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Mohamad Zamberi NN, Abuhamad AY, Low TY, Mohtar MA, Syafruddin SE. dCas9 Tells Tales: Probing Gene Function and Transcription Regulation in Cancer. CRISPR J 2024; 7:73-87. [PMID: 38635328 DOI: 10.1089/crispr.2023.0078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing is evolving into an essential tool in the field of biological and medical research. Notably, the development of catalytically deactivated Cas9 (dCas9) enzyme has substantially broadened its traditional boundaries in gene editing or perturbation. The conjugation of dCas9 with various molecular effectors allows precise control over transcriptional processes, epigenetic modifications, visualization of chromosomal dynamics, and several other applications. This expanded repertoire of CRISPR-Cas9 applications has emerged as an invaluable molecular tool kit that empowers researchers to comprehensively interrogate and gain insights into health and diseases. This review delves into the advancements in Cas9 protein engineering, specifically on the generation of various dCas9 tools that have significantly enhanced the CRISPR-based technology capability and versatility. We subsequently discuss the multifaceted applications of dCas9, especially in interrogating the regulation and function of genes that involve in supporting cancer pathogenesis. In addition, we also delineate the designing and utilization of dCas9-based tools as well as highlighting its current constraints and transformative potentials in cancer research.
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Affiliation(s)
- Nurul Nadia Mohamad Zamberi
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Asmaa Y Abuhamad
- Bionanotechnology Research Group, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - M Aiman Mohtar
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Saiful Effendi Syafruddin
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Cheras, Malaysia, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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2
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Fu MP, Merrill SM, Sharma M, Gibson WT, Turvey SE, Kobor MS. Rare diseases of epigenetic origin: Challenges and opportunities. Front Genet 2023; 14:1113086. [PMID: 36814905 PMCID: PMC9939656 DOI: 10.3389/fgene.2023.1113086] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Rare diseases (RDs), more than 80% of which have a genetic origin, collectively affect approximately 350 million people worldwide. Progress in next-generation sequencing technology has both greatly accelerated the pace of discovery of novel RDs and provided more accurate means for their diagnosis. RDs that are driven by altered epigenetic regulation with an underlying genetic basis are referred to as rare diseases of epigenetic origin (RDEOs). These diseases pose unique challenges in research, as they often show complex genetic and clinical heterogeneity arising from unknown gene-disease mechanisms. Furthermore, multiple other factors, including cell type and developmental time point, can confound attempts to deconvolute the pathophysiology of these disorders. These challenges are further exacerbated by factors that contribute to epigenetic variability and the difficulty of collecting sufficient participant numbers in human studies. However, new molecular and bioinformatics techniques will provide insight into how these disorders manifest over time. This review highlights recent studies addressing these challenges with innovative solutions. Further research will elucidate the mechanisms of action underlying unique RDEOs and facilitate the discovery of treatments and diagnostic biomarkers for screening, thereby improving health trajectories and clinical outcomes of affected patients.
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Affiliation(s)
- Maggie P. Fu
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Sarah M. Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Mehul Sharma
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - William T. Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Stuart E. Turvey
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada,*Correspondence: Michael S. Kobor,
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3
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Wiedner HJ, Torres EV, Blue RE, Tsai Y, Parker J, Giudice J. SET domain containing 2 (SETD2) influences metabolism and alternative splicing during myogenesis. FEBS J 2022; 289:6799-6816. [PMID: 35724320 PMCID: PMC9796740 DOI: 10.1111/febs.16553] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/13/2022] [Accepted: 06/10/2022] [Indexed: 01/14/2023]
Abstract
Epigenetic regulatory mechanisms are increasingly recognized as crucial determinants of cellular specification and differentiation. During muscle cell differentiation (myogenesis), extensive remodelling of histone acetylation and methylation occurs. Several of these histone modifications aid in the expression of muscle-specific genes and the silencing of genes that block lineage commitment. Therefore, the identification of new epigenetic regulatory mechanisms is of high interest. Still, the functional relevance of numerous histone modifications during myogenesis remain completely uncertain. In this study, we focus on the function of H3K36me3 and its epigenetic writer, SET domain containing 2 (SETD2), in the context of muscle cell differentiation. We first observed that SETD2 expression increases during myogenesis. Targeted depletion of SETD2 in undifferentiated (myoblasts) and differentiated (myotubes) muscle cells reduced H3K36me3 levels and induced profound changes in gene expression and slight alterations in alternative splicing, as determined by deep RNA-sequencing analysis. Enzymes that function in metabolic pathways were upregulated in response to SETD2 depletion. Furthermore, we demonstrated that upregulation of several glycolytic enzymes was associated with an increase in intracellular pyruvate levels in SETD2-depleted cells, indicating a novel role for SETD2 in metabolic programming during myogenesis. Together, our results provide new insight into the signalling pathways controlled by chromatin-modifying enzymes and their associated histone modifications during muscle cell differentiation.
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Affiliation(s)
- Hannah J. Wiedner
- Department of Cell Biology and PhysiologyThe University of North Carolina at Chapel HillUSA,Curriculum in Genetics and Molecular Biology (GMB)The University of North Carolina at Chapel HillUSA
| | - Eduardo V. Torres
- Department of Cell Biology and PhysiologyThe University of North Carolina at Chapel HillUSA
| | - R. Eric Blue
- Department of Cell Biology and PhysiologyThe University of North Carolina at Chapel HillUSA
| | - Yi‐Hsuan Tsai
- Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillUSA
| | - Joel Parker
- Curriculum in Genetics and Molecular Biology (GMB)The University of North Carolina at Chapel HillUSA,Lineberger Comprehensive Cancer CenterThe University of North Carolina at Chapel HillUSA
| | - Jimena Giudice
- Department of Cell Biology and PhysiologyThe University of North Carolina at Chapel HillUSA,Curriculum in Genetics and Molecular Biology (GMB)The University of North Carolina at Chapel HillUSA,McAllister Heart Institute, School of MedicineThe University of North Carolina at Chapel HillUSA
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4
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Yang J, Song C, Zhan X. The role of protein acetylation in carcinogenesis and targeted drug discovery. Front Endocrinol (Lausanne) 2022; 13:972312. [PMID: 36171897 PMCID: PMC9510633 DOI: 10.3389/fendo.2022.972312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/23/2022] [Indexed: 12/01/2022] Open
Abstract
Protein acetylation is a reversible post-translational modification, and is involved in many biological processes in cells, such as transcriptional regulation, DNA damage repair, and energy metabolism, which is an important molecular event and is associated with a wide range of diseases such as cancers. Protein acetylation is dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs) in homeostasis. The abnormal acetylation level might lead to the occurrence and deterioration of a cancer, and is closely related to various pathophysiological characteristics of a cancer, such as malignant phenotypes, and promotes cancer cells to adapt to tumor microenvironment. Therapeutic modalities targeting protein acetylation are a potential therapeutic strategy. This article discussed the roles of protein acetylation in tumor pathology and therapeutic drugs targeting protein acetylation, which offers the contributions of protein acetylation in clarification of carcinogenesis, and discovery of therapeutic drugs for cancers, and lays the foundation for precision medicine in oncology.
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Affiliation(s)
- Jingru Yang
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Cong Song
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- *Correspondence: Xianquan Zhan,
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5
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Morales-Tarré O, Alonso-Bastida R, Arcos-Encarnación B, Pérez-Martínez L, Encarnación-Guevara S. Protein lysine acetylation and its role in different human pathologies: a proteomic approach. Expert Rev Proteomics 2021; 18:949-975. [PMID: 34791964 DOI: 10.1080/14789450.2021.2007766] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Lysine acetylation is a reversible post-translational modification (PTM) regulated through the action of specific types of enzymes: lysine acetyltransferases (KATs) and lysine deacetylases (HDACs), in addition to bromodomains, which are a group of conserved domains which identify acetylated lysine residues, several of the players in the process of protein acetylation, including enzymes and bromodomain-containing proteins, have been related to the progression of several diseases. The combination of high-resolution mass spectrometry-based proteomics, and immunoprecipitation to enrich acetylated peptides has contributed in recent years to expand the knowledge about this PTM described initially in histones and nuclear proteins, and is currently reported in more than 5000 human proteins, that are regulated by this PTM. AREAS COVERED This review presents an overview of the main participant elements, the scenario in the development of protein lysine acetylation, and its role in different human pathologies. EXPERT OPINION Acetylation targets are practically all cellular processes in eukaryotes and prokaryotes organisms. Consequently, this modification has been linked to many pathologies like cancer, viral infection, obesity, diabetes, cardiovascular, and nervous system-associated diseases, to mention a few relevant examples. Accordingly, some intermediate mediators in the acetylation process have been projected as therapeutic targets.
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Affiliation(s)
- Orlando Morales-Tarré
- Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ramiro Alonso-Bastida
- Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Bolivar Arcos-Encarnación
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular Y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Leonor Pérez-Martínez
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular Y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sergio Encarnación-Guevara
- Laboratorio de Proteómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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6
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The GCN5: its biological functions and therapeutic potentials. Clin Sci (Lond) 2021; 135:231-257. [PMID: 33443284 DOI: 10.1042/cs20200986] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022]
Abstract
General control non-depressible 5 (GCN5) or lysine acetyltransferase 2A (KAT2A) is one of the most highly studied histone acetyltransferases. It acts as both histone acetyltransferase (HAT) and lysine acetyltransferase (KAT). As an HAT it plays a pivotal role in the epigenetic landscape and chromatin modification. Besides, GCN5 regulates a wide range of biological events such as gene regulation, cellular proliferation, metabolism and inflammation. Imbalance in the GCN5 activity has been reported in many disorders such as cancer, metabolic disorders, autoimmune disorders and neurological disorders. Therefore, unravelling the role of GCN5 in different diseases progression is a prerequisite for both understanding and developing novel therapeutic agents of these diseases. In this review, we have discussed the structural features, the biological function of GCN5 and the mechanical link with the diseases associated with its imbalance. Moreover, the present GCN5 modulators and their limitations will be presented in a medicinal chemistry perspective.
