1
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Kalra P, Zahid H, Ayoub A, Dou Y, Pomerantz WCK. Alternative Mechanisms for DNA Engagement by BET Bromodomain-Containing Proteins. Biochemistry 2022; 61:1260-1272. [PMID: 35748495 PMCID: PMC9682295 DOI: 10.1021/acs.biochem.2c00157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Epigenetic reader domains regulate chromatin structure and modulate gene expression through the recognition of post-translational modifications on histones. Recently, reader domains have also been found to harbor double-stranded (ds) DNA-binding activity, which is as functionally critical as histone association. Here, we explore the dsDNA recognition of the N-terminal bromodomain of the bromodomain and extra-terminal (BET) protein, BRD4. Using protein-observed 19F NMR, 1H-15N HSQC NMR, electrophoretic mobility shift assays (EMSA), and competitive-inhibition assays, we establish the binding surface of dsDNA and find it to be largely overlapping with the acetylated histone (KAc)-binding site. Rather than engaging in electrostatic contacts, we find dsDNA to interact competitively within the KAc-binding pocket. These interactions are distinct from the highly homologous BET bromodomain, BRDT. Nine additional bromodomains have also been characterized for interacting with dsDNA, including tandem BET bromodomains. Together, these studies help establish a binding model for dsDNA interactions with BRD4 bromodomains and elucidate the chromatin-recognition mechanisms of the BRD4 protein for regulating gene expression.
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Affiliation(s)
- Prakriti Kalra
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Huda Zahid
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Alex Ayoub
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yali Dou
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California 90089, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Neuhaus D. Zinc finger structure determination by NMR: Why zinc fingers can be a handful. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 130-131:62-105. [PMID: 36113918 PMCID: PMC7614390 DOI: 10.1016/j.pnmrs.2022.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/09/2022] [Accepted: 07/10/2022] [Indexed: 06/07/2023]
Abstract
Zinc fingers can be loosely defined as protein domains containing one or more tetrahedrally-co-ordinated zinc ions whose role is to stabilise the structure rather than to be involved in enzymatic chemistry; such zinc ions are often referred to as "structural zincs". Although structural zincs can occur in proteins of any size, they assume particular significance for very small protein domains, where they are often essential for maintaining a folded state. Such small structures, that sometimes have only marginal stability, can present particular difficulties in terms of sample preparation, handling and structure determination, and early on they gained a reputation for being resistant to crystallisation. As a result, NMR has played a more prominent role in structural studies of zinc finger proteins than it has for many other types of proteins. This review will present an overview of the particular issues that arise for structure determination of zinc fingers by NMR, and ways in which these may be addressed.
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Affiliation(s)
- David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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3
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Li J, Bergmann L, Rafael de Almeida A, Webb KM, Gogol M, Voigt P, Liu Y, Liang H, Smolle M. H3K36 methylation and DNA-binding both promote Ioc4 recruitment and Isw1b remodeler function. Nucleic Acids Res 2022; 50:2549-2565. [PMID: 35188579 PMCID: PMC8934638 DOI: 10.1093/nar/gkac077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 01/20/2022] [Accepted: 02/15/2022] [Indexed: 11/23/2022] Open
Abstract
The Isw1b chromatin-remodeling complex is specifically recruited to gene bodies to help retain pre-existing histones during transcription by RNA polymerase II. Recruitment is dependent on H3K36 methylation and the Isw1b subunit Ioc4, which contains an N-terminal PWWP domain. Here, we present the crystal structure of the Ioc4-PWWP domain, including a detailed functional characterization of the domain on its own as well as in the context of full-length Ioc4 and the Isw1b remodeler. The Ioc4-PWWP domain preferentially binds H3K36me3-containing nucleosomes. Its ability to bind DNA is required for nucleosome binding. It is also furthered by the unique insertion motif present in Ioc4-PWWP. The ability to bind H3K36me3 and DNA promotes the interaction of full-length Ioc4 with nucleosomes in vitro and they are necessary for its recruitment to gene bodies in vivo. Furthermore, a fully functional Ioc4-PWWP domain promotes efficient remodeling by Isw1b and the maintenance of ordered chromatin in vivo, thereby preventing the production of non-coding RNAs.
