1
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Patel R, Onyema A, Tang PK, Loverde SM. Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations. J Chem Inf Model 2024; 64:4709-4726. [PMID: 38865599 PMCID: PMC11200259 DOI: 10.1021/acs.jcim.4c00059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024]
Abstract
Epigenetic modifications of histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and DNA repair. One of the key post-translational modifications (PTMs) is the acetylation of lysine residues on histone tails. Epigenetic modifications are ubiquitous in the development of diseases, such as cancer and neurological disorders. Histone H2B tails are critical regulators of nucleosome dynamics, biological processes, and certain diseases. Here, we report all-atomistic molecular dynamics (MD) simulations of the nucleosome to demonstrate that acetylation of the histone tails changes their conformational space and interaction with DNA. We perform simulations of H2B tails, critical regulators of gene regulation, in both the lysine-acetylated (ACK) and unacetylated wild type (WT) states. To explore the effects of salt concentration, we use two different NaCl concentrations to perform simulations at microsecond time scales. Salt can modulate the effects of electrostatic interactions between the DNA phosphate backbone and histone tails. Upon acetylation, H2B tails shift their secondary structure helical propensity. The number of contacts between the DNA and the H2B tail decreases. We characterize the conformational dynamics of the H2B tails by principal component analysis (PCA). The ACK tails become more compact at increased salt concentrations, but conformations from the WT tails display the most contacts with DNA at both salt concentrations. Mainly, H2B acetylation may increase the DNA accessibility for regulatory proteins to bind, which can aid in gene regulation and NCP stability.
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Affiliation(s)
- Rutika Patel
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Augustine Onyema
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Phu K. Tang
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Sharon M. Loverde
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Ph.D.
Program in Physics, The Graduate Center
of the City University of New York, New York, New York 10016, United States
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2
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Tsuruta Y, Senmatsu S, Oe H, Hoffman CS, Hirota K. Metabolic stress-induced long ncRNA transcription governs the formation of meiotic DNA breaks in the fission yeast fbp1 gene. PLoS One 2024; 19:e0294191. [PMID: 38252660 PMCID: PMC10802949 DOI: 10.1371/journal.pone.0294191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/26/2023] [Indexed: 01/24/2024] Open
Abstract
Meiotic recombination is a pivotal process that ensures faithful chromosome segregation and contributes to the generation of genetic diversity in offspring, which is initiated by the formation of double-strand breaks (DSBs). The distribution of meiotic DSBs is not uniform and is clustered at hotspots, which can be affected by environmental conditions. Here, we show that non-coding RNA (ncRNA) transcription creates meiotic DSBs through local chromatin remodeling in the fission yeast fbp1 gene. The fbp1 gene is activated upon glucose starvation stress, in which a cascade of ncRNA-transcription in the fbp1 upstream region converts the chromatin configuration into an open structure, leading to the subsequent binding of transcription factors. We examined the distribution of meiotic DSBs around the fbp1 upstream region in the presence and absence of glucose and observed several new DSBs after chromatin conversion under glucose starvation conditions. Moreover, these DSBs disappeared when cis-elements required for ncRNA transcription were mutated. These results indicate that ncRNA transcription creates meiotic DSBs in response to stress conditions in the fbp1 upstream region. This study addressed part of a long-standing unresolved mechanism underlying meiotic recombination plasticity in response to environmental fluctuation.
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Affiliation(s)
- Yusuke Tsuruta
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Satoshi Senmatsu
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Hana Oe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
| | - Charles S. Hoffman
- Biology Department, Boston College, Chestnut Hill, MA, United States of America
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Tokyo, Japan
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3
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Zhang L, Chai R, Tai Z, Miao F, Shi X, Chen Z, Zhu Q. Noval advance of histone modification in inflammatory skin diseases and related treatment methods. Front Immunol 2024; 14:1286776. [PMID: 38235133 PMCID: PMC10792063 DOI: 10.3389/fimmu.2023.1286776] [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: 09/01/2023] [Accepted: 12/08/2023] [Indexed: 01/19/2024] Open
Abstract
Inflammatory skin diseases are a group of diseases caused by the disruption of skin tissue due to immune system disorders. Histone modification plays a pivotal role in the pathogenesis and treatment of chronic inflammatory skin diseases, encompassing a wide range of conditions, including psoriasis, atopic dermatitis, lupus, systemic sclerosis, contact dermatitis, lichen planus, and alopecia areata. Analyzing histone modification as a significant epigenetic regulatory approach holds great promise for advancing our understanding and managing these complex disorders. Additionally, therapeutic interventions targeting histone modifications have emerged as promising strategies for effectively managing inflammatory skin disorders. This comprehensive review provides an overview of the diverse types of histone modification. We discuss the intricate association between histone modification and prevalent chronic inflammatory skin diseases. We also review current and potential therapeutic approaches that revolve around modulating histone modifications. Finally, we investigated the prospects of research on histone modifications in the context of chronic inflammatory skin diseases, paving the way for innovative therapeutic interventions and improved patient outcomes.
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Affiliation(s)
- Lichen Zhang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Rongrong Chai
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Zongguang Tai
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Fengze Miao
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Xinwei Shi
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Zhongjian Chen
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
| | - Quangang Zhu
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of External Chinese Medicine, Shanghai, China
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4
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Maeshima K, Iida S, Shimazoe MA, Tamura S, Ide S. Is euchromatin really open in the cell? Trends Cell Biol 2024; 34:7-17. [PMID: 37385880 DOI: 10.1016/j.tcb.2023.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 07/01/2023]
Abstract
Genomic DNA is wrapped around a core histone octamer and forms a nucleosome. In higher eukaryotic cells, strings of nucleosomes are irregularly folded as chromatin domains that act as functional genome units. According to a typical textbook model, chromatin can be categorized into two types, euchromatin and heterochromatin, based on its degree of compaction. Euchromatin is open, while heterochromatin is closed and condensed. However, is euchromatin really open in the cell? New evidence from genomics and advanced imaging studies has revealed that euchromatin consists of condensed liquid-like domains. Condensed chromatin seems to be the default chromatin state in higher eukaryotic cells. We discuss this novel view of euchromatin in the cell and how the revealed organization is relevant to genome functions.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan.
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Masa A Shimazoe
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Satoru Ide
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Graduate Institute for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
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5
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Beljkas M, Ilic A, Cebzan A, Radovic B, Djokovic N, Ruzic D, Nikolic K, Oljacic S. Targeting Histone Deacetylases 6 in Dual-Target Therapy of Cancer. Pharmaceutics 2023; 15:2581. [PMID: 38004560 PMCID: PMC10674519 DOI: 10.3390/pharmaceutics15112581] [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: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Histone deacetylases (HDACs) are the major regulators of the balance of acetylation of histone and non-histone proteins. In contrast to other HDAC isoforms, HDAC6 is mainly involved in maintaining the acetylation balance of many non-histone proteins. Therefore, the overexpression of HDAC6 is associated with tumorigenesis, invasion, migration, survival, apoptosis and growth of various malignancies. As a result, HDAC6 is considered a promising target for cancer treatment. However, none of selective HDAC6 inhibitors are in clinical use, mainly because of the low efficacy and high concentrations used to show anticancer properties, which may lead to off-target effects. Therefore, HDAC6 inhibitors with dual-target capabilities represent a new trend in cancer treatment, aiming to overcome the above problems. In this review, we summarize the advances in tumor treatment with dual-target HDAC6 inhibitors.
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Affiliation(s)
| | | | | | | | | | | | - Katarina Nikolic
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (M.B.); (A.I.); (A.C.); (B.R.); (N.D.); (D.R.)
| | - Slavica Oljacic
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Belgrade, Vojvode Stepe 450, 11221 Belgrade, Serbia; (M.B.); (A.I.); (A.C.); (B.R.); (N.D.); (D.R.)
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6
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Das SK, Huynh MT, Lee TH. Spontaneous histone exchange between nucleosomes. J Biol Chem 2023; 299:105037. [PMID: 37442235 PMCID: PMC10406861 DOI: 10.1016/j.jbc.2023.105037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/26/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023] Open
Abstract
The nucleosome is the fundamental gene-packing unit in eukaryotes. Nucleosomes comprise ∼147 bp DNA wrapped around an octameric histone protein core composed of two H2A-H2B dimers and one (H3-H4)2 tetramer. The strong yet flexible DNA-histone interactions are the physical basis of the dynamic regulation of genes packaged in chromatin. The dynamic nature of DNA-histone interactions also implies that nucleosomes dissociate DNA-histone contacts both transiently and repeatedly. This kinetic instability may lead to spontaneous nucleosome disassembly or histone exchange between nucleosomes. At high nucleosome concentrations, nucleosome-nucleosome collisions and subsequent histone exchange would be a more likely event, where nucleosomes could act as their own histone chaperone. This spontaneous histone exchange could serve as a mechanism for maintaining overall chromatin stability, although it has never been reported. Here we employed three-color single-molecule FRET (smFRET) to demonstrate that histone H2A-H2B dimers are exchanged spontaneously between nucleosomes on a time scale of a few tens of seconds at a physiological nucleosome concentration. We show that the rate of histone exchange increases at a higher monovalent salt concentration, with histone-acetylated nucleosomes, and in the presence of histone chaperone Nap1, while it remains unchanged at a higher temperature, and decreases upon DNA methylation. These results support the notion of histone exchange via transient and repetitive partial disassembly of the nucleosome and corroborate spontaneous histone diffusion in a compact chromatin context, modulating the local concentrations of histone modifications and variants.