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7
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Daled S, Willems S, Van Puyvelde B, Corveleyn L, Verhelst S, De Clerck L, Deforce D, Dhaenens M. Histone Sample Preparation for Bottom-Up Mass Spectrometry: A Roadmap to Informed Decisions. Proteomes 2021; 9:17. [PMID: 33919160 PMCID: PMC8167631 DOI: 10.3390/proteomes9020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/08/2021] [Accepted: 04/19/2021] [Indexed: 11/16/2022] Open
Abstract
Histone-based chromatin organization enabled eukaryotic genome complexity. This epigenetic control mechanism allowed for the differentiation of stable gene-expression and thus the very existence of multicellular organisms. This existential role in biology makes histones one of the most complexly modified molecules in the biotic world, which makes these key regulators notoriously hard to analyze. We here provide a roadmap to enable fast and informed selection of a bottom-up mass spectrometry sample preparation protocol that matches a specific research question. We therefore propose a two-step assessment procedure: (i) visualization of the coverage that is attained for a given workflow and (ii) direct alignment between runs to assess potential pitfalls at the ion level. To illustrate the applicability, we compare four different sample preparation protocols while adding a new enzyme to the toolbox, i.e., RgpB (GingisREX®, Genovis, Lund, Sweden), an endoproteinase that selectively and efficiently cleaves at the c-terminal end of arginine residues. Raw data are available via ProteomeXchange with identifier PXD024423.
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Affiliation(s)
- Simon Daled
- Laboratory of Pharmaceutical Biotechnology/ProGenTomics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; (S.D.); (B.V.P.); (L.C.); (S.V.); (L.D.C.); (D.D.)
| | - Sander Willems
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Bart Van Puyvelde
- Laboratory of Pharmaceutical Biotechnology/ProGenTomics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; (S.D.); (B.V.P.); (L.C.); (S.V.); (L.D.C.); (D.D.)
| | - Laura Corveleyn
- Laboratory of Pharmaceutical Biotechnology/ProGenTomics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; (S.D.); (B.V.P.); (L.C.); (S.V.); (L.D.C.); (D.D.)
| | - Sigrid Verhelst
- Laboratory of Pharmaceutical Biotechnology/ProGenTomics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; (S.D.); (B.V.P.); (L.C.); (S.V.); (L.D.C.); (D.D.)
| | - Laura De Clerck
- Laboratory of Pharmaceutical Biotechnology/ProGenTomics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; (S.D.); (B.V.P.); (L.C.); (S.V.); (L.D.C.); (D.D.)
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology/ProGenTomics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; (S.D.); (B.V.P.); (L.C.); (S.V.); (L.D.C.); (D.D.)
| | - Maarten Dhaenens
- Laboratory of Pharmaceutical Biotechnology/ProGenTomics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; (S.D.); (B.V.P.); (L.C.); (S.V.); (L.D.C.); (D.D.)
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8
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Harachi M, Masui K, Cavenee WK, Mischel PS, Shibata N. Protein Acetylation at the Interface of Genetics, Epigenetics and Environment in Cancer. Metabolites 2021; 11:216. [PMID: 33916219 PMCID: PMC8066013 DOI: 10.3390/metabo11040216] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 02/07/2023] Open
Abstract
Metabolic reprogramming is an emerging hallmark of cancer and is driven by abnormalities of oncogenes and tumor suppressors. Accelerated metabolism causes cancer cell aggression through the dysregulation of rate-limiting metabolic enzymes as well as by facilitating the production of intermediary metabolites. However, the mechanisms by which a shift in the metabolic landscape reshapes the intracellular signaling to promote the survival of cancer cells remain to be clarified. Recent high-resolution mass spectrometry-based proteomic analyses have spotlighted that, unexpectedly, lysine residues of numerous cytosolic as well as nuclear proteins are acetylated and that this modification modulates protein activity, sublocalization and stability, with profound impact on cellular function. More importantly, cancer cells exploit acetylation as a post-translational protein for microenvironmental adaptation, nominating it as a means for dynamic modulation of the phenotypes of cancer cells at the interface between genetics and environments. The objectives of this review were to describe the functional implications of protein lysine acetylation in cancer biology by examining recent evidence that implicates oncogenic signaling as a strong driver of protein acetylation, which might be exploitable for novel therapeutic strategies against cancer.
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Affiliation(s)
- Mio Harachi
- Department of Pathology, Division of Pathological Neuroscience, Tokyo Women’s Medical University, Tokyo 162-8666, Japan; (M.H.); (N.S.)
| | - Kenta Masui
- Department of Pathology, Division of Pathological Neuroscience, Tokyo Women’s Medical University, Tokyo 162-8666, Japan; (M.H.); (N.S.)
| | - Webster K. Cavenee
- Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, CA 92093, USA;
| | - Paul S. Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Noriyuki Shibata
- Department of Pathology, Division of Pathological Neuroscience, Tokyo Women’s Medical University, Tokyo 162-8666, Japan; (M.H.); (N.S.)
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9
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Raeisossadati R, Ferrari MFR, Kihara AH, AlDiri I, Gross JM. Epigenetic regulation of retinal development. Epigenetics Chromatin 2021; 14:11. [PMID: 33563331 PMCID: PMC7871400 DOI: 10.1186/s13072-021-00384-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/28/2021] [Indexed: 01/10/2023] Open
Abstract
In the developing vertebrate retina, retinal progenitor cells (RPCs) proliferate and give rise to terminally differentiated neurons with exquisite spatio-temporal precision. Lineage commitment, fate determination and terminal differentiation are controlled by intricate crosstalk between the genome and epigenome. Indeed, epigenetic regulation plays pivotal roles in numerous cell fate specification and differentiation events in the retina. Moreover, aberrant chromatin structure can contribute to developmental disorders and retinal pathologies. In this review, we highlight recent advances in our understanding of epigenetic regulation in the retina. We also provide insight into several aspects of epigenetic-related regulation that should be investigated in future studies of retinal development and disease. Importantly, focusing on these mechanisms could contribute to the development of novel treatment strategies targeting a variety of retinal disorders.
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Affiliation(s)
- Reza Raeisossadati
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil.,Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Merari F R Ferrari
- Departamento de Genética E Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Rua Do Matao, 277, Cidade Universitaria, Sao Paulo, SP, 05508-090, Brazil
| | | | - Issam AlDiri
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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10
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Zhou Y, Sun W, Qin Z, Guo S, Kang Y, Zeng S, Yu L. LncRNA regulation: New frontiers in epigenetic solutions to drug chemoresistance. Biochem Pharmacol 2020; 189:114228. [PMID: 32976832 DOI: 10.1016/j.bcp.2020.114228] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/09/2023]
Abstract
Long-noncoding RNAs (lncRNAs) have been shown to participate in sensitizing or de-sensitizing cancer cells to chemical drugs during cancer therapeutics. Notably, a plethora of lncRNAs have been confirmed to be associated with epigenetic controllers and regulate histone protein modification or DNA methylation states in the process of gene transcription. This correlation between lncRNAs and epigenetic regulators can induce the expression of core genes to trigger drug resistance. In addition, epigenetic signatures are considered to be effective and attractive biomarkers for monitoring drug therapeutic effects because they are inheritable, dynamic, and reversible. Therefore, the regulatory mechanism between lncRNAs and epigenetic machinery can serve as a novel indicator and target to overcome or reverse drug resistance in cancer therapy. In this review, we also presented a curated selection of computational tools (including online databases and network analysis) in the area of epigenetics. A classic workflow for lncRNA expression network analysis is presented, providing guidance for non-bioinformaticians to identify significant correlation between lncRNAs and other biomolecules.
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Affiliation(s)
- Ying Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Wen Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhiyuan Qin
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Suhang Guo
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
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11
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Germline genomes have a dominant-heritable contribution to cancer immune evasion and immunotherapy response. QUANTITATIVE BIOLOGY 2020. [DOI: 10.1007/s40484-020-0212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Neural metabolic imbalance induced by MOF dysfunction triggers pericyte activation and breakdown of vasculature. Nat Cell Biol 2020; 22:828-841. [PMID: 32541879 DOI: 10.1038/s41556-020-0526-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
Mutations in chromatin-modifying complexes and metabolic enzymes commonly underlie complex human developmental syndromes affecting multiple organs. A major challenge is to determine how disease-causing genetic lesions cause deregulation of homeostasis in unique cell types. Here we show that neural-specific depletion of three members of the non-specific lethal (NSL) chromatin complex-Mof, Kansl2 or Kansl3-unexpectedly leads to severe vascular defects and brain haemorrhaging. Deregulation of the epigenetic landscape induced by the loss of the NSL complex in neural cells causes widespread metabolic defects, including an accumulation of free long-chain fatty acids (LCFAs). Free LCFAs induce a Toll-like receptor 4 (TLR4)-NFκB-dependent pro-inflammatory signalling cascade in neighbouring vascular pericytes that is rescued by TLR4 inhibition. Pericytes display functional changes in response to LCFA-induced activation that result in vascular breakdown. Our work establishes that neurovascular function is determined by the neural metabolic environment.
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13
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Dai S, Holt MV, Horton JR, Woodcock CB, Patel A, Zhang X, Young NL, Wilkinson AW, Cheng X. Characterization of SETD3 methyltransferase-mediated protein methionine methylation. J Biol Chem 2020; 295:10901-10910. [PMID: 32503840 DOI: 10.1074/jbc.ra120.014072] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/03/2020] [Indexed: 12/20/2022] Open
Abstract
Most characterized protein methylation events encompass arginine and lysine N-methylation, and only a few cases of protein methionine thiomethylation have been reported. Newly discovered oncohistone mutations include lysine-to-methionine substitutions at positions 27 and 36 of histone H3.3. In these instances, the methionine substitution localizes to the active-site pocket of the corresponding histone lysine methyltransferase, thereby inhibiting the respective transmethylation activity. SET domain-containing 3 (SETD3) is a protein (i.e. actin) histidine methyltransferase. Here, we generated an actin variant in which the histidine target of SETD3 was substituted with methionine. As for previously characterized histone SET domain proteins, the methionine substitution substantially (76-fold) increased binding affinity for SETD3 and inhibited SETD3 activity on histidine. Unexpectedly, SETD3 was active on the substituted methionine, generating S-methylmethionine in the context of actin peptide. The ternary structure of SETD3 in complex with the methionine-containing actin peptide at 1.9 Å resolution revealed that the hydrophobic thioether side chain is packed by the aromatic rings of Tyr312 and Trp273, as well as the hydrocarbon side chain of Ile310 Our results suggest that placing methionine properly in the active site-within close proximity to and in line with the incoming methyl group of SAM-would allow some SET domain proteins to selectively methylate methionine in proteins.