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Affiliation(s)
- Jian Li
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Lena Bergmann
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Andreia Rafael de Almeida
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
| | - Kimberly M Webb
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Madelaine M Gogol
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO 64110, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Yingfang Liu
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- School of Medicine, Sun Yat-Sen University, Guangzhou 510275, China
| | - Huanhuan Liang
- State Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
- Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510275, China
| | - Michaela M Smolle
- Physiological Chemistry, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
- BioPhysics Core Facility, Biomedical Center, Medical Faculty, Ludwig-Maximilian-University Munich, Grosshaderner Str. 9, 82152 Martinsried-Planegg, Germany
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4
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Mechanistic similarities in recognition of histone tails and DNA by epigenetic readers. Curr Opin Struct Biol 2021; 71:1-6. [PMID: 33993059 DOI: 10.1016/j.sbi.2021.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/03/2021] [Accepted: 04/08/2021] [Indexed: 11/21/2022]
Abstract
The past two decades have witnessed rapid advances in the identification and characterization of epigenetic readers, capable of recognizing or reading post-translational modifications in histones. More recently, a new set of readers with the ability to interact with the nucleosome through concomitant binding to histones and DNA has emerged. In this review, we discuss mechanistic insights underlying bivalent histone and DNA recognition by newly characterized readers and highlight the importance of binding to DNA for their association with chromatin.
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5
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Iyer H, Wahul AB, P K A, Sawant BS, Kumar A. A BRD's (BiRD's) eye view of BET and BRPF bromodomains in neurological diseases. Rev Neurosci 2021; 32:403-426. [PMID: 33661583 DOI: 10.1515/revneuro-2020-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/11/2020] [Indexed: 01/18/2023]
Abstract
Neurological disorders (NLDs) are among the top leading causes for disability worldwide. Dramatic changes in the epigenetic topography of the brain and nervous system have been found in many NLDs. Histone lysine acetylation has prevailed as one of the well characterised epigenetic modifications in these diseases. Two instrumental components of the acetylation machinery are the evolutionarily conserved Bromodomain and PHD finger containing (BRPF) and Bromo and Extra terminal domain (BET) family of proteins, also referred to as acetylation 'readers'. Several reasons, including their distinct mechanisms of modulation of gene expression and their property of being highly tractable small molecule targets, have increased their translational relevance. Thus, compounds which demonstrated promising results in targeting these proteins have advanced to clinical trials. They have been established as key role players in pathologies of cancer, cardiac diseases, renal diseases and rheumatic diseases. In addition, studies implicating the role of these bromodomains in NLDs are gaining pace. In this review, we highlight the findings of these studies, and reason for the plausible roles of all BET and BRPF members in NLDs. A comprehensive understanding of their multifaceted functions would be radical in the development of therapeutic interventions.
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Affiliation(s)
- Harish Iyer
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
| | - Abhipradnya B Wahul
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
| | - Annapoorna P K
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Bharvi S Sawant
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
| | - Arvind Kumar
- Epigenetics and Neuropsychiatric Disorders' Laboratory, CSIR - Centre for Cellular and Molecular Biology (CCMB), Hyderabad500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
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6
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Kirtana R, Manna S, Patra SK. Molecular mechanisms of KDM5A in cellular functions: Facets during development and disease. Exp Cell Res 2020; 396:112314. [PMID: 33010254 DOI: 10.1016/j.yexcr.2020.112314] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 12/12/2022]
Abstract
Gene expression is influenced at many layers by a fine-tuned crosstalk between multiple extrinsic signalling pathways and intrinsic regulatory molecules that respond to environmental stimuli. Epigenetic modifiers like DNA methyltransferases, histone modifying enzymes and chromatin remodellers are reported to act as triggering factors in many scenarios by exhibiting their control over most of the cellular processes. These epigenetic players can either directly regulate gene expression or interact with some effector molecules that harmonize the expression of downstream genes. One such epigenetic regulator which exhibits multifaceted regulation over gene expression is KDM5A. It is classically a transcriptional repressor acting as H3K4me3 demethylase, but also is reported to act as an activator in many contexts either by loss of activity due to inhibition manifested by other interacting proteins or by downregulating the negative players of a given physiological process thereby escalating the framework. Through this review, we draw attention to the remarkable modes of functioning laid by KDM5A on transcriptional and translational processes, affecting gene expression during differentiation and development and finally summing up on role in disease causation (Fig. 1). We also shed light on different orthologs of KDM5A and their organism specific roles, along with comparison of the sequence similarity to extrapolate some unanswered questions about this protein.