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Affiliation(s)
- Subhra Kanti Das
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Mai Thao Huynh
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Tae-Hee Lee
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
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7
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Mayer V, Frank AC, Preinsperger S, Csar P, Steppert P, Jungbauer A, Pereira Aguilar P. Removal of chromatin by salt-tolerant endonucleases for production of recombinant measles virus. Biotechnol Prog 2023; 39:e3342. [PMID: 36974026 DOI: 10.1002/btpr.3342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/27/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
Host cell DNA is a critical impurity in downstream processing of enveloped viruses. Especially, DNA in the form of chromatin is often neglected. Endonuclease treatment is an almost mandatory step in manufacturing of viral vaccines. In order to find the optimal performer, four different endonucleases, two of them salt tolerant, were evaluated in downstream processing of recombinant measles virus. Endonuclease treatment was performed under optimal temperature conditions after clarification and before the purification by flow-through chromatography with a core shell chromatography medium: Capto™ Core 700. Virus infectivity was measured by TCID50. DNA and histone presence in process and purified samples was determined using PicoGreen™ assay and Western blot analysis using an anti-histone antibody, respectively. All tested endonucleases allowed the reduction of DNA content improving product purity. The salt-tolerant endonucleases SAN and M-SAN were more efficient in the removal of chromatin compared with the non-salt-tolerant endonucleases Benzonase® and DENARASE®. Removal of chromatin using M-SAN was also possible without the addition of extra salt to the cell culture supernatant. The combination of the endonuclease treatment, using salt-tolerant endonucleases with flow-through chromatography, using core-shell particles, resulted in high purity and purification efficiency. This strategy has all features for a platform downstream process of recombinant measles virus and beyond.
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Affiliation(s)
- Viktoria Mayer
- acib - Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Anna-Carina Frank
- acib - Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Shirin Preinsperger
- acib - Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Patrick Csar
- Themis Bioscience GmbH (A Subsidiary of Merck & Co., Inc, Kenilworth, NJ, USA), Vienna, Austria
| | - Petra Steppert
- Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Alois Jungbauer
- acib - Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Patricia Pereira Aguilar
- acib - Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Institute of Bioprocess Science and Engineering, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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8
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Das SK, Huynh MT, Lee TH. Spontaneous Histone Exchange Between Nucleosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.540004. [PMID: 37215040 PMCID: PMC10197660 DOI: 10.1101/2023.05.09.540004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The nucleosome is the fundamental gene-packing unit in eukaryotes. Nucleosomes comprise ∼147 bp DNA wrapped around an octameric histone protein core composed of two H2A-H2B dimers and one (H3-H4) 2 tetramer. The strong yet flexible DNA-histone interactions are a physical basis of the dynamic regulation of genes packaged in chromatin. The dynamic nature of DNA-histone interactions implies that nucleosomes dissociate DNA-histone contacts transiently and repeatedly. This kinetic instability may lead to spontaneous nucleosome disassembly or histone exchange between nucleosomes. At a high nucleosome concentration, nucleosome-nucleosome collisions and subsequent histone exchange would be a more likely pathway, where nucleosomes act as their own histone chaperone. The spontaneous histone exchange would serve as a mechanism for maintaining the overall chromatin stability although it has never been reported. We employed three-color single-molecule FRET (smFRET) to demonstrate that histone H2A-H2B dimers are exchanged spontaneously between nucleosomes and that the time scale is on a few tens of seconds at a physiological nucleosome concentration. The rate of histone exchange increases at a higher monovalent salt concentration, with histone acetylated nucleosomes, and in the presence of histone chaperone Nap1, while it remains unchanged at a higher temperature, and decreases upon DNA methylation. These results support histone exchange via transient and repetitive partial disassembly of the nucleosome and corroborate spontaneous histone diffusion in a compact chromatin context, modulating the local concentrations of histone modifications and variants.
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9
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Nunez-Vazquez R, Desvoyes B, Gutierrez C. Histone variants and modifications during abiotic stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:984702. [PMID: 36589114 PMCID: PMC9797984 DOI: 10.3389/fpls.2022.984702] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/28/2022] [Indexed: 06/17/2023]
Abstract
Plants have developed multiple mechanisms as an adaptive response to abiotic stresses, such as salinity, drought, heat, cold, and oxidative stress. Understanding these regulatory networks is critical for coping with the negative impact of abiotic stress on crop productivity worldwide and, eventually, for the rational design of strategies to improve plant performance. Plant alterations upon stress are driven by changes in transcriptional regulation, which rely on locus-specific changes in chromatin accessibility. This process encompasses post-translational modifications of histone proteins that alter the DNA-histones binding, the exchange of canonical histones by variants that modify chromatin conformation, and DNA methylation, which has an implication in the silencing and activation of hypervariable genes. Here, we review the current understanding of the role of the major epigenetic modifications during the abiotic stress response and discuss the intricate relationship among them.
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10
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Zhou JJ, Cho KWY. Epigenomic dynamics of early Xenopus Embryos. Dev Growth Differ 2022; 64:508-516. [PMID: 36168140 PMCID: PMC10550391 DOI: 10.1111/dgd.12813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 12/31/2022]
Abstract
How the embryonic genome regulates accessibility to transcription factors is one of the major questions in understanding the spatial and temporal dynamics of gene expression during embryogenesis. Epigenomic analyses of embryonic chromatin provide molecular insights into cell-specific gene activities and genomic architectures. In recent years, significant advances have been made to elucidate the dynamic changes behind the activation of the zygotic genome in various model organisms. Here we provide an overview of the recent epigenomic studies pertaining to early Xenopus development.
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Affiliation(s)
- Jeff Jiajing Zhou
- Developmental and Cell Biology, University of California, Irvine, California, USA
| | - Ken W Y Cho
- Developmental and Cell Biology, University of California, Irvine, California, USA
- Center for Complex Biological Systems, University of California, Irvine, California, USA
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11
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Bhat JA, Balliano AJ, Hayes JJ. Histone protein surface accessibility dictates direction of RSC-dependent nucleosome mobilization. Nucleic Acids Res 2022; 50:10376-10384. [PMID: 36161493 PMCID: PMC9561379 DOI: 10.1093/nar/gkac790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/23/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Chromatin remodeling enzymes use energy derived from ATP hydrolysis to mobilize nucleosomes and alter their structure to facilitate DNA access. The Remodels the Structure of Chromatin (RSC) complex has been extensively studied, yet aspects of how this complex functionally interacts with nucleosomes remain unclear. We introduce a steric mapping approach to determine how RSC activity depends on interaction with specific surfaces within the nucleosome. We find that blocking SHL + 4.5/–4.5 via streptavidin binding to the H2A N-terminal tail domains results in inhibition of RSC nucleosome mobilization. However, restriction enzyme assays indicate that remodeling-dependent exposure of an internal DNA site near the nucleosome dyad is not affected. In contrast, occlusion of both protein faces of the nucleosome by streptavidin attachment near the acidic patch completely blocks both remodeling-dependent nucleosome mobilization and internal DNA site exposure. However, we observed partial inhibition when only one protein surface is occluded, consistent with abrogation of one of two productive RSC binding orientations. Our results indicate that nucleosome mobilization requires RSC access to the trailing but not the leading protein surface, and reveals a mechanism by which RSC and related complexes may drive unidirectional movement of nucleosomes to regulate cis-acting DNA sequences in vivo.