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Affiliation(s)
- Shaobo Dai
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Matthew V Holt
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Clayton B Woodcock
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
| | - Nicolas L Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Alex W Wilkinson
- Department of Biology, Stanford University, Stanford, California, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas M. D. Anderson Cancer Center, Houston, Texas, USA
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14
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Mitchell CM, Hirst JJ, Mitchell MD, Murray HG, Zakar T. Genes upregulated in the amnion at labour are bivalently marked by activating and repressive histone modifications. Mol Hum Reprod 2020; 25:228-240. [PMID: 30753586 DOI: 10.1093/molehr/gaz007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 01/17/2019] [Accepted: 02/08/2019] [Indexed: 12/19/2022] Open
Abstract
Inflammatory genes are expressed increasingly in the foetal membranes at late gestation triggering birth. Here we have examined whether epigenetic histone modifications contribute to the upregulation of proinflammatory genes in the amnion in late pregnancy and at labour. Amnion samples were collected from early pregnancy, at term in the absence of labour and after spontaneous birth. The expression of the labour-associated proinflammatory genes PTGS2, BMP2 and NAMPT was determined by reverse transcription-coupled quantitative real-time PCR (qRT-PCR). Chromatin immunoprecipitation (ChIP) and sequential double ChIP were performed to determine the levels and co-occurrence of activating histone-3, lysine-4 trimethylation (H3K4me3) and repressive histone-3, lysine-27 trimethylation (H3K27me3) at the gene promoters. H3K4 methyltransferase, H3K27me3 demethylase and H3K27 methyltransferase expression was determined by qRT-PCR and immunofluorescence confocal microscopy. PTGS2, BMP2 and NAMPT expression was upregulated robustly between early pregnancy and term (P < 0.05). The promoters were marked bivalently by both the H3K4me3 and H3K27me3 modifications. Bivalence was reduced at term by the decrease of the H3K27me3-modified fraction of promoter copies marked by H3K4me3 indicating epigenetic activation. Messenger RNAs encoding the H3K4-specific methyl transferases MLL1,-2,-3,-4, SETD1A,-B and the H3K27me3-specific demethylases KDM6A,-B were expressed increasingly while the H3K27 methyl transferase EZH2 was expressed decreasingly at term. Histone modifying enzyme proteins were detected in amnion epithelial and mesenchymal cells. These results with prototypical proinflammatory genes suggest that nucleosomes at labour-promoting genes are marked bivalently in the amnion, which is shifted towards monovalent H3K4me3 modification at term when the genes are upregulated. Bivalent epigenetic regulation by histone modifying enzymes may control the timing of labour.
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Affiliation(s)
- Carolyn M Mitchell
- Mothers and Babies Research Centre, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Faculty of Medicine and Public Health, The University of Newcastle, Callaghan, Australia
| | - Jonathan J Hirst
- Mothers and Babies Research Centre, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Faculty of Medicine and Public Health, The University of Newcastle, Callaghan, Australia
| | - Murray D Mitchell
- Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Henry G Murray
- Department of Obstetrics and Gynaecology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia.,Faculty of Medicine and Public Health, The University of Newcastle, Callaghan, Australia
| | - Tamas Zakar
- Mothers and Babies Research Centre, Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Department of Obstetrics and Gynaecology, John Hunter Hospital, New Lambton Heights, New South Wales, Australia.,Faculty of Medicine and Public Health, The University of Newcastle, Callaghan, Australia
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15
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Zhang S, Lu Y, Jiang C. Inhibition of histone demethylase JMJD1C attenuates cardiac hypertrophy and fibrosis induced by angiotensin II. J Recept Signal Transduct Res 2020; 40:339-347. [PMID: 32122211 DOI: 10.1080/10799893.2020.1734819] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Pathological cardiac hypertrophy is a major risk factor for cardiovascular morbidity and mortality. Histone demethylases (KDMs) are emerging regulators of transcriptional reprograming in cancer, however, their potential role in abnormal heart growth and fibrosis remains largely unknown. The aim of this current study was to examine the role of JMJD1C, an H3K9me2 specific demethylase, in angiotensin II (Ang II) induced cardiac hypertrophy and fibrosis. In this study, we observed that Ang II could increase the expression of JMJD1C detected by Western blot and RT-qPCR in vitro and in vivo. Immunofluorescence staining showed that the treatment of Ang II could increase cardiomyocyte size. RT-qPCR results have shown that Ang II could increase the expression of cell hypertrophic and fibrotic markers in H9c2 cells. Whereas, inhibition of JMJD1C by shRNA and JIB-04, a small molecule histone demethylase inhibitor, significantly reduced Ang II-induced cell hypertrophy, and hypertrophic and fibrotic marker overexpression. Furthermore, cardiomyocyte JMJD1C knockdown decreased Tissue Inhibitor of Metalloproteinases 1 (TIMP1) transcription with pro-fibrotic activity. In conclusion, JMJD1C plays an important role in Ang II-induced cardiac hypertrophy and fibrosis by activating TIMP1 transcription, targeting of JMJD1C may be an effective strategy for the treatment of Ang II-associated cardiac diseases.
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Affiliation(s)
- Shenqian Zhang
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Electrocardiogram Room of Department of Functional Examination, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Ying Lu
- Electrocardiogram Room of Department of Functional Examination, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Chenyang Jiang
- Department of Cardiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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16
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Stolzenbach F, Valdivia S, Ojeda-Provoste P, Toledo F, Sobrevia L, Kerr B. DNA methylation changes in genes coding for leptin and insulin receptors during metabolic-altered pregnancies. Biochim Biophys Acta Mol Basis Dis 2020; 1866:165465. [DOI: 10.1016/j.bbadis.2019.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/19/2019] [Accepted: 05/02/2019] [Indexed: 01/07/2023]
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17
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Lizák B, Szarka A, Kim Y, Choi KS, Németh CE, Marcolongo P, Benedetti A, Bánhegyi G, Margittai É. Glucose Transport and Transporters in the Endomembranes. Int J Mol Sci 2019; 20:ijms20235898. [PMID: 31771288 PMCID: PMC6929180 DOI: 10.3390/ijms20235898] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/16/2019] [Accepted: 11/21/2019] [Indexed: 12/18/2022] Open
Abstract
Glucose is a basic nutrient in most of the creatures; its transport through biological membranes is an absolute requirement of life. This role is fulfilled by glucose transporters, mediating the transport of glucose by facilitated diffusion or by secondary active transport. GLUT (glucose transporter) or SLC2A (Solute carrier 2A) families represent the main glucose transporters in mammalian cells, originally described as plasma membrane transporters. Glucose transport through intracellular membranes has not been elucidated yet; however, glucose is formed in the lumen of various organelles. The glucose-6-phosphatase system catalyzing the last common step of gluconeogenesis and glycogenolysis generates glucose within the lumen of the endoplasmic reticulum. Posttranslational processing of the oligosaccharide moiety of glycoproteins also results in intraluminal glucose formation in the endoplasmic reticulum (ER) and Golgi. Autophagic degradation of polysaccharides, glycoproteins, and glycolipids leads to glucose accumulation in lysosomes. Despite the obvious necessity, the mechanism of glucose transport and the molecular nature of mediating proteins in the endomembranes have been hardly elucidated for the last few years. However, recent studies revealed the intracellular localization and functional features of some glucose transporters; the aim of the present paper was to summarize the collected knowledge.
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Affiliation(s)
- Beáta Lizák
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 1094 Budapest, Hungary; (B.L.); (C.E.N.); (G.B.)
| | - András Szarka
- Laboratory of Biochemistry and Molecular Biology, Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, 1111 Budapest, Hungary;
| | - Yejin Kim
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary; (Y.K.); (K.-s.C.)
| | - Kyu-sung Choi
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary; (Y.K.); (K.-s.C.)
| | - Csilla E. Németh
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 1094 Budapest, Hungary; (B.L.); (C.E.N.); (G.B.)
| | - Paola Marcolongo
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (P.M.); (A.B.)
| | - Angelo Benedetti
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (P.M.); (A.B.)
| | - Gábor Bánhegyi
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, 1094 Budapest, Hungary; (B.L.); (C.E.N.); (G.B.)
| | - Éva Margittai
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary; (Y.K.); (K.-s.C.)
- Correspondence: ; Tel.: +36-459-1500 (ext. 60311); Fax: +36-1-2662615
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18
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Wang F, Kang P, Li Z, Niu Q. Role of MLL in the modification of H3K4me3 in aluminium-induced cognitive dysfunction. CHEMOSPHERE 2019; 232:121-129. [PMID: 31152896 DOI: 10.1016/j.chemosphere.2019.05.099] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 06/09/2023]
Abstract
It is widely accepted that aluminium is neurotoxic; it primarily causes cognitive dysfunction, which has been confirmed in human and animal tissue and cell experiments (Bondy, 2010), but its toxic mechanism has yet to be fully elucidated. Epigenetics is the study of changes in gene expression that may be triggered by both genetic and environmental factors and is independent from changes in the underlying DNA sequence, resulting in a change in phenotype without a change in genotype, which in turn affects how cells read genes. Some findings emphasize the potential significance of histone lysine methylation for orderly brain development and as a molecular toolbox to study chromatin function in vivo and in vitro. The H3K4-specific methyltransferase MLL is essential for hippocampal synaptic plasticity and might be involved in cognitive dysfunction. In the present study, we established that chronic aluminium exposure results in cognitive dysfunction, causing deficits in exploratory behaviour and learning and memory, in a dose- and time-dependent manner. Furthermore, we demonstrated in vivo and in vitro that chronic aluminium exposure reduces expression of histone H3K4 tri-methylation (H3K4me3) and the activity and expression of MLL. Taken together, these results indicate that chronic aluminium exposure may reduce H3K4me3 levels through suppressing activation of MLL, which in turn affects cognitive ability.
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Affiliation(s)
- Fei Wang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Pan Kang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Zhaoyang Li
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China
| | - Qiao Niu
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, 030001, China.