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Affiliation(s)
- R Kirtana
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Soumen Manna
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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7
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Soshnikova NV, Sheynov AA, Tatarskiy EV, Georgieva SG. The DPF Domain As a Unique Structural Unit Participating in Transcriptional Activation, Cell Differentiation, and Malignant Transformation. Acta Naturae 2020; 12:57-65. [PMID: 33456978 PMCID: PMC7800603 DOI: 10.32607/actanaturae.11092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022] Open
Abstract
The DPF (double PHD finger) domain consists of two PHD fingers organized in tandem. The two PHD-finger domains within a DPF form a single structure that interacts with the modification of the N-terminal histone fragment in a way different from that for single PHD fingers. Several histone modifications interacting with the DPF domain have already been identified. They include acetylation of H3K14 and H3K9, as well as crotonylation of H3K14. These modifications are found predominantly in transcriptionally active chromatin. Proteins containing DPF belong to two classes of protein complexes, which are the transcriptional coactivators involved in the regulation of the chromatin structure. These are the histone acetyltransferase complex belonging to the MYST family and the SWI/SNF chromatin-remodeling complex. The DPF domain is responsible for the specificity of the interactions between these complexes and chromatin. Proteins containing DPF play a crucial role in the activation of the transcription of a number of genes expressed during the development of an organism. These genes are important in the differentiation and malignant transformation of mammalian cells.
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Affiliation(s)
- N. V. Soshnikova
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
| | - A. A. Sheynov
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
| | - Eu. V. Tatarskiy
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
| | - S. G. Georgieva
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
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8
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Kane M, Mele V, Liberatore RA, Bieniasz PD. Inhibition of spumavirus gene expression by PHF11. PLoS Pathog 2020; 16:e1008644. [PMID: 32678836 PMCID: PMC7390438 DOI: 10.1371/journal.ppat.1008644] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 07/29/2020] [Accepted: 05/19/2020] [Indexed: 01/05/2023] Open
Abstract
The foamy viruses (FV) or spumaviruses are an ancient subfamily of retroviruses that infect a variety of vertebrates. FVs are endemic, but apparently apathogenic, in modern non-human primates. Like other retroviruses, FV replication is inhibited by type-I interferon (IFN). In a previously described screen of IFN-stimulated genes (ISGs), we identified the macaque PHD finger domain protein-11 (PHF11) as an inhibitor of prototype foamy virus (PFV) replication. Here, we show that human and macaque PHF11 inhibit the replication of multiple spumaviruses, but are inactive against several orthoretroviruses. Analysis of other mammalian PHF11 proteins revealed that antiviral activity is host species dependent. Using multiple reporter viruses and cell lines, we determined that PHF11 specifically inhibits a step in the replication cycle that is unique to FVs, namely basal transcription from the FV internal promoter (IP). In so doing, PHF11 prevents expression of the viral transactivator Tas and subsequent activation of the viral LTR promoter. These studies reveal a previously unreported inhibitory mechanism in mammalian cells, that targets a family of ancient viruses and may promote viral latency.
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Affiliation(s)
- Melissa Kane
- Department of Pediatrics, Infectious Diseases Division, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Microbial Pathogenesis, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Vincent Mele
- Department of Pediatrics, Infectious Diseases Division, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Microbial Pathogenesis, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Rachel A. Liberatore
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
| | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, United States of America
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9
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Naseer MI, Abdulkareem AA, Guzmán-Vega FJ, Arold ST, Pushparaj PN, Chaudhary AG, AlQahtani MH. Novel Missense Variant in Heterozygous State in the BRPF1 Gene Leading to Intellectual Developmental Disorder With Dysmorphic Facies and Ptosis. Front Genet 2020; 11:368. [PMID: 32457794 PMCID: PMC7221184 DOI: 10.3389/fgene.2020.00368] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/25/2020] [Indexed: 12/15/2022] Open
Abstract
Intellectual developmental disorder with dysmorphic facies and ptosis is an autosomal dominant condition characterized by delayed psychomotor development, intellectual disability, delayed speech, and dysmorphic facial features, mostly ptosis. Heterozygous mutations in bromodomain and plant homeodomain (PHD) finger containing one (BRPF1) gene have been reported. In this study, whole exome sequencing (WES) was performed as a molecular diagnostic test. Bioinformatics of WES data and candidate gene prioritization identified a novel variant in heterozygous state in the exon 3 of BRPF1 gene (ENST383829: c.1054G > C and p.Val352Leu). Autosomal dominant inheritance in the family affected individuals and exclusion of non-pathogenicity in the ethnically matched healthy controls (n = 100) were performed by Sanger sequencing. To the best of our knowledge, this is the first evidence of BRPF1 variant in a Saudi family. Whole exome sequencing analysis has been proven as a valuable tool in the molecular diagnostics. Our findings further expand the role of WES in efficient disease diagnosis in Arab families and explained that the mutation in BRPF1 gene plays an important role for the development of IDDFP syndrome.
