affect many important biological processes and changes to these important regulation mechanisms can initiate or significantly contribute to the development of many serious pathological states. Therefore, recognition and determination of chromatin modifications is an important goal in basic and clinical research. Two of the most promising tools for this purpose are optical probes and sensors, especially colourimetric and fluorescence devices. The use of optical probes and sensors is simple, without highly expensive instrumentation, and with excellent sensitivity and specificity for target structural motifs. Accordingly, the application of various probes and sensors in the recognition and determination of cytosine modifications and structure of histones and histone posttranslational modifications, are discussed in detail in this review.
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Affiliation(s)
- Zdeněk Kejík
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Robert Kaplánek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Martin Havlík
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Tomáš Bříza
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Milan Jakubek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Jarmila Králová
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Ivan Mikula
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Pavel Martásek
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic
| | - Vladimír Král
- First Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague 2, Czech Republic.
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Bayarsaihan D. Deciphering the Epigenetic Code in Embryonic and Dental Pulp Stem Cells. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:539-563. [PMID: 28018144 PMCID: PMC5168831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
A close cooperation between chromatin states, transcriptional modulation, and epigenetic modifications is required for establishing appropriate regulatory circuits underlying self-renewal and differentiation of adult and embryonic stem cells. A growing body of research has established that the epigenome topology provides a structural framework for engaging genes in the non-random chromosomal interactions to orchestrate complex processes such as cell-matrix interactions, cell adhesion and cell migration during lineage commitment. Over the past few years, the functional dissection of the epigenetic landscape has become increasingly important for understanding gene expression dynamics in stem cells naturally found in most tissues. Adult stem cells of the human dental pulp hold great promise for tissue engineering, particularly in the skeletal and tooth regenerative medicine. It is therefore likely that progress towards pulp regeneration will have a substantial impact on the clinical research. This review summarizes the current state of knowledge regarding epigenetic cues that have evolved to regulate the pluripotent differentiation potential of embryonic stem cells and the lineage determination of developing dental pulp progenitors.
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Affiliation(s)
- Dashzeveg Bayarsaihan
- Institute for System Genomics and Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health Center, Farmington, CT, USA
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23
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Ferreira WAS, Pinheiro DDR, Costa Junior CAD, Rodrigues-Antunes S, Araújo MD, Leão Barros MB, Teixeira ACDS, Faro TAS, Burbano RR, Oliveira EHCD, Harada ML, Borges BDN. An update on the epigenetics of glioblastomas. Epigenomics 2016; 8:1289-305. [PMID: 27585647 DOI: 10.2217/epi-2016-0040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glioblastomas, also known as glioblastoma multiforme (GBM), are the most aggressive and malignant type of primary brain tumor in adults, exhibiting notable variability at the histopathological, genetic and epigenetic levels. Recently, epigenetic alterations have emerged as a common hallmark of many tumors, including GBM. Considering that a deeper understanding of the epigenetic modifications that occur in GBM may increase the knowledge regarding the tumorigenesis, progression and recurrence of this disease, in this review we discuss the recent major advances in GBM epigenetics research involving histone modification, glioblastoma stem cells, DNA methylation, noncoding RNAs expression, including their main alterations and the use of epigenetic therapy as a valid option for GBM treatment.
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Affiliation(s)
- Wallax Augusto Silva Ferreira
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Danilo do Rosário Pinheiro
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Carlos Antonio da Costa Junior
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Symara Rodrigues-Antunes
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Mariana Diniz Araújo
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Mariceli Baia Leão Barros
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Adriana Corrêa de Souza Teixeira
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Thamirys Aline Silva Faro
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | | | | | - Maria Lúcia Harada
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Bárbara do Nascimento Borges
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
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Abstract
PURPOSE OF REVIEW The activation of inflammatory response is dependent upon genetic factors and epigenetic control mechanisms. This overview will highlight recent advances in the understanding of epigenetic dynamics during cellular inflammation. RECENT FINDINGS There is a growing body of evidence indicating that alterations of the chromatin state associate with an increased risk of chronic disease development and inflammation. Epigenetic alterations respond rapidly to environmental changes and have a profound effect on gene regulatory cross-wirings and transcriptional regulation. SUMMARY Systematic dissection of the mechanisms underlying epigenetic effects during inflammatory response is a critical step toward elucidation of the cell's molecular processes and holds potential for the development of novel therapies for the treatment of chronic diseases.