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19
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Yang Y, Wilson MJ. Genome-wide analysis of H3K4me3 and H3K27me3 modifications throughout the mouse urogenital ridge at E11.5. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Şanlı E, Kabaran S. Maternal Obesity, Maternal Overnutrition and Fetal Programming: Effects of Epigenetic Mechanisms on the Development of Metabolic Disorders. Curr Genomics 2019; 20:419-427. [PMID: 32476999 PMCID: PMC7235386 DOI: 10.2174/1389202920666191030092225] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 10/12/2019] [Accepted: 10/21/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Maternal obesity and maternal overnutrition, can lead to epigenetic alterations during pregnancy and these alterations can influence fetal and neonatal phenotype which increase the risk of metabolic disorders in later stages of life. OBJECTIVE The effects of maternal obesity on fetal programming and potential mechanisms of maternal epigenetic regulation of gene expression which have persistent effects on fetal health and development were investigated. METHODS Review of the literature was carried out in order to discuss the effects of maternal obesity and epigenetic mechanisms in fetal programming of metabolic disorders. All abstracts and full-text articles were examined and the most relevant articles were included in this review. RESULTS Maternal obesity and maternal overnutrition during fetal period has important overall effects on long-term health. Maternal metabolic alterations during early stages of fetal development can lead to permanent changes in organ structures, cell numbers and metabolism. Epigenetic modifications (DNA methylation, histone modifications, microRNAs) play an important role in disease susceptibility in the later stages of human life. Maternal nutrition alter expression of hypothalamic genes which can increase fetal and neonatal energy intake. Epigenetic modifications may affect the increasing rate of obesity and other metabolic disorders worldwide since the impact of these changes can be passed through generations. CONCLUSION Weight management before and during pregnancy, together with healthy nutritional intakes may improve the maternal metabolic environment, which can reduce the risks of fetal programming of metabolic diseases. Further evidence from long-term follow-up studies are needed in order to determine the role of maternal obesity on epigenetic mechanisms.
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Affiliation(s)
- Ezgi Şanlı
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Eastern Mediterranean University, Famagusta, T.R. North Cyprus via Mersin 10, Turkey
| | - Seray Kabaran
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Eastern Mediterranean University, Famagusta, T.R. North Cyprus via Mersin 10, Turkey
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21
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Roatsch M, Hoffmann I, Abboud MI, Hancock RL, Tarhonskaya H, Hsu KF, Wilkins SE, Yeh TL, Lippl K, Serrer K, Moneke I, Ahrens TD, Robaa D, Wenzler S, Barthes NPF, Franz H, Sippl W, Lassmann S, Diederichs S, Schleicher E, Schofield CJ, Kawamura A, Schüle R, Jung M. The Clinically Used Iron Chelator Deferasirox Is an Inhibitor of Epigenetic JumonjiC Domain-Containing Histone Demethylases. ACS Chem Biol 2019; 14:1737-1750. [PMID: 31287655 DOI: 10.1021/acschembio.9b00289] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fe(II)- and 2-oxoglutarate (2OG)-dependent JumonjiC domain-containing histone demethylases (JmjC KDMs) are "epigenetic eraser" enzymes involved in the regulation of gene expression and are emerging drug targets in oncology. We screened a set of clinically used iron chelators and report that they potently inhibit JMJD2A (KDM4A) in vitro. Mode of action investigations revealed that one compound, deferasirox, is a bona fide active site-binding inhibitor as shown by kinetic and spectroscopic studies. Synthesis of derivatives with improved cell permeability resulted in significant upregulation of histone trimethylation and potent cancer cell growth inhibition. Deferasirox was also found to inhibit human 2OG-dependent hypoxia inducible factor prolyl hydroxylase activity. Therapeutic effects of clinically used deferasirox may thus involve transcriptional regulation through 2OG oxygenase inhibition. Deferasirox might provide a useful starting point for the development of novel anticancer drugs targeting 2OG oxygenases and a valuable tool compound for investigations of KDM function.
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Affiliation(s)
- Martin Roatsch
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Inga Hoffmann
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Martine I Abboud
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Rebecca L Hancock
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Hanna Tarhonskaya
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kuo-Feng Hsu
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Sarah E Wilkins
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Tzu-Lan Yeh
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kerstin Lippl
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kerstin Serrer
- Institute of Physical Chemistry , Albert-Ludwigs-Universität Freiburg , Albertstraße 21 , 79104 Freiburg i.Br. , Germany
| | - Isabelle Moneke
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine , University of Freiburg , German Cancer Consortium (DKTK)-Partner Site Freiburg, Breisacher Straße 115 , 79106 Freiburg i.Br. , Germany
| | - Theresa D Ahrens
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 115a , 79106 Freiburg i.Br. , Germany
| | - Dina Robaa
- Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , Wolfgang-Langenbeck-Straße 4 , 06120 Halle (Saale) , Germany
| | - Sandra Wenzler
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Nicolas P F Barthes
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Henriette Franz
- Central Clinical Research, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 66 , 79106 Freiburg i.Br. , Germany
| | - Wolfgang Sippl
- Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , Wolfgang-Langenbeck-Straße 4 , 06120 Halle (Saale) , Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 115a , 79106 Freiburg i.Br. , Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine , University of Freiburg , German Cancer Consortium (DKTK)-Partner Site Freiburg, Breisacher Straße 115 , 79106 Freiburg i.Br. , Germany
- Division of RNA Biology & Cancer , German Cancer Research Center (DKFZ) , Im Neuenheimer Feld 280 , 69120 Heidelberg , Germany
| | - Erik Schleicher
- Institute of Physical Chemistry , Albert-Ludwigs-Universität Freiburg , Albertstraße 21 , 79104 Freiburg i.Br. , Germany
| | - Christopher J Schofield
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Akane Kawamura
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Roland Schüle
- Central Clinical Research, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 66 , 79106 Freiburg i.Br. , Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
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22
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Brunk CF, Martin WF. Archaeal Histone Contributions to the Origin of Eukaryotes. Trends Microbiol 2019; 27:703-714. [PMID: 31076245 DOI: 10.1016/j.tim.2019.04.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/01/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022]
Abstract
The eukaryotic lineage arose from bacterial and archaeal cells that underwent a symbiotic merger. At the origin of the eukaryote lineage, the bacterial partner contributed genes, metabolic energy, and the building blocks of the endomembrane system. What did the archaeal partner donate that made the eukaryotic experiment a success? The archaeal partner provided the potential for complex information processing. Archaeal histones were crucial in that regard by providing the basic functional unit with which eukaryotes organize DNA into nucleosomes, exert epigenetic control of gene expression, transcribe genes with CCAAT-box promoters, and a manifest cell cycle with condensed chromosomes. While mitochondrial energy lifted energetic constraints on eukaryotic protein production, histone-based chromatin organization paved the path to eukaryotic genome complexity, a critical hurdle en route to the evolution of complex cells.
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Affiliation(s)
- Clifford F Brunk
- Department of Ecology and Evolutionary Biology and Molecular Biology Institute University of California Los Angeles, Los Angeles, USA
| | - William F Martin
- Institute of Molecular Evolution Heinrich-Heine-Universitaet Duesseldorf, Dusseldorf, Germany.
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23
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One-Carbon Metabolism Links Nutrition Intake to Embryonic Development via Epigenetic Mechanisms. Stem Cells Int 2019; 2019:3894101. [PMID: 30956668 PMCID: PMC6431457 DOI: 10.1155/2019/3894101] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/06/2019] [Accepted: 01/28/2019] [Indexed: 02/06/2023] Open
Abstract
Beyond energy production, nutrient metabolism plays a crucial role in stem cell lineage determination. Changes in metabolism based on nutrient availability and dietary habits impact stem cell identity. Evidence suggests a strong link between metabolism and epigenetic mechanisms occurring during embryonic development and later life of offspring. Metabolism regulates epigenetic mechanisms such as modifications of DNA, histones, and microRNAs. In turn, these epigenetic mechanisms regulate metabolic pathways to modify the metabolome. One-carbon metabolism (OCM) is a crucial metabolic process involving transfer of the methyl groups leading to regulation of multiple cellular activities. OCM cycles and its related micronutrients are ubiquitously present in stem cells and feed into the epigenetic mechanisms. In this review, we briefly introduce the OCM process and involved micronutrients and discuss OCM-associated epigenetic modifications, including DNA methylation, histone modification, and microRNAs. We further consider the underlying OCM-mediated link between nutrition and epigenetic modifications in embryonic development.
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24
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Restellini C, Cuomo A, Lupia M, Giordano M, Bonaldi T, Noberini R. Alternative digestion approaches improve histone modification mapping by mass spectrometry in clinical samples. Proteomics Clin Appl 2018; 13:e1700166. [PMID: 30471193 DOI: 10.1002/prca.201700166] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/03/2018] [Indexed: 12/14/2022]
Abstract
PURPOSE Profiling histone posttranslational modifications (PTMs) in clinical samples holds great potential for the identification of epigenetic biomarkers and the discovery of novel epigenetic targets. MS-based approaches to analyze histone PTMs in clinical samples usually rely on SDS-PAGE separation following histone enrichment in order to eliminate detergents and further isolate histones. However, this limits the digestions options and hence the modification coverage. EXPERIMENTAL DESIGN AND RESULTS The aim of this study is the implementation of a procedure involving acetone protein precipitation followed by histone enrichment through a C18 StageTip column to obtain histone preparations suitable for various in-solution digestion protocols. Among them, the Arg-C digestion, which allows profiling histone H4 modifications, and the Prop-PIC method, which improves the detection of short and hydrophilic peptides, are tested. This approach is validated on different types of samples, including formalin-fixed paraffin-embedded pathology tissues, and employed to profile histone H4 modifications in cancer samples and normal tissues, identifying previously reported differences, as well as novel ones. CONCLUSIONS AND CLINICAL RELEVANCE This protocol widens the number of applications available in the toolbox of clinical epigenomics, allowing the investigation of a larger spectrum of histone marks in patient samples.