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Affiliation(s)
- Javeed Ahmad Bhat
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Angela J Balliano
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
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12
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Li Y, Quan L, Zhou Y, Jiang Y, Li K, Wu T, Lyu Q. Identifying modifications on DNA-bound histones with joint deep learning of multiple binding sites in DNA sequence. Bioinformatics 2022; 38:4070-4077. [PMID: 35809058 DOI: 10.1093/bioinformatics/btac489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 06/15/2022] [Accepted: 07/07/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Histone modifications are epigenetic markers that impact gene expression by altering the chromatin structure or recruiting histone modifiers. Their accurate identification is key to unraveling the mechanisms by which they regulate gene expression. However, the solutions for this task can be improved by exploiting multiple relationships from dataset and exploring designs of learning models, for example jointly learning technology. RESULTS This article proposes a deep learning-based multi-objective computational approach, iHMnBS, to identify which of the seven typical histone modifications a DNA sequence may choose to bind, and which parts of the DNA sequence bind to them. iHMnBS employs a customized dataset that allows the marking of modifications contained in histones that may bind to any position in the DNA sequence. iHMnBS tries to mine the information implicit in this richer data by means of deep neural networks. In comprehensive comparisons, iHMnBS outperforms a baseline method, and the probability of binding to modified histones assigned to a representative nucleotide of a DNA sequence can serve as a reference for biological experiments. Since the interaction between transcription factors and histone modifications has an important role in gene expression, we extracted a number of sequence patterns that may bind to transcription factors, and explored their possible impact on disease. AVAILABILITY AND IMPLEMENTATION The source code is available at https://github.com/lennylv/iHMnBS. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yan Li
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Lijun Quan
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China.,Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China.,Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
| | - Yiting Zhou
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Yelu Jiang
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Kailong Li
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China
| | - Tingfang Wu
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China.,Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China.,Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
| | - Qiang Lyu
- School of Computer Science and Technology, Soochow University, Suzhou 215006, China.,Province Key Lab for Information Processing Technologies, Soochow University, Suzhou 215006, China.,Collaborative Innovation Center of Novel Software Technology and Industrialization, Nanjing 210000, China
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13
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Ide S, Tamura S, Maeshima K. Chromatin behavior in living cells: Lessons from single‐nucleosome imaging and tracking. Bioessays 2022; 44:e2200043. [DOI: 10.1002/bies.202200043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Satoru Ide
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
- Department of Genetics School of Life Science SOKENDAI Mishima Shizuoka Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory National Institute of Genetics, ROIS Mishima Shizuoka Japan
- Department of Genetics School of Life Science SOKENDAI Mishima Shizuoka Japan
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14
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The Use of Inhaled Corticosteroids for Patients with COPD Who Continue to Smoke Cigarettes: An Evaluation of Current Practice. Am J Med 2022; 135:302-312. [PMID: 34655541 DOI: 10.1016/j.amjmed.2021.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 09/17/2021] [Accepted: 09/20/2021] [Indexed: 11/22/2022]
Abstract
The use of inhaled corticosteroids (ICS) in combination with inhaled bronchodilators for patients with chronic obstructive pulmonary disease (COPD) is a common practice in primary care settings. However, ICS-containing therapies may be less effective in patients with COPD compared with asthma, and in individuals with COPD who continue to smoke cigarettes. Preclinical studies suggest that inflammation in COPD is very different from in asthma. Glucocorticoid receptor functioning and other innate anti-inflammatory mechanisms are altered in cells exposed to cigarette smoke. COPD may be relatively insensitive to ICS, especially in individuals who continue to smoke. ICS-containing therapies in patients with asthma who continue to smoke may also be less effective compared with patients who do not smoke. ICS-containing therapies may be inappropriately used in some patients with COPD, and their long-term use is associated with an increased risk for side effects, including pneumonia and bone fractures in some patients. Treatment for patients with COPD should be carefully evaluated, and anti-inflammatory/bronchodilatory strategies should be chosen based on individual patient characteristics and recommendations in current guidelines.
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15
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Abstract
Significance: Epigenetic dysregulation plays an important role in the pathogenesis and development of autoimmune diseases. Oxidative stress is associated with autoimmunity and is also known to alter epigenetic mechanisms. Understanding the interplay between oxidative stress and epigenetics will provide insights into the role of environmental triggers in the development of autoimmunity in genetically susceptible individuals. Recent Advances: Abnormal DNA and histone methylation patterns in genes and pathways involved in interferon and tumor necrosis factor signaling, cellular survival, proliferation, metabolism, organ development, and autoantibody production have been described in autoimmunity. Inhibitors of DNA and histone methyltransferases showed potential therapeutic effects in animal models of autoimmune diseases. Oxidative stress can regulate epigenetic mechanisms via effects on DNA damage repair mechanisms, cellular metabolism and the local redox environment, and redox-sensitive transcription factors and pathways. Critical Issues: Studies looking into oxidative stress and epigenetics in autoimmunity are relatively limited. The number of available longitudinal studies to explore the role of DNA methylation in the development of autoimmune diseases is small. Future Directions: Exploring the relationship between oxidative stress and epigenetics in autoimmunity will provide clues for potential preventative measures and treatment strategies. Inception cohorts with longitudinal follow-up would help to evaluate epigenetic marks as potential biomarkers for disease development, progression, and treatment response in autoimmunity. Antioxid. Redox Signal. 36, 423-440.
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Affiliation(s)
- Xiaoqing Zheng
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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16
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Niu J, Yang J, Feng J, Feng Z, Wang X, Yu B, Wang G. Ubiquitin-proteasome pathway plays an essential regulatory role during spermatangium formation in Neopyropia yezoensis. ALGAL RES 2022. [DOI: 10.1016/j.algal.2021.102623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Arole AH, Deshmukh P, Sridhar A, Padmanabhan B. Structural investigation of a pyrano-1,3-oxazine derivative and the phenanthridinone core moiety against BRD2 bromodomains. Acta Crystallogr F Struct Biol Commun 2022; 78:119-127. [PMID: 35234137 PMCID: PMC8900734 DOI: 10.1107/s2053230x22001066] [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: 12/01/2021] [Accepted: 01/31/2022] [Indexed: 11/11/2022] Open
Abstract
The BET (bromodomain and extra-terminal) family of proteins recognize the acetylated histone code on chromatin and play important roles in transcriptional co-regulation. BRD2 and BRD4, which belong to the BET family, are promising drug targets for the management of chronic diseases. The discovery of new scaffold molecules, a pyrano-1,3-oxazine derivative (NSC 328111; NS5) and phenanthridinone-based derivatives (L10 and its core moiety L10a), as inhibitors of BRD2 bromodomains BD1 and BD2, respectively, has recently been reported. The compound NS5 has a significant inhibitory effect on BRD2 in glioblastoma. Here, the crystal structure of BRD2 BD2 in complex with NS5, refined to 2.0 Å resolution, is reported. Moreover, as the previously reported crystal structures of the BD1-NS5 complex and the BD2-L10a complex possess moderate electron density corresponding to the respective ligands, the crystal structures of these complexes were re-evaluated using new X-ray data. Together with biochemical studies using wild-type BRD2 BD1 and BD2 and various mutants, it is confirmed that the pyrano-1,3-oxazine and phenanthridinone derivatives are indeed potent inhibitors of BRD2 bromodomains.
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Affiliation(s)
- Aishwarya H. Arole
- Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Main Road, Bengaluru 560 029, India
| | - Prashant Deshmukh
- Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Main Road, Bengaluru 560 029, India
| | - Ashok Sridhar
- Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Main Road, Bengaluru 560 029, India
| | - Balasundaram Padmanabhan
- Department of Biophysics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Main Road, Bengaluru 560 029, India,Correspondence e-mail: ,
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18
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Dubey R, Prabhakar PK, Gupta J. Epigenetics: key to improve delayed wound healing in type 2 diabetes. Mol Cell Biochem 2022; 477:371-383. [PMID: 34739665 DOI: 10.1007/s11010-021-04285-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/23/2021] [Indexed: 12/13/2022]
Abstract
Diabetes-related delayed wound healing is a multifactorial, nuanced, and intertwined complication that causes substantial clinical morbidity. The etiology of diabetes and its related microvascular complications is affected by genes, diet, and lifestyle factors. Epigenetic modifications such as DNA methylation, histone modifications, and post-transcriptional RNA regulation (microRNAs) are subsequently recognized as key facilitators of the complicated interaction between genes and the environment. Current research suggests that diabetes-persuaded dysfunction of epigenetic pathways, which results in changed expression of genes in target cells and cause diabetes-related complications including cardiomyopathy, nephropathy, retinopathy, delayed wound healing, etc., which are foremost drivers to diabetes-related adverse outcomes. In this paper, we discuss the role of epigenetic mechanisms in controlling tissue repair, angiogenesis, and expression of growth factors, as well as recent findings that show the alteration of epigenetic events during diabetic wound healing.
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Affiliation(s)
- Rupal Dubey
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University (LPU), Jalandhar-Delhi G.T. Road, 144411, Phagwara, Punjab, India
| | - Pranav Kumar Prabhakar
- Department of Medical Laboratory Sciences, School of Physiotherapy and Paramedical Sciences, Lovely Professional University, 144411, Phagwara, Punjab, India
| | - Jeena Gupta
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University (LPU), Jalandhar-Delhi G.T. Road, 144411, Phagwara, Punjab, India.
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19
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Halabian R, Valizadeh Arshad, Ahmadi A, Saeedi P, Azimzadeh Jamalkandi S, Alivand MR. Laboratory methods to decipher epigenetic signatures: a comparative review. Cell Mol Biol Lett 2021; 26:46. [PMID: 34763654 PMCID: PMC8582164 DOI: 10.1186/s11658-021-00290-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics refers to nucleotide sequence-independent events, and heritable changes, including DNA methylation and histone modification (as the two main processes), contributing to the phenotypic features of the cell. Both genetics and epigenetics contribute to determining the outcome of regulatory gene expression systems. Indeed, the flexibility of epigenetic effects and stability of genetic coding lead to gene regulation complexity in response signals. Since some epigenetic changes are significant in abnormalities such as cancers and neurodegenerative diseases, the initial changes, dynamic and reversible properties, and diagnostic potential of epigenomic phenomena are subject to epigenome-wide association studies (EWAS) for therapeutic aims. Based on recent studies, methodological developments are necessary to improve epigenetic research. As a result, several methods have been developed to explore epigenetic alterations at low, medium, and high scales, focusing on DNA methylation and histone modification detection. In this research field, bisulfite-, enzyme sensitivity- and antibody specificity-based techniques are used for DNA methylation, whereas histone modifications are gained based on antibody recognition. This review provides a mechanism-based understanding and comparative overview of the most common techniques for detecting the status of epigenetic effects, including DNA methylation and histone modifications, for applicable approaches from low- to high-throughput scales.