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Affiliation(s)
- Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Francisco J Guzmán-Vega
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Stefan T Arold
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Peter Natesan Pushparaj
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Adeel G Chaudhary
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Center for Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad H AlQahtani
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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10
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Zhang Z, Sun D, Chen F. Comparative transcriptome analysis revealing the mechanisms underlying light-induced total fatty acid and carotenoid accumulation in Crypthecodinium sp. SUN. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Weaver TM, Morrison EA, Musselman CA. Reading More than Histones: The Prevalence of Nucleic Acid Binding among Reader Domains. Molecules 2018; 23:molecules23102614. [PMID: 30322003 PMCID: PMC6222470 DOI: 10.3390/molecules23102614] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/02/2018] [Accepted: 10/07/2018] [Indexed: 01/09/2023] Open
Abstract
The eukaryotic genome is packaged into the cell nucleus in the form of chromatin, a complex of genomic DNA and histone proteins. Chromatin structure regulation is critical for all DNA templated processes and involves, among many things, extensive post-translational modification of the histone proteins. These modifications can be “read out” by histone binding subdomains known as histone reader domains. A large number of reader domains have been identified and found to selectively recognize an array of histone post-translational modifications in order to target, retain, or regulate chromatin-modifying and remodeling complexes at their substrates. Interestingly, an increasing number of these histone reader domains are being identified as also harboring nucleic acid binding activity. In this review, we present a summary of the histone reader domains currently known to bind nucleic acids, with a focus on the molecular mechanisms of binding and the interplay between DNA and histone recognition. Additionally, we highlight the functional implications of nucleic acid binding in chromatin association and regulation. We propose that nucleic acid binding is as functionally important as histone binding, and that a significant portion of the as yet untested reader domains will emerge to have nucleic acid binding capabilities.
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Affiliation(s)
- Tyler M Weaver
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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12
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Du Z, Li J. Expression, purification and molecular characterization of a novel transcription factor KcCBF3 from Kandelia candel. Protein Expr Purif 2018; 153:26-34. [PMID: 30118861 DOI: 10.1016/j.pep.2018.08.006] [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: 02/26/2018] [Revised: 08/06/2018] [Accepted: 08/13/2018] [Indexed: 11/28/2022]
Abstract
Kandelia candel, a major species of mangrove in the tropical and subtropical area, is susceptible to low temperature in winter. K. candel was introduced into Zhejiang Province (the northern margin of South China) several decades ago, and suffered from low temperature causing growth retardation, in server cases, even death. To explore the molecular mechanisms of cold acclimation in K. candel, a novel C-repeat binding factor gene KcCBF3 (Genbank accession no. KF111715) of 729 bp open reading frame (ORF) encoding a protein of 242 amino acid residues was isolated, expressed, purified and characterized. Multiple sequence alignment analysis revealed that KcCBF3 contained a highly conserved AP2/EREBP DNA-binding domain which consisting of 79 amino acid residues, as well as two CBF signature sequences. Phylogenetic analysis indicated that KcCBF3 belonged to the A-1 subgroup of DREB subfamily based on the classification of AP2/EREBP transcription factors in Arabidopsis. Semi-quantitative RT-PCR showed that KcCBF3 transcripts were highly accumulated in roots and leaves, and could be induced by low temperature. Electrophoresis mobility shift assay (EMSA) demonstrated KcCBF3 could bind to the core sequence (CCGAC) of cis-acting element C-repeat (CRT)/dehydration-responsive element (DRE) in vitro. These results implied that KcCBF3 might participate in the adaptation of K. candel to low-temperature stress by binding to CRT/DRE element.