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Affiliation(s)
- Camilla Restellini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Michela Lupia
- Unit of Gynecological Oncology Research, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Marco Giordano
- Unit of Gynecological Oncology Research, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
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25
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Padalino G, Ferla S, Brancale A, Chalmers IW, Hoffmann KF. Combining bioinformatics, cheminformatics, functional genomics and whole organism approaches for identifying epigenetic drug targets in Schistosoma mansoni. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2018; 8:559-570. [PMID: 30455056 PMCID: PMC6288008 DOI: 10.1016/j.ijpddr.2018.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/22/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
Abstract
Schistosomiasis endangers the lives of greater than 200 million people every year and is predominantly controlled by a single class chemotherapy, praziquantel (PZQ). Development of PZQ replacement (to combat the threat of PZQ insensitivity/resistance arising) or combinatorial (to facilitate the killing of PZQ-insensitive juvenile schistosomes) chemotherapies would help sustain this control strategy into the future. Here, we re-categorise two families of druggable epigenetic targets in Schistosoma mansoni, the histone methyltransferases (HMTs) and the histone demethylases (HDMs). Amongst these, a S. mansoni Lysine Specific Demethylase 1 (SmLSD1, Smp_150560) homolog was selected for further analyses. Homology modelling of SmLSD1 and in silico docking of greater than four thousand putative inhibitors identified seven (L1 – L7) showing more favourable binding to the target pocket of SmLSD1 vs Homo sapiens HsLSD1; six of these seven (L1 – L6) plus three structural analogues of L7 (L8 – L10) were subsequently screened against schistosomula using the Roboworm anthelmintic discovery platform. The most active compounds (L10 - pirarubicin > L8 – danunorubicin hydrochloride) were subsequently tested against juvenile (3 wk old) and mature (7 wk old) schistosome stages and found to impede motility, suppress egg production and affect tegumental surfaces. When compared to a surrogate human cell line (HepG2), a moderate window of selectivity was observed for the most active compound L10 (selectivity indices - 11 for schistosomula, 9 for juveniles, 1.5 for adults). Finally, RNA interference of SmLSD1 recapitulated the egg-laying defect of schistosomes co-cultivated in the presence of L10 and L8. These preliminary results suggest that SmLSD1 represents an attractive new target for schistosomiasis; identification of more potent and selective SmLSD1 compounds, however, is essential. Nevertheless, the approaches described herein highlight an interdisciplinary strategy for selecting and screening novel/repositioned anti-schistosomals, which can be applied to any druggable (epigenetic) target encoded by the parasite's genome. Schistosoma mansoni contains 27 histone methyltransferases (HMTs) and 14 histone demethylases (HDMs). S. mansoni lysine specific demethylase 1 (SmLSD1) is a druggable target. Schistosomes treated with the putative SmLSD1 inhibitor pirarubicin or siRNAs targeting SmLSD1 are less fecund.
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Affiliation(s)
- Gilda Padalino
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY23 3DA, Wales, UK.
| | - Salvatore Ferla
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, United Kingdom.
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, CF10 3NB, United Kingdom.
| | - Iain W Chalmers
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY23 3DA, Wales, UK.
| | - Karl F Hoffmann
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, SY23 3DA, Wales, UK.
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Viaene AN, Santi M, Rosenbaum J, Li MM, Surrey LF, Nasrallah MP. SETD2 mutations in primary central nervous system tumors. Acta Neuropathol Commun 2018; 6:123. [PMID: 30419952 PMCID: PMC6231273 DOI: 10.1186/s40478-018-0623-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 10/21/2018] [Indexed: 02/07/2023] Open
Abstract
Mutations in SETD2 are found in many tumors, including central nervous system (CNS) tumors. Previous work has shown these mutations occur specifically in high grade gliomas of the cerebral hemispheres in pediatric and young adult patients. We investigated SETD2 mutations in a cohort of approximately 640 CNS tumors via next generation sequencing; 23 mutations were detected across 19 primary CNS tumors. Mutations were found in a wide variety of tumors and locations at a broad range of allele frequencies. SETD2 mutations were seen in both low and high grade gliomas as well as non-glial tumors, and occurred in patients greater than 55 years of age, in addition to pediatric and young adult patients. High grade gliomas at first occurrence demonstrated either frameshift/truncating mutations or point mutations at high allele frequencies, whereas recurrent high grade gliomas frequently harbored subclones with point mutations in SETD2 at lower allele frequencies in the setting of higher mutational burdens. Comparison with the TCGA dataset demonstrated consistent findings. Finally, immunohistochemistry showed decreased staining for H3K36me3 in our cohort of SETD2 mutant tumors compared to wildtype controls. Our data further describe the spectrum of tumors in which SETD2 mutations are found and provide a context for interpretation of these mutations in the clinical setting.
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27
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Blank spots on the map: some current questions on nuclear organization and genome architecture. Histochem Cell Biol 2018; 150:579-592. [PMID: 30238154 DOI: 10.1007/s00418-018-1726-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
The past decades have provided remarkable insights into how the eukaryotic cell nucleus and the genome within it are organized. The combined use of imaging, biochemistry and molecular biology approaches has revealed several basic principles of nuclear architecture and function, including the existence of chromatin domains of various sizes, the presence of a large number of non-membranous intranuclear bodies, non-random positioning of genes and chromosomes in 3D space, and a prominent role of the nuclear lamina in organizing genomes. Despite this tremendous progress in elucidating the biological properties of the cell nucleus, many questions remain. Here, we highlight some of the key open areas of investigation in the field of nuclear organization and genome architecture with a particular focus on the mechanisms and principles of higher-order genome organization, the emerging role of liquid phase separation in cellular organization, and the functional role of the nuclear lamina in physiological processes.
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28
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Lu X, Jia H, Yan X, Wang J, Wang Y, Liu C. Label-free detection of histone based on cationic conjugated polymer-mediated fluorescence resonance energy transfer. Talanta 2018; 180:150-155. [DOI: 10.1016/j.talanta.2017.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/28/2017] [Accepted: 12/02/2017] [Indexed: 12/30/2022]
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29
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Milstone ZJ, Lawson G, Trivedi CM. Histone deacetylase 1 and 2 are essential for murine neural crest proliferation, pharyngeal arch development, and craniofacial morphogenesis. Dev Dyn 2017; 246:1015-1026. [PMID: 28791750 DOI: 10.1002/dvdy.24563] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/02/2017] [Accepted: 08/07/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Craniofacial anomalies involve defective pharyngeal arch development and neural crest function. Copy number variation at 1p35, containing histone deacetylase 1 (Hdac1), or 6q21-22, containing Hdac2, are implicated in patients with craniofacial defects, suggesting an important role in guiding neural crest development. However, the roles of Hdac1 and Hdac2 within neural crest cells remain unknown. RESULTS The neural crest and its derivatives express both Hdac1 and Hdac2 during early murine development. Ablation of Hdac1 and Hdac2 within murine neural crest progenitor cells cause severe hemorrhage, atrophic pharyngeal arches, defective head morphogenesis, and complete embryonic lethality. Embryos lacking Hdac1 and Hdac2 in the neural crest exhibit decreased proliferation and increased apoptosis in both the neural tube and the first pharyngeal arch. Mechanistically, loss of Hdac1 and Hdac2 upregulates cyclin-dependent kinase inhibitors Cdkn1a, Cdkn1b, Cdkn1c, Cdkn2b, Cdkn2c, and Tp53 within the first pharyngeal arch. CONCLUSIONS Our results show that Hdac1 and Hdac2 function redundantly within the neural crest to regulate proliferation and the development of the pharyngeal arches by means of repression of cyclin-dependent kinase inhibitors. Developmental Dynamics 246:1015-1026, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Zachary J Milstone
- Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts.,Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Grace Lawson
- Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Chinmay M Trivedi
- Cardiovascular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts.,Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts.,Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts
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30
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Wang L, Song G, Zhang X, Feng T, Pan J, Chen W, Yang M, Bai X, Pang Y, Yu J, Han J, Han B. PADI2-Mediated Citrullination Promotes Prostate Cancer Progression. Cancer Res 2017; 77:5755-5768. [DOI: 10.1158/0008-5472.can-17-0150] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/31/2017] [Accepted: 08/11/2017] [Indexed: 11/16/2022]
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31
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Yu C, Yao X, Zhao L, Wang P, Zhang Q, Zhao C, Yao S, Wei Y. Wolf-Hirschhorn Syndrome Candidate 1 (whsc1) Functions as a Tumor Suppressor by Governing Cell Differentiation. Neoplasia 2017; 19:606-616. [PMID: 28654864 PMCID: PMC5487304 DOI: 10.1016/j.neo.2017.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/25/2017] [Accepted: 05/02/2017] [Indexed: 02/07/2023]
Abstract
Wolf–Hirschhorn syndrome candidate 1 (WHSC1) is a histone 3 lysine 36 (H3K36) specific methyltransferase that is frequently deleted in Wolf–Hirschhorn syndrome (WHS). Whsc1 is also found mutated in a subgroup of B-cell derived malignant diseases by genomic translocation or point mutation, both of which resulted in hyperactivity of WHSC1 mediated H3K36 methylation and uncontrolled cell proliferation, suggesting that whsc1 functions as an oncogene. However, here we provided evidences to show that whsc1 also has tumor suppressor functions. We used zebrafish as an in vivo model and generated homozygous whsc1 mutant lines via clustered regularly interspaced short palindromic repeats-associated protein Cas9 (CRISPR/Cas9) technology. Then western-blot (WB) and immunofluorescence (IF) were performed to analysis the expression level of H3K36Me2 and H3K36Me3, and we identified the diseased tissue via hematoxylin–eosin (HE) staining, IF staining or immunohistochemistry (IHC). Whsc1 lose-of-function led to significant decrease in di- and tri-methylation of H3K36. A series of WHS related phenotypes were found in whsc1−/− zebrafish, including growth retardation, neural development defects and heart failure. In addition, loss of function of whsc1 led to defects in the development of swim bladder, possibly through the dis-regulation of key genes in swim bladder organogenesis and inhibition of progenitor cell differentiation, which was correlated with its expression in this organ during embryonic development. At later stage, these whsc1−/− zebrafishes are inclined to grow tumors in the swim bladder. Our work suggested that whsc1 may function as a tumor suppressor by governing progenitor cell differentiation.
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Affiliation(s)
- Chuan Yu
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, College of Life Science, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Xiaomin Yao
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, College of Life Science, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Linjie Zhao
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, College of Life Science, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Ping Wang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, College of Life Science, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Qian Zhang
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, College of Life Science, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Chengjian Zhao
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, College of Life Science, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Shaohua Yao
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, College of Life Science, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Yuquan Wei
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, College of Life Science, Sichuan University, Chengdu, 610041, People's Republic of China.