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Affiliation(s)
- Raheleh Halabian
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Valizadeh Arshad
- Department of Stem Cell and Developmental Biology, Cell Science Research Center, Royan Institute For Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Ali Ahmadi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Pardis Saeedi
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Sadegh Azimzadeh Jamalkandi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Mollasadra Ave., 14359-16471, Tehran, Iran.
| | - Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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20
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Itoh Y, Woods EJ, Minami K, Maeshima K, Collepardo-Guevara R. Liquid-like chromatin in the cell: What can we learn from imaging and computational modeling? Curr Opin Struct Biol 2021; 71:123-135. [PMID: 34303931 DOI: 10.1016/j.sbi.2021.06.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/08/2021] [Indexed: 12/23/2022]
Abstract
Chromatin in eukaryotic cells is a negatively charged long polymer consisting of DNA, histones, and various associated proteins. With its highly charged and heterogeneous nature, chromatin structure varies greatly depending on various factors (e.g. chemical modifications and protein enrichment) and the surrounding environment (e.g. cations): from a 10-nm fiber, a folded 30-nm fiber, to chromatin condensates/droplets. Recent advanced imaging has observed that chromatin exhibits a dynamic liquid-like behavior and undergoes structural variations within the cell. Current computational modeling has made it possible to reconstruct the liquid-like chromatin in the cell by dealing with a number of nucleosomes on multiscale levels and has become a powerful technique to inspect the molecular mechanisms giving rise to the observed behavior, which imaging methods cannot do on their own. Based on new findings from both imaging and modeling studies, we discuss the dynamic aspect of chromatin in living cells and its functional relevance.
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Affiliation(s)
- Yuji Itoh
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Esmae J Woods
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK
| | - Katsuhiko Minami
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan.
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE, UK; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK; Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
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21
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Hogg SJ, Motorna O, Cluse LA, Johanson TM, Coughlan HD, Raviram R, Myers RM, Costacurta M, Todorovski I, Pijpers L, Bjelosevic S, Williams T, Huskins SN, Kearney CJ, Devlin JR, Fan Z, Jabbari JS, Martin BP, Fareh M, Kelly MJ, Dupéré-Richer D, Sandow JJ, Feran B, Knight D, Khong T, Spencer A, Harrison SJ, Gregory G, Wickramasinghe VO, Webb AI, Taberlay PC, Bromberg KD, Lai A, Papenfuss AT, Smyth GK, Allan RS, Licht JD, Landau DA, Abdel-Wahab O, Shortt J, Vervoort SJ, Johnstone RW. Targeting histone acetylation dynamics and oncogenic transcription by catalytic P300/CBP inhibition. Mol Cell 2021; 81:2183-2200.e13. [PMID: 34019788 PMCID: PMC8183601 DOI: 10.1016/j.molcel.2021.04.015] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 01/19/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023]
Abstract
To separate causal effects of histone acetylation on chromatin accessibility and transcriptional output, we used integrated epigenomic and transcriptomic analyses following acute inhibition of major cellular lysine acetyltransferases P300 and CBP in hematological malignancies. We found that catalytic P300/CBP inhibition dynamically perturbs steady-state acetylation kinetics and suppresses oncogenic transcriptional networks in the absence of changes to chromatin accessibility. CRISPR-Cas9 screening identified NCOR1 and HDAC3 transcriptional co-repressors as the principal antagonists of P300/CBP by counteracting acetylation turnover kinetics. Finally, deacetylation of H3K27 provides nucleation sites for reciprocal methylation switching, a feature that can be exploited therapeutically by concomitant KDM6A and P300/CBP inhibition. Overall, this study indicates that the steady-state histone acetylation-methylation equilibrium functions as a molecular rheostat governing cellular transcription that is amenable to therapeutic exploitation as an anti-cancer regimen.
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Affiliation(s)
- Simon J Hogg
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Olga Motorna
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Leonie A Cluse
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Hannah D Coughlan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | | | - Robert M Myers
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Matteo Costacurta
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Izabela Todorovski
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Lizzy Pijpers
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Stefan Bjelosevic
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Tobias Williams
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Shannon N Huskins
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, 7000, Australia
| | - Conor J Kearney
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Jennifer R Devlin
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Zheng Fan
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Jafar S Jabbari
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Australia
| | - Ben P Martin
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Mohamed Fareh
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Madison J Kelly
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia
| | - Daphné Dupéré-Richer
- Division of Hematology/Oncology, The University of Florida Health Cancer Center, Gainesville, FL 32608, USA
| | - Jarrod J Sandow
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Breon Feran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Deborah Knight
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia
| | - Tiffany Khong
- Australian Center for Blood Diseases, Monash University, Melbourne, 3004, Australia
| | - Andrew Spencer
- Australian Center for Blood Diseases, Monash University, Melbourne, 3004, Australia
| | - Simon J Harrison
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Clinical Hematology, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Royal Melbourne Hospital, Melbourne, 3000, Australia
| | - Gareth Gregory
- Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Vihandha O Wickramasinghe
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, 3000, Australia
| | - Andrew I Webb
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Phillippa C Taberlay
- Tasmanian School of Medicine, College of Health and Medicine, University of Tasmania, Hobart, 7000, Australia
| | - Kenneth D Bromberg
- Discovery, Global Pharmaceutical Research and Development, AbbVie, North Chicago, IL 60064, USA
| | - Albert Lai
- Discovery, Global Pharmaceutical Research and Development, AbbVie, North Chicago, IL 60064, USA
| | - Anthony T Papenfuss
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Gordon K Smyth
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; School of Mathematics and Statistics, The University of Melbourne, Parkville, 3010, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, 3010, Australia
| | - Jonathan D Licht
- Division of Hematology/Oncology, The University of Florida Health Cancer Center, Gainesville, FL 32608, USA
| | - Dan A Landau
- New York Genome Center, New York, NY 10013, USA; Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jake Shortt
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia; Monash Haematology, Monash Health, Clayton, 3168, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, 3800, Australia
| | - Stephin J Vervoort
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia.
| | - Ricky W Johnstone
- Translational Hematology Program, Gene Regulation Laboratory, Peter MacCallum Cancer Center, Melbourne, 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3000, Australia.
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22
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Abstract
Genomic information is encoded on long strands of DNA, which are folded into chromatin and stored in a tiny nucleus. Nuclear chromatin is a negatively charged polymer composed of DNA, histones, and various nonhistone proteins. Because of its highly charged nature, chromatin structure varies greatly depending on the surrounding environment (e.g., cations, molecular crowding, etc.). New technologies to capture chromatin in living cells have been developed over the past 10 years. Our view on chromatin organization has drastically shifted from a regular and static one to a more variable and dynamic one. Chromatin forms numerous compact dynamic domains that act as functional units of the genome in higher eukaryotic cells and locally appear liquid-like. By changing DNA accessibility, these domains can govern various functions. Based on new evidences from versatile genomics and advanced imaging studies, we discuss the physical nature of chromatin in the crowded nuclear environment and how it is regulated.
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Affiliation(s)
- Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Shiori Iida
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka 411-8540, Japan
| | - Sachiko Tamura
- Genome Dynamics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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23
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Lu Y, Wu Y, Liu Y, Li Y, Jing R, Li M. Prediction of disease-associated functional variants in noncoding regions through a comprehensive analysis by integrating datasets and features. Hum Mutat 2021; 42:667-684. [PMID: 33822436 DOI: 10.1002/humu.24203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 02/01/2021] [Accepted: 03/31/2021] [Indexed: 02/01/2023]
Abstract
One of the greatest challenges in human genetics is deciphering the link between functional variants in noncoding sequences and the pathophysiology of complex diseases. To address this issue, many methods have been developed to sort functional single-nucleotide variants (SNVs) for neutral SNVs in noncoding regions. In this study, we integrated well-established features and commonly used datasets and merged them into large-scale datasets based on a random forest model, which yielded promising performance and outperformed some cutting-edge approaches. Our analyses of feature importance and data coverage also provide certain clues for future research in enhancing the prediction of functional noncoding SNVs.
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Affiliation(s)
- Yu Lu
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Yiming Wu
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yuan Liu
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Yizhou Li
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
| | - Runyu Jing
- College of Cybersecurity, Sichuan University, Chengdu, Sichuan, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, Sichuan, China
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24
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Duc C, Thiriet C. Replication-Coupled Chromatin Remodeling: An Overview of Disassembly and Assembly of Chromatin during Replication. Int J Mol Sci 2021; 22:1113. [PMID: 33498649 PMCID: PMC7865951 DOI: 10.3390/ijms22031113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/08/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
The doubling of genomic DNA during the S-phase of the cell cycle involves the global remodeling of chromatin at replication forks. The present review focuses on the eviction of nucleosomes in front of the replication forks to facilitate the passage of replication machinery and the mechanism of replication-coupled chromatin assembly behind the replication forks. The recycling of parental histones as well as the nuclear import and the assembly of newly synthesized histones are also discussed with regard to the epigenetic inheritance.