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Affiliation(s)
- Zhaokui Du
- Zhejiang Provincial Key Laboratory of Plant Evolutionary and Conservation, Taizhou University, Taizhou, Zhejiang, 318000, PR China; Institute of Ecology, Taizhou University, Taizhou, Zhejiang, 318000, PR China
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary and Conservation, Taizhou University, Taizhou, Zhejiang, 318000, PR China; Institute of Ecology, Taizhou University, Taizhou, Zhejiang, 318000, PR China.
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13
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Morellet N, Li X, Wieninger SA, Taylor JL, Bischerour J, Moriau S, Lescop E, Bardiaux B, Mathy N, Assrir N, Bétermier M, Nilges M, Hickman AB, Dyda F, Craig NL, Guittet E. Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase. Nucleic Acids Res 2018; 46:2660-2677. [PMID: 29385532 PMCID: PMC5861402 DOI: 10.1093/nar/gky044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 01/12/2018] [Accepted: 01/17/2018] [Indexed: 12/16/2022] Open
Abstract
The piggyBac transposase (PB) is distinguished by its activity and utility in genome engineering, especially in humans where it has highly promising therapeutic potential. Little is known, however, about the structure-function relationships of the different domains of PB. Here, we demonstrate in vitro and in vivo that its C-terminal Cysteine-Rich Domain (CRD) is essential for DNA breakage, joining and transposition and that it binds to specific DNA sequences in the left and right transposon ends, and to an additional unexpectedly internal site at the left end. Using NMR, we show that the CRD adopts the specific fold of the cross-brace zinc finger protein family. We determine the interaction interfaces between the CRD and its target, the 5'-TGCGT-3'/3'-ACGCA-5' motifs found in the left, left internal and right transposon ends, and use NMR results to propose docking models for the complex, which are consistent with our site-directed mutagenesis data. Our results provide support for a model of the PB/DNA interactions in the context of the transpososome, which will be useful for the rational design of PB mutants with increased activity.
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Affiliation(s)
- Nelly Morellet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Xianghong Li
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Silke A Wieninger
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Jennifer L Taylor
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Julien Bischerour
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Séverine Moriau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Benjamin Bardiaux
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Nathalie Mathy
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Nadine Assrir
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Mireille Bétermier
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
| | - Michael Nilges
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Alison B Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy L Craig
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Eric Guittet
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198 Gif sur Yvette cedex, France
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14
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Cai QQ, Dong YW, Qi B, Shao XT, Wang R, Chen ZY, He BM, Wu XZ. BRD1-Mediated Acetylation Promotes Integrin αV Gene Expression Via Interaction with Sulfatide. Mol Cancer Res 2018; 16:610-622. [PMID: 29453316 DOI: 10.1158/1541-7786.mcr-17-0527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/16/2017] [Accepted: 01/26/2018] [Indexed: 11/16/2022]
Abstract
Integrin αV gene expression is often dysregulated in cancers especially in hepatocellular carcinoma (HCC); however, the mechanism of regulation is poorly understood. Here, it is demonstrated that sulfatide activated integrin αV gene transcription, through histone H3K9/14 acetylation at the promoter, and high integrin αV expression are closely associated with poor prognosis. To elucidate the mechanism of regulation of acetylation, sulfatide-bound proteins were screened by mass spectrometry (MS), and bromodomain containing protein 1 (BRD1) was identified as an interacting protein that also colocalized with sulfatide in HCC cells. BRD1 was also formed a complex with Sp1, which was recruited to the integrin αV gene promoter. Sulfatide was also found to induce BRD1, monocytic leukemia zinc finger (MOZ) and histone acetyltransferase binding to ORC1 (HBO1) acetyltransferase multiprotein complex recruitment to the integrin αV promoter, which is responsible for histone H3K9/14 acetylation. Finally, knockdown of BRD1 limited sulfatide-induced H3K9/14 acetylation and occupancy of MOZ or HBO1 on integrin αV gene promoter.Implications: This study demonstrates that sulfatide interaction with BRD1 mediates acetylation and is important for regulation of integrin αV gene expression. Mol Cancer Res; 16(4); 610-22. ©2018 AACR.