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32
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Sundar IK, Rahman I. Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer. Am J Physiol Lung Cell Mol Physiol 2016; 311:L1245-L1258. [PMID: 27793800 DOI: 10.1152/ajplung.00253.2016] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 10/23/2016] [Indexed: 01/23/2023] Open
Abstract
Chromatin-modifying enzymes mediate DNA methylation and histone modifications on recruitment to specific target gene loci in response to various stimuli. The key enzymes that regulate chromatin accessibility for maintenance of modifications in DNA and histones, and for modulation of gene expression patterns in response to cigarette smoke (CS), are not known. We hypothesize that CS exposure alters the gene expression patterns of chromatin-modifying enzymes, which then affects multiple downstream pathways involved in the response to CS. We have, therefore, analyzed chromatin-modifying enzyme profiles and validated by quantitative real-time PCR (qPCR). We also performed immunoblot analysis of targeted histone marks in C57BL/6J mice exposed to acute and subchronic CS, and of lungs from nonsmokers, smokers, and patients with chronic obstructive pulmonary disease (COPD). We found a significant increase in expression of several chromatin modification enzymes, including DNA methyltransferases, histone acetyltransferases, histone methyltransferases, and SET domain proteins, histone kinases, and ubiquitinases. Our qPCR validation data revealed a significant downregulation of Dnmt1, Dnmt3a, Dnmt3b, Hdac2, Hdac4, Hat1, Prmt1, and Aurkb We identified targeted chromatin histone marks (H3K56ac and H4K12ac), which are induced by CS. Thus CS-induced genotoxic stress differentially affects the expression of epigenetic modulators that regulate transcription of target genes via DNA methylation and site-specific histone modifications. This may have implications in devising epigenetic-based therapies for COPD and lung cancer.
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Affiliation(s)
- Isaac K Sundar
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York
| | - Irfan Rahman
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York
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33
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Shabbir MAB, Hao H, Shabbir MZ, Hussain HI, Iqbal Z, Ahmed S, Sattar A, Iqbal M, Li J, Yuan Z. Survival and Evolution of CRISPR-Cas System in Prokaryotes and Its Applications. Front Immunol 2016; 7:375. [PMID: 27725818 PMCID: PMC5035730 DOI: 10.3389/fimmu.2016.00375] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/07/2016] [Indexed: 12/12/2022] Open
Abstract
Prokaryotes have developed numerous innate immune mechanisms in order to fend off bacteriophage or plasmid attack. One of these immune systems is clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR-associated proteins play a key role in survival of prokaryotes against invaders, as these systems cleave DNA of foreign genetic elements. Beyond providing immunity, these systems have significant impact in altering the bacterial physiology in term of its virulence and pathogenicity, as well as evolution. Also, due to their diverse nature of functionality, cas9 endoribonuclease can be easily reprogrammed with the help of guide RNAs, showing unprecedented potential and significance for gene editing in treating genetic diseases. Here, we also discuss the use of NgAgo–gDNA system in genome editing of human cells.
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Affiliation(s)
- Muhammad Abu Bakr Shabbir
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Muhammad Zubair Shabbir
- Quality Operations Laboratory at University of Veterinary and Animal Sciences Lahore , Pakistan
| | - Hafiz Iftikhar Hussain
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Zahid Iqbal
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Saeed Ahmed
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Adeel Sattar
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, China; MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Mujahid Iqbal
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, China; MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Jun Li
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University , Wuhan , China
| | - Zonghui Yuan
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China; National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agricultural University, Wuhan, China; MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
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Substituted 2-(2-aminopyrimidin-4-yl)pyridine-4-carboxylates as potent inhibitors of JumonjiC domain-containing histone demethylases. Future Med Chem 2016; 8:1553-71. [DOI: 10.4155/fmc.15.188] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background: Aberrant expression of iron(II)- and 2-oxoglutarate-dependent JumonjiC histone demethylases has been linked to cancer. Potent demethylase inhibitors are drug candidates and biochemical tools to elucidate the functional impact of demethylase inhibition. Methods & results: Virtual screening identified a novel lead scaffold against JMJD2A with low-micromolar potency in vitro. Analogs were acquired from commercial sources respectively synthesized in feedback with biological testing. Optimized compounds were transformed into cell-permeable prodrugs. A cocrystal x-ray structure revealed the mode of binding of these compounds as competitive to 2-oxoglutarate and confirmed kinetic experiments. Selectivity studies revealed a preference for JMJD2A and JARID1A over JMJD3. Conclusion: Virtual screening and rational structural optimization led to a novel scaffold for highly potent and selective JMJD2A inhibitors.
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35
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Gole H, Chuk R, Coman D. Persistent Hyperinsulinism in Kabuki Syndrome 2: Case Report and Literature Review. Clin Pract 2016; 6:848. [PMID: 27777708 PMCID: PMC5067400 DOI: 10.4081/cp.2016.848] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 08/04/2016] [Accepted: 08/10/2016] [Indexed: 12/17/2022] Open
Abstract
Kabuki syndrome is a clinically and genetically heterogeneous congenital malformation syndrome with protean clinical manifestations. This reflects the important epigenetic role in embryonic development of the two genes currently known to be associated with Kabuki syndrome i.e., KMT2D and KDM6A, which are responsible for Kabuki syndrome 1 and Kabuki syndrome 2, respectively. Hypoglycemia is thought to be a rare manifestation of Kabuki syndrome; however it may be under diagnosed. Herein we describe the case of a 5-year-old girl with Kabuki syndrome 2 in whom persistent hyperinsulinism was diagnosed at 4 years of age. We postulate an epigenetic mechanism for hyperinsulinism where specific loss KDM6A demethylation of the H3K27me3/me2 mark may lead to deregulated pancreatic ß-cell development.
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36
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Kidd CDA, Thompson PJ, Barrett L, Baltic S. Histone Modifications and Asthma. The Interface of the Epigenetic and Genetic Landscapes. Am J Respir Cell Mol Biol 2016; 54:3-12. [PMID: 26397168 DOI: 10.1165/rcmb.2015-0050tr] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Complex lung diseases, such as asthma, are influenced by both genetic predisposition and environmental stimuli. The epigenetic landscape of such diseases is attracting increasing interest and research. Epigenetics broadly covers the transient and the inheritable changes to gene expression that are not directly due to changes in nucleotide sequences. Epigenetic mechanisms could have significant impact on asthma-related allergic, immune, and regulatory pathways, as well as on the generation of biomarkers and the heritable transmission of asthma phenotypes. Recent technological advances have allowed mapping of the epigenome and analysis of genome-wide epigenetic contributors to disease. As a result, ground-breaking observations regarding histone post-translational modifications in a number of immunological diseases have emerged. In this review, we look beyond the biological information coded by DNA and review the epigenetic modifications made to histones, with evidence suggesting a role for their modification in asthma.
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Affiliation(s)
- Courtney D A Kidd
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and
| | - Philip J Thompson
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and.,3 Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Western Australia, Perth, Western Australia, Australia
| | - Lucy Barrett
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and
| | - Svetlana Baltic
- 1 Institute for Respiratory Health, Perth, Western Australia, Australia.,2 Centre for Respiratory Health, School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia; and
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37
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Burg JM, Gonzalez JJ, Maksimchuk KR, McCafferty DG. Lysine-Specific Demethylase 1A (KDM1A/LSD1): Product Recognition and Kinetic Analysis of Full-Length Histones. Biochemistry 2016; 55:1652-62. [PMID: 26673564 DOI: 10.1021/acs.biochem.5b01135] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lysine-specific demethylase 1A (KDM1A/LSD1) is a FAD-dependent enzyme that catalyzes the oxidative demethylation of histone H3K4me1/2 and H3K9me1/2 repressing and activating transcription, respectively. Although the active site is expanded compared to that of members of the greater amine oxidase superfamily, it is too sterically restricted to encompass the minimal 21-mer peptide substrate footprint. The remainder of the substrate/product is therefore expected to extend along the surface of KDM1A. We show that full-length histone H3, which lacks any posttranslational modifications, is a tight-binding, competitive inhibitor of KDM1A demethylation activity with a Ki of 18.9 ± 1.2 nM, a value that is approximately 100-fold higher than that of the 21-mer peptide product. The relative H3 affinity is independent of preincubation time, suggesting that H3 rapidly reaches equilibrium with KDM1A. Jump dilution experiments confirmed the increased binding affinity of full-length H3 was at least partially due to a slow off rate (koff) of 1.2 × 10(-3) s(-1), corresponding to a half-life (t1/2) of 9.63 min, and a residence time (τ) of 13.9 min. Independent affinity capture surface plasmon resonance experiments confirmed the tight-binding nature of the H3/KDM1A interaction, revealing a Kd of 9.02 ± 2.3 nM, a kon of (9.3 ± 1.5) × 10(4) M(-1) s(-1), and a koff of (8.4 ± 0.3) × 10(-4) s(-1). Additionally, no other core histones exhibited inhibition of KDM1A demethylation activity, which is consistent with H3 being the preferred histone substrate of KDM1A versus H2A, H2B, and H4. Together, these data suggest that KDM1A likely contains a histone H3 secondary specificity element on the enzyme surface that contributes significantly to its recognition of substrates and products.
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Affiliation(s)
- Jonathan M Burg
- Department of Chemistry, Duke University , B120 Levine Science Research Center, Box 90317, Durham, North Carolina 27708, United States
| | - Julie J Gonzalez
- Trinity College of Arts & Sciences, Duke University , Durham, North Carolina 27708, United States
| | - Kenneth R Maksimchuk
- Department of Biochemistry, Duke University Medical Center , 255 Nanaline H. Duke, Box 3711, Durham, North Carolina 27710, United States
| | - Dewey G McCafferty
- Department of Chemistry, Duke University , B120 Levine Science Research Center, Box 90317, Durham, North Carolina 27708, United States
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38
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Shanle EK, Tsun IK, Strahl BD. A course-based undergraduate research experience investigating p300 bromodomain mutations. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:68-74. [PMID: 26537758 PMCID: PMC4982466 DOI: 10.1002/bmb.20927] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/15/2015] [Accepted: 09/29/2015] [Indexed: 05/31/2023]
Abstract
Course-based undergraduate research experiences (CUREs) provide an opportunity for students to engage in experiments with outcomes that are unknown to both the instructor and students. These experiences allow students and instructors to collaboratively bridge the research laboratory and classroom, and provide research experiences for a large number of students relative to traditional individual mentored research. Here, we describe a molecular biology CURE investigating the impact of clinically relevant mutations found in the bromodomain of the p300 transcriptional regulator on acetylated histone interaction. In the CURE, students identified missense mutations in the p300 bromodomain using the Catalogue of Somatic Mutations in Cancer (COSMIC) database and hypothesized the effects of the mutation on the acetyl-binding function of the domain. They cloned and purified the mutated bromodomain and performed peptide pulldown assays to define its potential to bind to acetylated histones. Upon completion of the course, students showed increased confidence performing molecular techniques and reported positively on doing a research project in class. In addition, results generated in the classroom were further validated in the research laboratory setting thereby providing a new model for faculty to engage in both course-based and individual undergraduate research experiences.