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Affiliation(s)
- Dashzeveg Bayarsaihan
- Institute for System Genomics and Center for Regenerative Medicine and Skeletal Development, University of Connecticut Health Center, Farmington, Connecticut, USA
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25
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Influenza A Virus Dysregulates Host Histone Deacetylase 1 That Inhibits Viral Infection in Lung Epithelial Cells. J Virol 2016; 90:4614-4625. [PMID: 26912629 DOI: 10.1128/jvi.00126-16] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/16/2016] [Indexed: 01/17/2023] Open
Abstract
UNLABELLED Viruses dysregulate the host factors that inhibit virus infection. Here, we demonstrate that human enzyme, histone deacetylase 1 (HDAC1) is a new class of host factor that inhibits influenza A virus (IAV) infection, and IAV dysregulates HDAC1 to efficiently replicate in epithelial cells. A time-dependent decrease in HDAC1 polypeptide level was observed in IAV-infected cells, reducing to <50% by 24 h of infection. A further depletion (97%) of HDAC1 expression by RNA interference increased the IAV growth kinetics, increasing it by >3-fold by 24 h and by >6-fold by 48 h of infection. Conversely, overexpression of HDAC1 decreased the IAV infection by >2-fold. Likewise, a time-dependent decrease in HDAC1 activity, albeit with slightly different kinetics to HDAC1 polypeptide reduction, was observed in infected cells. Nevertheless, a further inhibition of deacetylase activity increased IAV infection in a dose-dependent manner. HDAC1 is an important host deacetylase and, in addition to its role as a transcription repressor, HDAC1 has been lately described as a coactivator of type I interferon response. Consistent with this property, we found that inhibition of deacetylase activity either decreased or abolished the phosphorylation of signal transducer and activator of transcription I (STAT1) and expression of interferon-stimulated genes, IFITM3, ISG15, and viperin in IAV-infected cells. Furthermore, the knockdown of HDAC1 expression in infected cells decreased viperin expression by 58% and, conversely, the overexpression of HDAC1 increased it by 55%, indicating that HDAC1 is a component of IAV-induced host type I interferon antiviral response. IMPORTANCE Influenza A virus (IAV) continues to significantly impact global public health by causing regular seasonal epidemics, occasional pandemics, and zoonotic outbreaks. IAV is among the successful human viral pathogens that has evolved various strategies to evade host defenses, prevent the development of a universal vaccine, and acquire antiviral drug resistance. A comprehensive knowledge of IAV-host interactions is needed to develop a novel and alternative anti-IAV strategy. Host produces a variety of factors that are able to fight IAV infection by employing various mechanisms. However, the full repertoire of anti-IAV host factors and their antiviral mechanisms has yet to be identified. We have identified here a new host factor, histone deacetylase 1 (HDAC1) that inhibits IAV infection. We demonstrate that HDAC1 is a component of host innate antiviral response against IAV, and IAV undermines HDAC1 to limit its role in antiviral response.
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Fu I, Cai Y, Zhang Y, Geacintov NE, Broyde S. Entrapment of a Histone Tail by a DNA Lesion in a Nucleosome Suggests the Lesion Impacts Epigenetic Marking: A Molecular Dynamics Study. Biochemistry 2016; 55:239-42. [PMID: 26709619 PMCID: PMC4721520 DOI: 10.1021/acs.biochem.5b01166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 12/21/2015] [Indexed: 11/30/2022]
Abstract
Errors in epigenetic markings are associated with human diseases, including cancer. We have used molecular dynamics simulations of a nucleosome containing the 10S (+)-trans-anti-B[a]P-N(2)-dG lesion, derived from the environmental pro-carcinogen benzo[a]pyrene, to elucidate the impact of the lesion on the structure and dynamics of a nearby histone N-terminal tail. Our results show that a lysine-containing part of this H2B tail that is subject to post-translational modification is engulfed by the enlarged DNA minor groove imposed by the lesion. The tail entrapment suggests that epigenetic markings could be hampered by this lesion, thereby impacting critical cellular functions, including transcription and repair.