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Affiliation(s)
- Qian Qian Cai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Key Lab of Glycoconjugate Research, Ministry of Public Health, Shanghai, China
| | - Yi Wei Dong
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Key Lab of Glycoconjugate Research, Ministry of Public Health, Shanghai, China
| | - Bing Qi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Key Lab of Glycoconjugate Research, Ministry of Public Health, Shanghai, China
| | - Xiao-Ting Shao
- Yu Ying Hospital, Wenzhou Medical University, Wenzhou, China
| | - Rong Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Key Lab of Glycoconjugate Research, Ministry of Public Health, Shanghai, China
| | - Zhong Yi Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Key Lab of Glycoconjugate Research, Ministry of Public Health, Shanghai, China
| | - Bao Mei He
- Yu Ying Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xing Zhong Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Key Lab of Glycoconjugate Research, Ministry of Public Health, Shanghai, China.
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15
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Non-canonical reader modules of BAZ1A promote recovery from DNA damage. Nat Commun 2017; 8:862. [PMID: 29021563 PMCID: PMC5636791 DOI: 10.1038/s41467-017-00866-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 07/27/2017] [Indexed: 01/08/2023] Open
Abstract
Members of the ISWI family of chromatin remodelers mobilize nucleosomes to control DNA accessibility and, in some cases, are required for recovery from DNA damage. However, it remains poorly understood how the non-catalytic ISWI subunits BAZ1A and BAZ1B might contact chromatin to direct the ATPase SMARCA5. Here, we find that the plant homeodomain of BAZ1A, but not that of BAZ1B, has the unusual function of binding DNA. Furthermore, the BAZ1A bromodomain has a non-canonical gatekeeper residue and binds relatively weakly to acetylated histone peptides. Using CRISPR-Cas9-mediated genome editing we find that BAZ1A and BAZ1B each recruit SMARCA5 to sites of damaged chromatin and promote survival. Genetic engineering of structure-designed bromodomain and plant homeodomain mutants reveals that reader modules of BAZ1A and BAZ1B, even when non-standard, are critical for DNA damage recovery in part by regulating ISWI factors loading at DNA lesions and supporting transcriptional programs required for survival. ISWI chromatin remodelers regulate DNA accessibility and have been implicated in DNA damage repair. Here, the authors uncover functions, in response to DNA damage, for the bromodomain of the ISWI subunit BAZ1B and for the non-canonical PHD and bromodomain modules of the paralog BAZ1A.
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16
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Tao Y, Zhong C, Zhu J, Xu S, Ding J. Structural and mechanistic insights into regulation of HBO1 histone acetyltransferase activity by BRPF2. Nucleic Acids Res 2017; 45:5707-5719. [PMID: 28334966 PMCID: PMC5449618 DOI: 10.1093/nar/gkx142] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 02/21/2017] [Indexed: 12/15/2022] Open
Abstract
HBO1, a member of the MYST family of histone acetyltransferases (HATs), is required for global acetylation of histone H3K14 and embryonic development. It functions as a catalytic subunit in multisubunit complexes comprising a BRPF1/2/3 or JADE1/2/3 scaffold protein, and two accessory proteins. BRPF2 has been shown to be important for the HAT activity of HBO1 toward H3K14. Here we demonstrated that BRPF2 can regulate the HAT activity of HBO1 toward free H3 and H4, and nucleosomal H3. Particularly, a short N-terminal region of BRPF2 is sufficient for binding to HBO1 and can potentiate its activity toward H3K14. The crystal structure of the HBO1 MYST domain in complex with this segment of BRPF2 together with the biochemical and cell biological data revealed the key residues responsible for the HBO1–BRPF2 interaction. Our structural and functional data together indicate that the N-terminal region of BRPF2 plays an important role in the binding of HBO1 and a minor role in the binding of nucleosomes, which provide new mechanistic insights into the regulation of the HAT activity of HBO1 by BRPF2.