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Affiliation(s)
| | - Christophe Thiriet
- UFIP UMR-CNRS 6286, Épigénétique et Dynamique de la Chromatine, Université de Nantes, 2 rue de la Houssinière, 44322 Nantes, France;
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25
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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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26
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Rehman S, Aatif M, Rafi Z, Khan MY, Shahab U, Ahmad S, Farhan M. Effect of non-enzymatic glycosylation in the epigenetics of cancer. Semin Cancer Biol 2020; 83:543-555. [DOI: 10.1016/j.semcancer.2020.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/09/2023]
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Dong E, Pandey SC. Prenatal stress induced chromatin remodeling and risk of psychopathology in adulthood. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2020; 156:185-215. [PMID: 33461663 PMCID: PMC7864549 DOI: 10.1016/bs.irn.2020.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
New insights into the pathophysiology of psychiatric disorders suggest the existence of a complex interplay between genetics and environment. This notion is supported by evidence suggesting that exposure to stress during pregnancy exerts profound effects on the neurodevelopment and behavior of the offspring and predisposes them to psychiatric disorders later in life. Accumulated evidence suggests that vulnerability to psychiatric disorders may result from permanent negative effects of long-term changes in synaptic plasticity due to altered epigenetic mechanisms (histone modifications and DNA methylation) that lead to condensed chromatin architecture, thereby decreasing the expression of candidate genes during early brain development. In this chapter, we have summarized the literature of clinical studies on psychiatric disorders induced by maternal stress during pregnancy. We also discussed the epigenetic alterations of gene regulations induced by prenatal stress. Because the clinical manifestations of psychiatric disorders are complex, it is obvious that the biological progression of these diseases cannot be studied only in postmortem brains of patients and the use of animal models is required. Therefore, in this chapter, we have introduced a well-established mouse model of prenatal stress (PRS) generated in restrained pregnant dams. The behavioral phenotypes of the offspring (PRS mice) born to the stressed dam and underlying epigenetic changes in key molecules related to synaptic activity were described and highlighted. PRS mice may serve as a useful model for investigating the pathogenesis of psychiatric disorders and may be a useful tool for screening for the potential compounds that may normalize aberrant epigenetic mechanisms induced by prenatal stress.
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Affiliation(s)
- Erbo Dong
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States.
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States; Jesse Brown VA Medical Center, Chicago, IL, United States
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Swer PB, Sharma R. ATP-dependent chromatin remodelers in ageing and age-related disorders. Biogerontology 2020; 22:1-17. [PMID: 32968929 DOI: 10.1007/s10522-020-09899-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/16/2020] [Indexed: 11/27/2022]
Abstract
Ageing is characterized by the perturbation in cellular homeostasis associated with genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion and altered intracellular communication. Changes in the epigenome represent one of the crucial mechanisms during ageing and in age-related disorders. The ATP-dependent chromatin remodelers are an evolutionarily conserved family of nucleosome remodelling factors and generally regulate DNA repair, replication, recombination, transcription and cell cycle. Here, we review the chromatin based epigenetic changes that occur in ageing and age-related disorders with a specific reference to chromatin remodelers. We also discuss the link between dietary restriction and chromatin remodelers in regulating age-related processes with a view for consideration in future intervention studies.
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Affiliation(s)
- Pynskhem Bok Swer
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India
| | - Ramesh Sharma
- Department of Biochemistry, North-Eastern Hill University, Shillong, 793022, India.
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Chen R, Zhang M, Zhou Y, Guo W, Yi M, Zhang Z, Ding Y, Wang Y. The application of histone deacetylases inhibitors in glioblastoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:138. [PMID: 32682428 PMCID: PMC7368699 DOI: 10.1186/s13046-020-01643-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/13/2020] [Indexed: 12/14/2022]
Abstract
The epigenetic abnormality is generally accepted as the key to cancer initiation. Epigenetics that ensure the somatic inheritance of differentiated state is defined as a crucial factor influencing malignant phenotype without altering genotype. Histone modification is one such alteration playing an essential role in tumor formation, progression, and resistance to treatment. Notably, changes in histone acetylation have been strongly linked to gene expression, cell cycle, and carcinogenesis. The balance of two types of enzyme, histone acetyltransferases (HATs) and histone deacetylases (HDACs), determines the stage of histone acetylation and then the architecture of chromatin. Changes in chromatin structure result in transcriptional dysregulation of genes that are involved in cell-cycle progression, differentiation, apoptosis, and so on. Recently, HDAC inhibitors (HDACis) are identified as novel agents to keep this balance, leading to numerous researches on it for more effective strategies against cancers, including glioblastoma (GBM). This review elaborated influences on gene expression and tumorigenesis by acetylation and the antitumor mechanism of HDACis. Besdes, we outlined the preclinical and clinical advancement of HDACis in GBM as monotherapies and combination therapies.
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Affiliation(s)
- Rui Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Mengxian Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Yangmei Zhou
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wenjing Guo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ming Yi
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ziyan Zhang
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510000, Guangdong, China
| | - Yanpeng Ding
- Department of Oncology, Zhongnan Hospital, Wuhan University, Wuhan, 430030, China
| | - Yali Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
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Verza FA, Das U, Fachin AL, Dimmock JR, Marins M. Roles of Histone Deacetylases and Inhibitors in Anticancer Therapy. Cancers (Basel) 2020; 12:cancers12061664. [PMID: 32585896 PMCID: PMC7352721 DOI: 10.3390/cancers12061664] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 12/23/2022] Open
Abstract
Histones are the main structural proteins of eukaryotic chromatin. Histone acetylation/ deacetylation are the epigenetic mechanisms of the regulation of gene expression and are catalyzed by histone acetyltransferases (HAT) and histone deacetylases (HDAC). These epigenetic alterations of DNA structure influence the action of transcription factors which can induce or repress gene transcription. The HATs catalyze acetylation and the events related to gene transcription and are also responsible for transporting newly synthesized histones from the cytoplasm to the nucleus. The activity of HDACs is mainly involved in silencing gene expression and according to their specialized functions are divided into classes I, II, III and IV. The disturbance of the expression and mutations of HDAC genes causes the aberrant transcription of key genes regulating important cancer pathways such as cell proliferation, cell-cycle regulation and apoptosis. In view of their role in cancer pathways, HDACs are considered promising therapeutic targets and the development of HDAC inhibitors is a hot topic in the search for new anticancer drugs. The present review will focus on HDACs I, II and IV, the best known inhibitors and potential alternative inhibitors derived from natural and synthetic products which can be used to influence HDAC activity and the development of new cancer therapies.
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Affiliation(s)
- Flávia Alves Verza
- Biotechnology Unit, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil; (F.A.V.); (A.L.F.)
| | - Umashankar Das
- College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada;
| | - Ana Lúcia Fachin
- Biotechnology Unit, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil; (F.A.V.); (A.L.F.)
- Medicine School, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil
| | - Jonathan R. Dimmock
- College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada;
- Correspondence: (J.R.D.); (M.M.); Tel.: +1-306-966-6331 (J.R.D.); +55-16-3603-6728 (M.M.)
| | - Mozart Marins
- Biotechnology Unit, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil; (F.A.V.); (A.L.F.)
- College of Pharmacy and Nutrition, University of Saskatchewan, 110 Science Place, Saskatoon, SK S7N 5C9, Canada;
- Medicine School, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil
- Pharmaceutical Sciences School, University of Ribeirão Preto, Ribeirão Preto SP CEP 14096-900, Brazil
- Correspondence: (J.R.D.); (M.M.); Tel.: +1-306-966-6331 (J.R.D.); +55-16-3603-6728 (M.M.)
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Encinas-García T, Loreto-Quiroz DL, Mendoza-Cano F, Peña-Rodriguez A, Fimbres-Olivarria D, Re-Vega ED, Sánchez-Paz A. White spot syndrome virus down-regulates expression of histones H2A and H4 of Penaeus vannamei to promote viral replication. DISEASES OF AQUATIC ORGANISMS 2019; 137:73-79. [PMID: 31802744 DOI: 10.3354/dao03428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The white spot syndrome virus (WSSV) is a highly lethal and contagious pathogen to most cultivated shrimp species. The WSSV genome contains the ICP11 gene and its encoded protein acts as a multifunctinal DNA mimic protein that disrupts the nucleosome assembly by binding to the histone proteins H2A and H3. In addition, WSSV provokes severe nuclear hypertrophy and DNA damage. However, little is known about the influence of WSSV on the expression of the host's genes encoding for histones. Therefore, we investigated the effect of WSSV infection on the expression of the genes encoding histones in shrimp Penaeus vannamei. An RT-qPCR assay was performed to evaluate the temporal expression of H2A and H4 transcripts in the shrimp. Significant changes were observed in the expression of these genes, which coincided with the dynamics of replication of the virus. H2A reached its maximum expression levels at 12 hpi. Thus, it may be suggested that this is a viral strategy to evade the host's immune response in order to promote viral replication.