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Affiliation(s)
- Erin K. Shanle
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Biology, University of North Carolina at Pembroke, Pembroke, North Carolina
| | - Ian K. Tsun
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Brian D. Strahl
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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39
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Reynolds CM, Gray C, Li M, Segovia SA, Vickers MH. Early Life Nutrition and Energy Balance Disorders in Offspring in Later Life. Nutrients 2015; 7:8090-111. [PMID: 26402696 PMCID: PMC4586579 DOI: 10.3390/nu7095384] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/31/2015] [Accepted: 09/11/2015] [Indexed: 02/07/2023] Open
Abstract
The global pandemic of obesity and type 2 diabetes is often causally linked to changes in diet and lifestyle; namely increased intake of calorically dense foods and concomitant reductions in physical activity. Epidemiological studies in humans and controlled animal intervention studies have now shown that nutritional programming in early periods of life is a phenomenon that affects metabolic and physiological functions throughout life. This link is conceptualised as the developmental programming hypothesis whereby environmental influences during critical periods of developmental plasticity can elicit lifelong effects on the health and well-being of the offspring. The mechanisms by which early environmental insults can have long-term effects on offspring remain poorly defined. However there is evidence from intervention studies which indicate altered wiring of the hypothalamic circuits that regulate energy balance and epigenetic effects including altered DNA methylation of key adipokines including leptin. Studies that elucidate the mechanisms behind these associations will have a positive impact on the health of future populations and adopting a life course perspective will allow identification of phenotype and markers of risk earlier, with the possibility of nutritional and other lifestyle interventions that have obvious implications for prevention of non-communicable diseases.
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Affiliation(s)
- Clare M Reynolds
- Liggins Institute and Gravida: National Centre for Growth and Development, University of Auckland, Auckland 1142, New Zealand.
| | - Clint Gray
- Liggins Institute and Gravida: National Centre for Growth and Development, University of Auckland, Auckland 1142, New Zealand.
| | - Minglan Li
- Liggins Institute and Gravida: National Centre for Growth and Development, University of Auckland, Auckland 1142, New Zealand.
| | - Stephanie A Segovia
- Liggins Institute and Gravida: National Centre for Growth and Development, University of Auckland, Auckland 1142, New Zealand.
| | - Mark H Vickers
- Liggins Institute and Gravida: National Centre for Growth and Development, University of Auckland, Auckland 1142, New Zealand.
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40
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Brinkmeier ML, Geister KA, Jones M, Waqas M, Maillard I, Camper SA. The Histone Methyltransferase Gene Absent, Small, or Homeotic Discs-1 Like Is Required for Normal Hox Gene Expression and Fertility in Mice. Biol Reprod 2015; 93:121. [PMID: 26333994 DOI: 10.1095/biolreprod.115.131516] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 09/01/2015] [Indexed: 01/27/2023] Open
Abstract
Chromatin remodeling influences gene expression in developing and adult organisms. Active and repressive marks of histone methylation dictate the embryonic expression boundaries of developmentally regulated genes, including the Hox gene cluster. Drosophila ash1 (absent, small or homeotic discs 1) gene encodes a histone methyltransferase essential for regulation of Hox gene expression that interacts genetically with other members of the trithorax group (TrxG). While mammalian members of the mixed lineage leukemia (Mll) family of TrxG genes have roles in regulation of Hox gene expression, little is known about the expression and function of the mammalian ortholog of the Drosophila ash1 gene, Ash1-like (Ash1l). Here we report the expression of mouse Ash1l gene in specific structures within various organs and provide evidence that reduced Ash1l expression has tissue-specific effects on mammalian development and adult homeostasis. Mutants exhibit partially penetrant postnatal lethality and failure to thrive. Surviving mutants have growth insufficiency, skeletal transformations, and infertility associated with developmental defects in both male and female reproductive organs. Specifically, expression of Hoxa11 and Hoxd10 are altered in the epididymis of Ash1l mutant males and Hoxa10 is reduced in the uterus of Ash1l mutant females. In summary, we show that the histone methyltransferase Ash1l is important for the development and function of several tissues and for proper expression of homeotic genes in mammals.
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Affiliation(s)
| | - Krista A Geister
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan
| | - Morgan Jones
- Graduate Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan
| | - Meriam Waqas
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Ivan Maillard
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan Life Sciences Institute, University of Michigan, Ann Arbor, Michigan
| | - Sally A Camper
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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41
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Kimura H, Hayashi-Takanaka Y, Stasevich TJ, Sato Y. Visualizing posttranslational and epigenetic modifications of endogenous proteins in vivo. Histochem Cell Biol 2015; 144:101-9. [PMID: 26138929 PMCID: PMC4522274 DOI: 10.1007/s00418-015-1344-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2015] [Indexed: 01/29/2023]
Abstract
Protein localization and dynamics can now be visualized in living cells using the fluorescent protein fusion technique, but it is still difficult to selectively detect molecules with a specific function. As a posttranslational protein modification is often associated with a specific function, marking specifically modified protein molecules in living cells is a way to track an important fraction of protein. In the nucleus, histones are subjected to a variety of modifications such as acetylation and methylation that are associated with epigenetic gene regulation. RNA polymerase II, an enzyme that transcribes genes, is also differentially phosphorylated during the initiation and elongation of transcription. To understand the mechanism of gene regulation in vivo, we have developed methods to track histone and RNA polymerase II modifications using probes derived from modification-specific monoclonal antibodies. In Fab-based live endogenous modification labeling (FabLEM), fluorescently labeled antigen-binding fragments (Fabs) are loaded into cells. Fabs bind to target modifications in the nucleus with a binding time of a second to tens of seconds, and so the modification can be tracked without disturbing cell function. For tracking over longer periods of time or in living animals, we have also developed a genetically encoded system to express a modification-specific intracellular antibody (mintbody). Transgenic fruit fly and zebrafish that express histone H3 Lys9 acetylation-specific mintbody developed normally and remain fertile, suggesting that visualizing histone modifications in any tissue in live animals has become possible. These live cell modification tracking techniques will facilitate future studies on epigenetic regulation related to development, differentiation, and disease. Moreover, these techniques can be applied to any other protein modification, opening up new avenues in broad areas in biology and medicine.
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Affiliation(s)
- Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan,
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42
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Yao S, He Z, Chen C. CRISPR/Cas9-Mediated Genome Editing of Epigenetic Factors for Cancer Therapy. Hum Gene Ther 2015; 26:463-71. [PMID: 26075804 DOI: 10.1089/hum.2015.067] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Shaohua Yao
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University , Chengdu, China
| | - Zhiyao He
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University , Chengdu, China
| | - Chong Chen
- State Key Laboratory of Biotherapy/Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University , Chengdu, China
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43
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KRAS and CREBBP mutations: a relapse-linked malicious liaison in childhood high hyperdiploid acute lymphoblastic leukemia. Leukemia 2015; 29:1656-67. [PMID: 25917266 PMCID: PMC4530204 DOI: 10.1038/leu.2015.107] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/16/2015] [Indexed: 12/24/2022]
Abstract
High hyperdiploidy defines the largest genetic entity of childhood acute lymphoblastic leukemia (ALL). Despite its relatively low recurrence risk, this subgroup generates a high proportion of relapses. The cause and origin of these relapses remains obscure. We therefore explored the mutational landscape in high hyperdiploid (HD) ALL with whole-exome (n=19) and subsequent targeted deep sequencing of 60 genes in 100 relapsing and 51 non-relapsing cases. We identified multiple clones at diagnosis that were primarily defined by a variety of mutations in receptor tyrosine kinase (RTK)/Ras pathway and chromatin-modifying genes. The relapse clones consisted of reappearing as well as new mutations, and overall contained more mutations. Although RTK/Ras pathway mutations were similarly frequent between diagnosis and relapse, both intergenic and intragenic heterogeneity was essentially lost at relapse. CREBBP mutations, however, increased from initially 18–30% at relapse, then commonly co-occurred with KRAS mutations (P<0.001) and these relapses appeared primarily early (P=0.012). Our results confirm the exceptional susceptibility of HD ALL to RTK/Ras pathway and CREBBP mutations, but, more importantly, suggest that mutant KRAS and CREBBP might cooperate and equip cells with the necessary capacity to evolve into a relapse-generating clone.
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44
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Chango A, Pogribny IP. Considering maternal dietary modulators for epigenetic regulation and programming of the fetal epigenome. Nutrients 2015; 7:2748-70. [PMID: 25875118 PMCID: PMC4425171 DOI: 10.3390/nu7042748] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/16/2015] [Accepted: 03/19/2015] [Indexed: 12/21/2022] Open
Abstract
Fetal life is characterized by a tremendous plasticity and ability to respond to various environmental and lifestyle factors, including maternal nutrition. Identification of the role of dietary factors that can modulate and reshape the cellular epigenome during development, including methyl group donors (e.g., folate, choline) and bioactive compounds (e.g., polyphenols) is of great importance; however, there is insufficient knowledge of a particular effect of each type of modulator and/or their combination on fetal life. To enhance the quality and safety of food products for proper fetal health and disease prevention in later life, a better understanding of the underlying mechanisms of dietary epigenetic modulators during the critical prenatal period is necessary. This review focuses on the influence of maternal dietary components on DNA methylation, histone modification, and microRNAs, and summarizes current knowledge of the effect and importance of dietary components on epigenetic mechanisms that control the proper expression of genetic information. Evidence reveals that some components in the maternal diet can directly or indirectly affect epigenetic mechanisms. Understanding the underlying mechanisms of how early-life nutritional environment affects the epigenome during development is of great importance for the successful prevention of adult chronic diseases through optimal maternal nutrition.