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Affiliation(s)
- Iwen Fu
- Department of Biology and Department of
Chemistry, New York University, New York, New York 10003, United States
| | - Yuqin Cai
- Department of Biology and Department of
Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Biology and Department of
Chemistry, New York University, New York, New York 10003, United States
- NYU-ECNU
Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Nicholas E. Geacintov
- Department of Biology and Department of
Chemistry, New York University, New York, New York 10003, United States
| | - Suse Broyde
- Department of Biology and Department of
Chemistry, New York University, New York, New York 10003, United States
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Reduced Histone H3 Acetylation in CD4(+) T Lymphocytes: Potential Mechanism of Latent Autoimmune Diabetes in Adults. DISEASE MARKERS 2015; 2015:285125. [PMID: 26839444 PMCID: PMC4709642 DOI: 10.1155/2015/285125] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 12/07/2015] [Accepted: 12/10/2015] [Indexed: 11/18/2022]
Abstract
Aims. Latent autoimmune diabetes in adults (LADA) is the result of gene-environment interactions. Histone acetylation regulates gene expression and maybe interpret how environmental factors modify LADA. Hence, we studied the histone acetylation patterns in CD4(+) T lymphocytes from LADA patients. Methods. Blood CD4(+) T lymphocytes from 28 patients with LADA and 28 healthy controls were obtained to detect histone H3 acetylation and H4 acetylation. The gene expression of histone acetyltransferases (P300 and CREBBP) and histone deacetylases (HDAC1, HDAC2, and HDAC7) was measured by real-time polymerase chain reaction (RT-PCR). Results. Compared to healthy controls, reduced global H3 acetylation was observed in LADA patients' CD4(+) T lymphocytes (P < 0.05). Global level of H4 acetylation was not statistically different. Among LADA, CD4(+) T lymphocytes H3 acetylation was associated with glycosylated hemoglobin (HbA1c) and GADA titer. Compared to healthy controls, the expression of histone acetyltransferases CREBBP in LADA patients was downregulated, and the expression of histone deacetylases HDAC1 and HDAC7 was upregulated. Conclusion. A concerted downregulation of histone H3 acetylation was found in CD4(+) T lymphocytes of LADA patients, and this might provide evidence of a novel epigenetic explanation for the pathogenesis of LADA and its complications.
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Ferri E, Petosa C, McKenna CE. Bromodomains: Structure, function and pharmacology of inhibition. Biochem Pharmacol 2015; 106:1-18. [PMID: 26707800 DOI: 10.1016/j.bcp.2015.12.005] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/08/2015] [Indexed: 12/22/2022]
Abstract
Bromodomains are epigenetic readers of histone acetylation involved in chromatin remodeling and transcriptional regulation. The human proteome comprises 46 bromodomain-containing proteins with a total of 61 bromodomains, which, despite highly conserved structural features, recognize a wide array of natural peptide ligands. Over the past five years, bromodomains have attracted great interest as promising new epigenetic targets for diverse human diseases, including inflammation, cancer, and cardiovascular disease. The demonstration in 2010 that two small molecule compounds, JQ1 and I-BET762, potently inhibit proteins of the bromodomain and extra-terminal (BET) family with translational potential for cancer and inflammatory disease sparked intense efforts in academia and pharmaceutical industry to develop novel bromodomain antagonists for therapeutic applications. Several BET inhibitors are already in clinical trials for hematological malignancies, solid tumors and cardiovascular disease. Currently, the field faces the challenge of single-target selectivity, especially within the BET family, and of overcoming problems related to the development of drug resistance. At the same time, new trends in bromodomain inhibitor research are emerging, including an increased interest in non-BET bromodomains and a focus on drug synergy with established antitumor agents to improve chemotherapeutic efficacy. This review presents an updated view of the structure and function of bromodomains, traces the development of bromodomain inhibitors and their potential therapeutic applications, and surveys the current challenges and future directions of this vibrant new field in drug discovery.
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Affiliation(s)
- Elena Ferri
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, CA 90089, United States
| | - Carlo Petosa
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, 38044 Grenoble, France; Centre National de la Recherche Scientifique, IBS, 38044 Grenoble, France; Commissariat à l'Energie Atomique et aux Energies Alternatives, IBS, 38044 Grenoble, France
| | - Charles E McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, CA 90089, United States.
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