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Affiliation(s)
- Trinidad Encinas-García
- Laboratorio de Análisis, Referencia y Diagnóstico en Sanidad Acuícola, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Calle Hermosa 101, Col. Los Ángeles, Hermosillo, Sonora 83106, México
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Kinyamu HK, Bennett BD, Bushel PR, Archer TK. Proteasome inhibition creates a chromatin landscape favorable to RNA Pol II processivity. J Biol Chem 2019; 295:1271-1287. [PMID: 31806706 DOI: 10.1074/jbc.ra119.011174] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/02/2019] [Indexed: 11/06/2022] Open
Abstract
Proteasome activity is required for diverse cellular processes, including transcriptional and epigenetic regulation. However, inhibiting proteasome activity can lead to an increase in transcriptional output that is correlated with enriched levels of trimethyl H3K4 and phosphorylated forms of RNA polymerase (Pol) II at the promoter and gene body. Here, we perform gene expression analysis and ChIP followed by sequencing (ChIP-seq) in MCF-7 breast cancer cells treated with the proteasome inhibitor MG132, and we further explore genome-wide effects of proteasome inhibition on the chromatin state and RNA Pol II transcription. Analysis of gene expression programs and chromatin architecture reveals that chemically inhibiting proteasome activity creates a distinct chromatin state, defined by spreading of the H3K4me3 mark into the gene bodies of differentially-expressed genes. The distinct H3K4me3 chromatin profile and hyperacetylated nucleosomes at transcription start sites establish a chromatin landscape that facilitates recruitment of Ser-5- and Ser-2-phosphorylated RNA Pol II. Subsequent transcriptional events result in diverse gene expression changes. Alterations of H3K36me3 levels in the gene body reflect productive RNA Pol II elongation of transcripts of genes that are induced, underscoring the requirement for proteasome activity at multiple phases of the transcriptional cycle. Finally, by integrating genomics data and pathway analysis, we find that the differential effects of proteasome inhibition on the chromatin state modulate genes that are fundamental for cancer cell survival. Together, our results uncover underappreciated downstream effects of proteasome inhibitors that may underlie targeting of distinct chromatin states and key steps of RNA Pol II-mediated transcription in cancer cells.
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Affiliation(s)
- H Karimi Kinyamu
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Brian D Bennett
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709.,Integrative Bioinformatics Support Group, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Pierre R Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
| | - Trevor K Archer
- Chromatin and Gene Expression Section, Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, North Carolina 27709
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Yang Q, Jiang W, Hou P. Emerging role of PI3K/AKT in tumor-related epigenetic regulation. Semin Cancer Biol 2019; 59:112-124. [DOI: 10.1016/j.semcancer.2019.04.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 03/14/2019] [Accepted: 04/01/2019] [Indexed: 01/23/2023]
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Harrison RM, Romano F, Ouldridge TE, Louis AA, Doye JPK. Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model. J Chem Theory Comput 2019; 15:4660-4672. [PMID: 31282669 PMCID: PMC6694408 DOI: 10.1021/acs.jctc.9b00112] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
DNA
cyclization is a powerful technique to gain insight into the nature
of DNA bending. While the wormlike chain model provides a good description
of small to moderate bending fluctuations, it is expected to break
down for large bending. Recent cyclization experiments on strongly
bent shorter molecules indeed suggest enhanced flexibility over and
above that expected from the wormlike chain. Here, we use a coarse-grained
model of DNA to investigate the subtle thermodynamics of DNA cyclization
for molecules ranging from 30 to 210 base pairs. As the molecules
get shorter, we find increasing deviations between our computed equilibrium j-factor and the classic wormlike chain predictions of Shimada
and Yamakawa for a torsionally aligned looped molecule. These deviations
are due to sharp kinking, first at nicks, and only subsequently in
the body of the duplex. At the shortest lengths, substantial fraying
at the ends of duplex domains is the dominant method of relaxation.
We also estimate the dynamic j-factor measured in
recent FRET experiments. We find that the dynamic j-factor is systematically larger than its equilibrium counterpart—with
the deviation larger for shorter molecules—because not all
the stress present in the fully cyclized state is present in the transition
state. These observations are important for the interpretation of
recent cyclization experiments, suggesting that measured anomalously
high j-factors may not necessarily indicate non-WLC
behavior in the body of duplexes.
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Affiliation(s)
- Ryan M Harrison
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi , Universitá Ca' Foscari Venezia , I-30123 Venezia , Italy
| | - Thomas E Ouldridge
- Imperial College Centre for Synthetic Biology and Department of Bioengineering , Imperial College London , 180 Queen's Road , London SW7 2AZ , United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, Department of Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
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Chase KA, Feiner B, Ramaker MJ, Hu E, Rosen C, Sharma RP. Examining the effects of the histone methyltransferase inhibitor BIX-01294 on histone modifications and gene expression in both a clinical population and mouse models. PLoS One 2019; 14:e0216463. [PMID: 31185023 PMCID: PMC6559633 DOI: 10.1371/journal.pone.0216463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 04/08/2019] [Indexed: 01/03/2023] Open
Abstract
Schizophrenia has been consistently characterized by abnormal patterns of gene down-regulation, increased restrictive chromatin assemblies, and reduced transcriptional activity. Histone methyltransferase (HMT) mRNA and H3K9me2 levels are elevated in postmortem brain and peripheral blood cells of persons with schizophrenia. Moreover, this epigenomic state likely contributes to the disease, as HMT levels correlate with clinical symptomatology. This manuscript sought to establish the potential therapeutic value of the HMT inhibitor BIX-01294 (BIX). Human peripheral mononuclear cells (PBMC) from 24 individuals with schizophrenia and 24 healthy individuals were cultured in the presence of BIX (5uM or 10uM). Mice were given once daily intraperitoneal injections of BIX (0.5 or 1mg/kg) for one week. Cultured cells, mouse cortex, or striatum was harvested, RNA extracted and RT-PCR conducted for several schizophrenia candidate genes: IL-6, Gad1, Nanog, KLF4, Reln, and Bdnf9a. Total H3K9me2 levels were measured using western blot while H3K9me2 binding to selected genes of interest was conducted using chromatin immunoprecipitation (ChIP). Neuronal subtype-specific BDNF conditional knockdown was conducted using the cre/lox system of mutant animals. Treatment with BIX decreased H3K9me2 and increased selected mRNA levels in cultured PBMCs from both normal controls and participants with schizophrenia. In mice, peripheral administration of BIX decreased cortical H3K9me2 levels and increased schizophrenia candidate gene expression. In BDNF conditional knockdown animals, BIX administration was able to significantly rescue Bdnf9a mRNA levels in ChAT and D1 Bdnf conditional knockdown mice. The results presented in this manuscript demonstrate a potential for further research into the clinical effectiveness of histone modifying pharmacology in the treatment of schizophrenia.
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Affiliation(s)
- Kayla A. Chase
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States of America
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States of America
| | - Benjamin Feiner
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Marcia J. Ramaker
- Department of Psychiatry, University of California, La Jolla, CA, United States of America
| | - Edward Hu
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Cherise Rosen
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Rajiv P. Sharma
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, United States of America
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL, United States of America
- * E-mail:
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Chistiakov DA, Chekhonin VP. Early-life adversity-induced long-term epigenetic programming associated with early onset of chronic physical aggression: Studies in humans and animals. World J Biol Psychiatry 2019; 20:258-277. [PMID: 28441915 DOI: 10.1080/15622975.2017.1322714] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Objectives: To examine whether chronic physical aggression (CPA) in adulthood can be epigenetically programmed early in life due to exposure to early-life adversity. Methods: Literature search of public databases such as PubMed/MEDLINE and Scopus. Results: Children/adolescents susceptible for CPA and exposed to early-life abuse fail to efficiently cope with stress that in turn results in the development of CPA later in life. This phenomenon was observed in humans and animal models of aggression. The susceptibility to aggression is a complex trait that is regulated by the interaction between environmental and genetic factors. Epigenetic mechanisms mediate this interaction. Subjects exposed to stress early in life exhibited long-term epigenetic programming that can influence their behaviour in adulthood. This programming affects expression of many genes not only in the brain but also in other systems such as neuroendocrine and immune. Conclusions: The propensity to adult CPA behaviour in subjects experienced to early-life adversity is mediated by epigenetic programming that involves long-term systemic epigenetic alterations in a whole genome.
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Affiliation(s)
- Dimitry A Chistiakov
- a Department of Fundamental and Applied Neurobiology , Serbsky Federal Medical Research Center of Psychiatry and Narcology , Moscow , Russia
| | - Vladimir P Chekhonin
- a Department of Fundamental and Applied Neurobiology , Serbsky Federal Medical Research Center of Psychiatry and Narcology , Moscow , Russia.,b Department of Medical Nanobiotechnology , Pirogov Russian State Medical University (RSMU) , Moscow , Russia
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Muratori M, De Geyter C. Chromatin condensation, fragmentation of DNA and differences in the epigenetic signature of infertile men. Best Pract Res Clin Endocrinol Metab 2019; 33:117-126. [PMID: 30420311 DOI: 10.1016/j.beem.2018.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Epidemiological studies report an increase of pathologies of male reproductive tracts and suggest a link between this trend and the increased exposure of men to endocrine disruptors (EDs). The mechanisms by which EDs impact male fertility are far to be elucidated although DNA, chromatin and epigenome of spermatozoa appear to be relevant targets for these molecules. Indeed, many studies report associations between increased levels of sperm DNA fragmentation (sDF) or aberrant chromatin condensation or epigenetic modifications and poor semen quality and/or infertile phenotype. In this scenario, therapies able to reduce sperm damage to DNA, chromatin and epigenome are sought. Currently, antioxidants and FSH administration is proposed for treating high levels of sDF, but whether or not such therapies are really effective is still debated. Further studies are necessary to understand the link between endocrine disruptor exposure and damage to sperm function and/or structure and thus to define effective therapeutic strategies.
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Affiliation(s)
- Monica Muratori
- Department of Experimental, Clinical and Biomedical Sciences, Unit of Sexual Medicine and Andrology, Center of Excellence DeNothe, University of Florence, Viale Pieraccini, 6, I-50139, Firenze, Italy.
| | - Christian De Geyter
- Reproductive Medicine and Gynecological Endocrinology (RME), University Hospital, University of Basel, Vogesenstrasse 134, CH-4031, Basel, Switzerland.