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Affiliation(s)
- Abalo Chango
- Polytechnic Institute LaSalle Beauvais, Department of Nutrition and Health Sciences, EGEAL UP:2012.10.101, F-60026 Beauvais Cedex, France.
| | - Igor P Pogribny
- Division of Biochemical Toxicology, Food and Drug Administration National Center for Toxicological Research, Jefferson, AR 72079, USA.
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45
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Huang B, Li G, Jiang XH. Fate determination in mesenchymal stem cells: a perspective from histone-modifying enzymes. Stem Cell Res Ther 2015; 6:35. [PMID: 25890062 PMCID: PMC4365520 DOI: 10.1186/s13287-015-0018-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mesenchymal stem cells (MSCs) hold great promise for therapeutic use in regenerative medicine and tissue engineering. A detailed understanding of the molecular processes governing MSC fate determination will be instrumental in the application of MSCs. Much progress has been made in recent years in defining the epigenetic events that control the differentiation of MSCs into different lineages. A complex network of transcription factors and histone modifiers, in concert with specific transcriptional co-activators and co-repressors, activates or represses MSC differentiation. In this review, we summarize recent progress in determining the effects of histone-modifying enzymes on the multilineage differentiation of MSCs. In addition, we propose that the manipulation of histone signatures associated with lineage-specific differentiation by small molecules has immense potential for the advancement of MSC-based regenerative medicine.
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Affiliation(s)
- Biao Huang
- Key Laboratory for Regenerative Medicine, Ministry of Education, Epithelial Cell Biology Research Centre, School of Biomedical Sciences, Lo Kwee-Seong Integrated Biomedical Sciences Building, Shatin, New Territories, Hong Kong, PR China.
| | - Gang Li
- Department of Orthopaedics & Traumatology, Li Ka Shing Institute of Health Science, Prince of Wales Hospital, 30-32 Ngan Shing Street, Shatin, New Territories, Hong Kong, PR China. .,Lui Che Woo Institute of Innovative Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China. .,School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
| | - Xiao Hua Jiang
- Key Laboratory for Regenerative Medicine, Ministry of Education, Epithelial Cell Biology Research Centre, School of Biomedical Sciences, Lo Kwee-Seong Integrated Biomedical Sciences Building, Shatin, New Territories, Hong Kong, PR China. .,Lui Che Woo Institute of Innovative Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China. .,School of Biomedical Sciences Core Laboratory, The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
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46
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Yang Y, Tang Q, Zhao M, Liang G, Wu H, Li D, Xie Y, Tan Y, Dai Y, Yung S, Chan TM, Lu Q. The effect of mycophenolic acid on epigenetic modifications in lupus CD4+T cells. Clin Immunol 2015; 158:67-76. [PMID: 25791245 DOI: 10.1016/j.clim.2015.03.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 01/26/2015] [Accepted: 03/09/2015] [Indexed: 12/17/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex systemic autoimmune disease involving multiple organs and characterized by overproduction of autoantibodies and T and B cell abnormalities. The treatment for SLE has been restricted to immunosuppressants and corticosteroids. Mycophenolate mofetil (MMF), as a relatively new immunosuppressant, is now widely used in the treatment of SLE patients, particularly those with nephritis. However, it is unclear whether mycophenolic acid (MPA) could modulate the reported disorders of epigenetic status in CD4(+)T cells from SLE patients. In this study, we demonstrated that MPA can upregulate the histone H3/H4 global acetylation status by regulating HATs and HDACs in lupus CD4(+)T cells. Furthermore, we found that MPA also affected the histone H4 acetylation and histone H3K4 tri-methylation levels in CD40L promoter region that inhibited the expression of CD40L. These findings indicate the potential epigenetic mechanism of therapeutic effects of MPA in SLE.
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Affiliation(s)
- Yang Yang
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Tang
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Gongping Liang
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Haijing Wu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Duo Li
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yubing Xie
- Changsha Blood Center, Changsha, Hunan, China
| | - Yixin Tan
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yong Dai
- Clinical Medical Research Center, the Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Susan Yung
- Division of Nephrology, Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Tak Mao Chan
- Division of Nephrology, Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
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47
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Farria A, Li W, Dent SYR. KATs in cancer: functions and therapies. Oncogene 2015; 34:4901-13. [PMID: 25659580 PMCID: PMC4530097 DOI: 10.1038/onc.2014.453] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/25/2014] [Accepted: 11/25/2014] [Indexed: 12/12/2022]
Abstract
Post-translational acetylation of lysines is most extensively studied in histones, but this modification is also found in many other proteins and is implicated in a wide range of biological processes in both the cell nucleus and the cytoplasm. Like phosphorylation, acetylation patterns and levels are often altered in cancer, therefore small molecule inhibition of enzymes that regulate acetylation and deacetylation offers much potential for inhibiting cancer cell growth, as does disruption of interactions between acetylated residues and ‘reader’ proteins. For more than a decade now, histone deacetylase (HDAC) inhibitors have been investigated for their ability to increase acetylation and promote expression of tumor suppressor genes. However, emerging evidence suggests that acetylation can also promote cancer, in part by enhancing the functions of oncogenic transcription factors. In this review we focus on how acetylation of both histone and non-histone proteins may drive cancer, and we will discuss the implications of such changes on how patients are assigned to therapeutic agents. Finally, we will explore what the future holds in the design of small molecule inhibitors for modulation of levels or functions of acetylation states.
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Affiliation(s)
- A Farria
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, Graduate School of Biomedical Sciences, University of Texas M.D Anderson Cancer Center Science Park, Smithville, Texas, USA
| | - W Li
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, Graduate School of Biomedical Sciences, University of Texas M.D Anderson Cancer Center Science Park, Smithville, Texas, USA
| | - S Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, Graduate School of Biomedical Sciences, University of Texas M.D Anderson Cancer Center Science Park, Smithville, Texas, USA
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48
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Eid W, Opitz L, Biason-Lauber A. Genome-wide identification of CBX2 targets: insights in the human sex development network. Mol Endocrinol 2015; 29:247-57. [PMID: 25569159 DOI: 10.1210/me.2014-1339] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chromobox homolog 2 (CBX2) is a chromatin modifier that plays an important role in sexual development and its disorders (disorders of sex development [DSD]), yet the exact rank and function of human CBX2 in this pathway remains unclear. Here, we performed large-scale mapping and analysis of in vivo target loci of the protein CBX2 in Sertoli-like NT-2D1 cells, using the DNA adenine methyltransferase identification technique. We identified close to 1600 direct targets for CBX2. Intriguingly, validation of selected candidate genes using qRT-PCR in cells overexpressing CBX2 or in which CBX2 has been knocked down indicated that several CBX2-responsive genes encode proteins that are involved in DSD. We further validated these effects on the candidate genes using a mutated CBX2 causing DSD in human patient. Overall, our findings suggest that CBX2 role in the sex development cascade is to stimulate the male pathway and concurrently inhibit the female pathway. These data provide fundamental insights into potential etiology of DSD.
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Affiliation(s)
- Wassim Eid
- Division of Endocrinology (W.E., A.B.-L.), Department of Medicine, University of Fribourg, 1700 Fribourg, Switzerland; and Functional Genomics Center Zurich (L.O.), University of Zurich/ETHZ, 8057 Zurich, Switzerland
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49
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Gordon JAR, Montecino MA, Aqeilan RI, Stein JL, Stein GS, Lian JB. Epigenetic pathways regulating bone homeostasis: potential targeting for intervention of skeletal disorders. Curr Osteoporos Rep 2014; 12:496-506. [PMID: 25260661 PMCID: PMC4216616 DOI: 10.1007/s11914-014-0240-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic regulation utilizes different mechanisms to convey heritable traits to progeny cells that are independent of DNA sequence, including DNA silencing, post-translational modifications of histone proteins, and the post-transcriptional modulation of RNA transcript levels by non-coding RNAs. Although long non-coding RNAs have recently emerged as important regulators of gene imprinting, their functions during osteogenesis are as yet unexplored. In contrast, microRNAs (miRNAs) are well characterized for their control of osteogenic and osteoclastic pathways; thus, further defining how gene regulatory networks essential for skeleton functions are coordinated and finely tuned through the activities of miRNAs. Roles of miRNAs are constantly expanding as new studies uncover associations with skeletal disorders. The distinct functions of epigenetic regulators and evidence for integrating their activities to control normal bone gene expression and bone disease will be presented. In addition, potential for using "signature miRNAs" to identify, manage, and therapeutically treat osteosarcoma will be discussed in this review.
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Affiliation(s)
- Jonathan A. R. Gordon
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Martin A. Montecino
- Centro de Investigaciones Biomedicas and FONDAP Center for Genome Regulation, Universidad Andres Bello, Avenida Republica 239, Santiago, Chile
| | - Rami I. Aqeilan
- Lautenberg Center for Immunology and Cancer Research-IMRIC, Hebrew University-Hadassah Medical School, PO Box 12272, Ein Karem Campus, Jerusalem 91120, Israel
| | - Janet L. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Gary S. Stein
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
| | - Jane B. Lian
- Department of Biochemistry and Vermont Cancer Center, University of Vermont College of Medicine, 89 Beaumont Avenue, Burlington, VT, USA
- Corresponding Author: Jane B. Lian – P: 802-656-4872, F: 802-656-8216,
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50
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HSP90 regulates DNA repair via the interaction between XRCC1 and DNA polymerase β. Nat Commun 2014; 5:5513. [PMID: 25423885 PMCID: PMC4246423 DOI: 10.1038/ncomms6513] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 10/07/2014] [Indexed: 02/06/2023] Open
Abstract
Cellular DNA repair processes are crucial to maintain genome stability and integrity. In DNA base excision repair, a tight heterodimer complex formed by DNA polymerase β (Polβ) and XRCC1 is thought to facilitate repair by recruiting Polβ to DNA damage sites. Here we show that disruption of the complex does not impact DNA damage response or DNA repair. Instead, the heterodimer formation is required to prevent ubiquitylation and degradation of Polβ. In contrast, the stability of the XRCC1 monomer is protected from CHIP-mediated ubiquitylation by interaction with the binding partner HSP90. In response to cellular proliferation and DNA damage, proteasome and HSP90-mediated regulation of Polβ and XRCC1 alters the DNA repair complex architecture. We propose that protein stability, mediated by DNA repair protein complex formation, functions as a regulatory mechanism for DNA repair pathway choice in the context of cell cycle progression and genome surveillance.
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