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den Dekker A, Davis FM, Kunkel SL, Gallagher KA. Targeting epigenetic mechanisms in diabetic wound healing. Transl Res 2019; 204:39-50. [PMID: 30392877 PMCID: PMC6331222 DOI: 10.1016/j.trsl.2018.10.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/02/2018] [Accepted: 10/02/2018] [Indexed: 02/07/2023]
Abstract
Impaired wound healing is a major secondary complication of type 2 diabetes that often results in limb loss and disability. Normal tissue repair progresses through discrete phases including hemostasis, inflammation, proliferation, and remodeling. In diabetes, normal progression through these phases is impaired resulting in a sustained inflammatory state and dysfunctional epithelialization in the wound. Due to their plasticity, macrophages play a critical role in the transition from the inflammation phase to the proliferation phase. Diabetes disrupts macrophage function by impairing monocyte recruitment to the wound, reducing phagocytosis, and prohibiting the transition of inflammatory macrophages to an anti-inflammatory state. Diabetes also impedes keratinocyte and fibroblast function during the later phases resulting in impaired epithelialization of the wound. Several recent studies suggest that altered epigenetic regulation of both immune and structural cells in wounds may influence cell phenotypes and healing, particularly in pathologic states, such as diabetes. Specifically, it has been shown that macrophage plasticity during wound repair is partly regulated epigenetically and that diabetes alters this epigenetic regulation and contributes to a sustained inflammatory state. Epigenetic regulation is also known to regulate keratinocyte and fibroblast function during wound repair. In this review, we provide an introduction to the epigenetic mechanisms that regulate tissue repair and highlight recent findings that demonstrate, how epigenetic events are altered during the course of diabetic wound healing.
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Affiliation(s)
- Aaron den Dekker
- Department of Surgery, University of Michigan, Ann Arbor, Michgan
| | - Frank M Davis
- Department of Surgery, University of Michigan, Ann Arbor, Michgan
| | - Steve L Kunkel
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
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40
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James E, Jenkins TG. Epigenetics, infertility, and cancer: future directions. Fertil Steril 2018; 109:27-32. [PMID: 29307396 DOI: 10.1016/j.fertnstert.2017.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/28/2017] [Accepted: 11/07/2017] [Indexed: 12/11/2022]
Abstract
Although direct correlates between cancer and infertile epigenetic profiles are rare, the general similarities between the two disease processes offer insights into the study of both abnormalities. Foremost among them is the nature of these pathologies, where one disease (cancer) is categorized by an inability to control or inhibit cellular proliferation, and the other (male infertility) is caused by an inability to maintain the normally efficient extreme proliferation of the male germ cell. Based on this similarity alone, the study of epigenetics in both male fertility and cancer has the potential to offer intriguing insights in both fields. The creative application of harmonious studies of both infertility and cancer is likely to yield useful and informative data that may aid in both the understanding and treatment of both pathologies.
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Affiliation(s)
- Emma James
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah
| | - Timothy G Jenkins
- Andrology and IVF Laboratories, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah.
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41
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N-terminal acetylation and methylation differentially affect the function of MYL9. Biochem J 2018; 475:3201-3219. [PMID: 30242065 DOI: 10.1042/bcj20180638] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 12/30/2022]
Abstract
Deciphering the histone code has illustrated that acetylation or methylation on the same residue can have analogous or opposing roles. However, little is known about the interplay between these post-translational modifications (PTMs) on the same nonhistone residues. We have recently discovered that N-terminal acetyltransferases (NATs) and N-terminal methyltransferases (NRMTs) can have overlapping substrates and identified myosin regulatory light chain 9 (MYL9) as the first confirmed protein to occur in either α-amino-methylated (Nα-methyl) or α-amino-acetylated (Nα-acetyl) states in vivo Here we aim to determine if these PTMs function similarly or create different MYL9 proteoforms with distinct roles. We use enzymatic assays to directly verify MYL9 is a substrate of both NRMT1 and NatA and generate mutants of MYL9 that are exclusive for Nα-acetylation or Nα-methylation. We then employ eukaryotic cell models to probe the regulatory functions of these Nα-PTMs on MYL9. Our results show that, contrary to prevailing dogma, neither of these modifications regulate the stability of MYL9. Rather, exclusive Nα-acetylation promotes cytoplasmic roles of MYL9, while exclusive Nα-methylation promotes the nuclear role of MYL9 as a transcription factor. The increased cytoplasmic activity of Nα-acetylated MYL9 corresponds with increased phosphorylation at serine 19, a key MYL9 activating PTM. Increased nuclear activity of Nα-methylated MYL9 corresponds with increased DNA binding. Nα-methylation also results in a decrease of interactions between the N-terminus of MYL9 and a host of cytoskeletal proteins. These results confirm that Nα-acetylation and Nα-methylation differentially affect MYL9 function by creating distinct proteoforms with different internal PTM patterns and binding properties.
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Csizmok V, Forman-Kay JD. Complex regulatory mechanisms mediated by the interplay of multiple post-translational modifications. Curr Opin Struct Biol 2018; 48:58-67. [DOI: 10.1016/j.sbi.2017.10.013] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 10/07/2017] [Accepted: 10/13/2017] [Indexed: 12/18/2022]
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Korolev N, Lyubartsev AP, Nordenskiöld L. A systematic analysis of nucleosome core particle and nucleosome-nucleosome stacking structure. Sci Rep 2018; 8:1543. [PMID: 29367745 PMCID: PMC5784010 DOI: 10.1038/s41598-018-19875-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022] Open
Abstract
Chromatin condensation is driven by the energetically favourable interaction between nucleosome core particles (NCPs). The close NCP-NCP contact, stacking, is a primary structural element of all condensed states of chromatin in vitro and in vivo. However, the molecular structure of stacked nucleosomes as well as the nature of the interactions involved in its formation have not yet been systematically studied. Here we undertake an investigation of both the structural and physico-chemical features of NCP structure and the NCP-NCP stacking. We introduce an “NCP-centred” set of parameters (NCP-NCP distance, shift, rise, tilt, and others) that allows numerical characterisation of the mutual positions of the NCPs in the stacking and in any other structures formed by the NCP. NCP stacking in more than 140 published NCP crystal structures were analysed. In addition, coarse grained (CG) MD simulations modelling NCP condensation was carried out. The CG model takes into account details of the nucleosome structure and adequately describes the long range electrostatic forces as well as excluded volume effects acting in chromatin. The CG simulations showed good agreement with experimental data and revealed the importance of the H2A and H4 N-terminal tail bridging and screening as well as tail-tail correlations in the stacked nucleosomes.
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Affiliation(s)
- Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, 10691, Stockholm, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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Shadrick WR, Slavish PJ, Chai SC, Waddell B, Connelly M, Low JA, Tallant C, Young BM, Bharatham N, Knapp S, Boyd VA, Morfouace M, Roussel MF, Chen T, Lee RE, Kiplin Guy R, Shelat AA, Potter PM. Exploiting a water network to achieve enthalpy-driven, bromodomain-selective BET inhibitors. Bioorg Med Chem 2018; 26:25-36. [PMID: 29170024 PMCID: PMC5733700 DOI: 10.1016/j.bmc.2017.10.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/20/2017] [Accepted: 10/30/2017] [Indexed: 12/24/2022]
Abstract
Within the last decade, the Bromodomain and Extra-Terminal domain family (BET) of proteins have emerged as promising drug targets in diverse clinical indications including oncology, auto-immune disease, heart failure, and male contraception. The BET family consists of four isoforms (BRD2, BRD3, BRD4, and BRDT/BRDT6) which are distinguished by the presence of two tandem bromodomains (BD1 and BD2) that independently recognize acetylated-lysine (KAc) residues and appear to have distinct biological roles. BET BD1 and BD2 bromodomains differ at five positions near the substrate binding pocket: the variation in the ZA channel induces different water networks nearby. We designed a set of congeneric 2- and 3-heteroaryl substituted tetrahydroquinolines (THQ) to differentially engage bound waters in the ZA channel with the goal of achieving bromodomain selectivity. SJ830599 (9) showed modest, but consistent, selectivity for BRD2-BD2. Using isothermal titration calorimetry, we showed that the binding of all THQ analogs in our study to either of the two bromodomains was enthalpy driven. Remarkably, the binding of 9 to BRD2-BD2 was marked by negative entropy and was entirely driven by enthalpy, consistent with significant restriction of conformational flexibility and/or engagement with bound waters. Co-crystallography studies confirmed that 9 did indeed stabilize a water-mediated hydrogen bond network. Finally, we report that 9 retained cytotoxicity against several pediatric cancer cell lines with EC50 values comparable to BET inhibitor (BETi) clinical candidates.
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Affiliation(s)
- William R Shadrick
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Peter J Slavish
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Sergio C Chai
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Brett Waddell
- Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Michele Connelly
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jonathan A Low
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Cynthia Tallant
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK; Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Brandon M Young
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Nagakumar Bharatham
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Stefan Knapp
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK; Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Vincent A Boyd
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Marie Morfouace
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Martine F Roussel
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Richard E Lee
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - R Kiplin Guy
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Anang A Shelat
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
| | - Philip M Potter
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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Acetylation- and Methylation-Related Epigenetic Proteins in the Context of Their Targets. Genes (Basel) 2017; 8:genes8080196. [PMID: 28783137 PMCID: PMC5575660 DOI: 10.3390/genes8080196] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/19/2017] [Accepted: 07/31/2017] [Indexed: 12/19/2022] Open
Abstract
The nucleosome surface is covered with multiple modifications that are perpetuated by eight different classes of enzymes. These enzymes modify specific target sites both on DNA and histone proteins, and these modifications have been well identified and termed “epigenetics”. These modifications play critical roles, either by affecting non-histone protein recruitment to chromatin or by disturbing chromatin contacts. Their presence dictates the condensed packaging of DNA and can coordinate the orderly recruitment of various enzyme complexes for DNA manipulation. This genetic modification machinery involves various writers, readers, and erasers that have unique structures, functions, and modes of action. Regarding human disease, studies have mainly focused on the genetic mechanisms; however, alteration in the balance of epigenetic networks can result in major pathologies including mental retardation, chromosome instability syndromes, and various types of cancers. Owing to its critical influence, great potential lies in developing epigenetic therapies. In this regard, this review has highlighted mechanistic and structural interactions of the main epigenetic families with their targets, which will help to identify more efficient and safe drugs against several diseases.
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Wang Y, van Merwyk L, Tönsing K, Walhorn V, Anselmetti D, Fernàndez-Busquets X. Biophysical characterization of the association of histones with single-stranded DNA. Biochim Biophys Acta Gen Subj 2017; 1861:2739-2749. [PMID: 28756274 DOI: 10.1016/j.bbagen.2017.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Despite the profound current knowledge of the architecture and dynamics of nucleosomes, little is known about the structures generated by the interaction of histones with single-stranded DNA (ssDNA), which is widely present during replication and transcription. METHODS Non-denaturing gel electrophoresis, transmission electron microscopy, atomic force microscopy, magnetic tweezers. RESULTS Histones have a high affinity for ssDNA in 0.15M NaCl ionic strength, with an apparent binding constant similar to that calculated for their association with double-stranded DNA (dsDNA). The length of DNA (number of nucleotides in ssDNA or base pairs in dsDNA) associated with a fixed core histone mass is the same for both ssDNA and dsDNA. Although histone-ssDNA complexes show a high tendency to aggregate, nucleosome-like structures are formed at physiological salt concentrations. Core histones are able to protect ssDNA from digestion by micrococcal nuclease, and a shortening of ssDNA occurs upon its interaction with histones. The purified (+) strand of a cloned DNA fragment of nucleosomal origin has a higher affinity for histones than the purified complementary (-) strand. CONCLUSIONS At physiological ionic strength histones have high affinity for ssDNA, possibly associating with it into nucleosome-like structures. GENERAL SIGNIFICANCE In the cell nucleus histones may spontaneously interact with ssDNA to facilitate their participation in the replication and transcription of chromatin.
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Affiliation(s)
- Ying Wang
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Luis van Merwyk
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Katja Tönsing
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Volker Walhorn
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Dario Anselmetti
- Experimental Biophysics and Applied Nanoscience, Faculty of Physics, Bielefeld University, Bielefeld 33615, Germany
| | - Xavier Fernàndez-Busquets
- Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain; Barcelona Institute for Global Health (ISGlobal), Barcelona Center for International Health Research (CRESIB, Hospital Clínic-Universitat de Barcelona), Rosselló 149-153, Barcelona 08036, Spain; Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, Barcelona 08028, Spain.
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Radwan M, Serya R. Fragment-Based Drug Discovery in the Bromodomain and Extra-Terminal Domain Family. Arch Pharm (Weinheim) 2017; 350. [PMID: 28714212 DOI: 10.1002/ardp.201700147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 12/21/2022]
Abstract
Bromodomain and extra-terminal domain (BET) inhibition has emerged recently as a potential therapeutic target for the treatment of many human disorders such as atherosclerosis, inflammatory disorders, chronic obstructive pulmonary disease (COPD), some viral infections, and cancer. Since the discovery of the two potent inhibitors, I-BET762 and JQ1, different research groups have used different techniques to develop novel potent and selective inhibitors. In this review, we will be concerned with the trials that used fragment-based drug discovery (FBDD) approaches to discover or optimize BET inhibitors, also showing fragments that can be further optimized in future projects to reach novel potent BET inhibitors.
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Affiliation(s)
| | - Rabah Serya
- Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
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48
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Berezhnoy NV, Liu Y, Allahverdi A, Yang R, Su CJ, Liu CF, Korolev N, Nordenskiöld L. The Influence of Ionic Environment and Histone Tails on Columnar Order of Nucleosome Core Particles. Biophys J 2017; 110:1720-1731. [PMID: 27119633 DOI: 10.1016/j.bpj.2016.03.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 02/04/2016] [Accepted: 03/07/2016] [Indexed: 01/08/2023] Open
Abstract
The nucleosome core particle (NCP) is the basic building block of chromatin. Nucleosome-nucleosome interactions are instrumental in chromatin compaction, and understanding NCP self-assembly is important for understanding chromatin structure and dynamics. Recombinant NCPs aggregated by multivalent cations form various ordered phases that can be studied by x-ray diffraction (small-angle x-ray scattering). In this work, the effects on the supramolecular structure of aggregated NCPs due to lysine histone H4 tail acetylations, histone H2A mutations (neutralizing the acidic patch of the histone octamer), and the removal of histone tails were investigated. The formation of ordered mainly hexagonal columnar NCP phases is in agreement with earlier studies; however, the highly homogeneous recombinant NCP systems used in this work display a more compact packing. The long-range order of the NCP columnar phase was found to be abolished or reduced by acetylation of the H4 tails, acidic patch neutralization, and removal of the H3 and H2B tails. Loss of nucleosome stacking upon removal of the H3 tails in combination with other tails was observed. In the absence of the H2A tails, the formation of an unknown highly ordered phase was observed.
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Affiliation(s)
- Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ying Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Abdollah Allahverdi
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Renliang Yang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chun-Jen Su
- National Synchrotron Radiation Research Center, Hsinchu, Taiwan
| | - Chuan-Fa Liu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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49
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Menil-Philippot V, Thiriet C. Physarum polycephalum for Studying the Function of Histone Modifications In Vivo. Methods Mol Biol 2017; 1528:245-256. [PMID: 27854026 DOI: 10.1007/978-1-4939-6630-1_15] [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: 06/06/2023]
Abstract
Histone modifications have been widely correlated with genetic activities. However, how these posttranslational modifications affect the dynamics and the structure of chromatin is poorly understood. Here, we describe the incorporation of the exogenous histone proteins into the slime mold Physarum polycephalum, which has been revealed to be a valuable tool for examining different facets of the function histones in chromatin dynamics like replication-coupled chromatin assembly, histone exchange, and nucleosome turnover.
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Affiliation(s)
- Vanessa Menil-Philippot
- UMR CNRS 6286 UFIP, Université de Nantes, Epigénétique: Prolifération et Différenciation, 2 rue de Houssinière, 44322, Nantes Cedex 03, France
| | - Christophe Thiriet
- UMR CNRS 6286 UFIP, Université de Nantes, Epigénétique: Prolifération et Différenciation, 2 rue de Houssinière, 44322, Nantes Cedex 03, France.
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50
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Li Y, Dong XM, Jin F, Shen Z, Chao Q, Wang BC. Histone Acetylation Modifications Affect Tissue-Dependent Expression of Poplar Homologs of C 4 Photosynthetic Enzyme Genes. FRONTIERS IN PLANT SCIENCE 2017; 8:950. [PMID: 28642769 PMCID: PMC5462996 DOI: 10.3389/fpls.2017.00950] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/22/2017] [Indexed: 05/18/2023]
Abstract
Histone modifications play important roles in regulating the expression of C4 photosynthetic genes. Given that all enzymes required for the C4 photosynthesis pathway are present in C3 plants, it has been hypothesized that this expression regulatory mechanism has been conserved. However, the relationship between histone modification and the expression of homologs of C4 photosynthetic enzyme genes has not been well determined in C3 plants. In the present study, we cloned nine hybrid poplar (Populus simonii × Populus nigra) homologs of maize (Zea mays) C4 photosynthetic enzyme genes, carbonic anhydrase (CA), pyruvate orthophosphate dikinase (PPDK), phosphoenolpyruvate carboxykinase (PCK), and phosphoenolpyruvate carboxylase (PEPC), and investigated the correlation between the expression levels of these genes and the levels of promoter histone acetylation modifications in four vegetative tissues. We found that poplar homologs of C4 homologous genes had tissue-dependent expression patterns that were mostly well-correlated with the level of histone acetylation modification (H3K9ac and H4K5ac) determined by chromatin immunoprecipitation assays. Treatment with the histone deacetylase inhibitor trichostatin A further confirmed the role of histone acetylation in the regulation of the nine target genes. Collectively, these results suggest that both H3K9ac and H4K5ac positively regulate the tissue-dependent expression pattern of the PsnCAs, PsnPPDKs, PsnPCKs, and PsnPEPCs genes and that this regulatory mechanism seems to be conserved among the C3 and C4 species. Our findings provide new insight that will aid efforts to modify the expression pattern of these homologs of C4 genes to engineer C4 plants from C3 plants.
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Affiliation(s)
- Yuan Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry UniversityHarbin, China
| | - Xiu-Mei Dong
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Feng Jin
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Zhuo Shen
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of SciencesBeijing, China
- *Correspondence: Bai-Chen Wang,
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