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Affiliation(s)
- Ye Tao
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, and University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Chen Zhong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, and University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Junjun Zhu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, and University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Shutong Xu
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, and University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | - Jianping Ding
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, and University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.,Shanghai Science Research Center, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, 2005 Songhu Road, Shanghai 200438, China
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17
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Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae. Genetics 2017; 205:1113-1123. [PMID: 28108585 DOI: 10.1534/genetics.116.199422] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 12/23/2016] [Indexed: 11/18/2022] Open
Abstract
Histone post-translational modifications (PTMs) alter chromatin structure by promoting the interaction of chromatin-modifying complexes with nucleosomes. The majority of chromatin-modifying complexes contain multiple domains that preferentially interact with modified histones, leading to speculation that these domains function in concert to target nucleosomes with distinct combinations of histone PTMs. In Saccharomyces cerevisiae, the NuA3 histone acetyltransferase complex contains three domains, the PHD finger in Yng1, the PWWP domain in Pdp3, and the YEATS domain in Taf14; which in vitro bind to H3K4 methylation, H3K36 methylation, and acetylated and crotonylated H3K9, respectively. While the in vitro binding has been well characterized, the relative in vivo contributions of these histone PTMs in targeting NuA3 is unknown. Here, through genome-wide colocalization and by mutational interrogation, we demonstrate that the PHD finger of Yng1, and the PWWP domain of Pdp3 independently target NuA3 to H3K4 and H3K36 methylated chromatin, respectively. In contrast, we find no evidence to support the YEATS domain of Taf14 functioning in NuA3 recruitment. Collectively our results suggest that the presence of multiple histone PTM binding domains within NuA3, rather than restricting it to nucleosomes containing distinct combinations of histone PTMs, can serve to increase the range of nucleosomes bound by the complex. Interestingly, however, the simple presence of NuA3 is insufficient to ensure acetylation of the associated nucleosomes, suggesting a secondary level of acetylation regulation that does not involve control of HAT-nucleosome interactions.
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18
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Mutations in the Chromatin Regulator Gene BRPF1 Cause Syndromic Intellectual Disability and Deficient Histone Acetylation. Am J Hum Genet 2017; 100:91-104. [PMID: 27939640 DOI: 10.1016/j.ajhg.2016.11.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/10/2016] [Indexed: 12/18/2022] Open
Abstract
Identification of over 500 epigenetic regulators in humans raises an interesting question regarding how chromatin dysregulation contributes to different diseases. Bromodomain and PHD finger-containing protein 1 (BRPF1) is a multivalent chromatin regulator possessing three histone-binding domains, one non-specific DNA-binding module, and several motifs for interacting with and activating three lysine acetyltransferases. Genetic analyses of fish brpf1 and mouse Brpf1 have uncovered an important role in skeletal, hematopoietic, and brain development, but it remains unclear how BRPF1 is linked to human development and disease. Here, we describe an intellectual disability disorder in ten individuals with inherited or de novo monoallelic BRPF1 mutations. Symptoms include infantile hypotonia, global developmental delay, intellectual disability, expressive language impairment, and facial dysmorphisms. Central nervous system and spinal abnormalities are also seen in some individuals. These clinical features overlap with but are not identical to those reported for persons with KAT6A or KAT6B mutations, suggesting that BRPF1 targets these two acetyltransferases and additional partners in humans. Functional assays showed that the resulting BRPF1 variants are pathogenic and impair acetylation of histone H3 at lysine 23, an abundant but poorly characterized epigenetic mark. We also found a similar deficiency in different lines of Brpf1-knockout mice. These data indicate that aberrations in the chromatin regulator gene BRPF1 cause histone H3 acetylation deficiency and a previously unrecognized intellectual disability syndrome.
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19
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Regulation of KAT6 Acetyltransferases and Their Roles in Cell Cycle Progression, Stem Cell Maintenance, and Human Disease. Mol Cell Biol 2016; 36:1900-7. [PMID: 27185879 DOI: 10.1128/mcb.00055-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The lysine acetyltransferase 6 (KAT6) histone acetyltransferase (HAT) complexes are highly conserved from yeast to higher organisms. They acetylate histone H3 and other nonhistone substrates and are involved in cell cycle regulation and stem cell maintenance. In addition, the human KAT6 HATs are recurrently mutated in leukemia and solid tumors. Therefore, it is important to understand the mechanisms underlying the regulation of KAT6 HATs and their roles in cell cycle progression. In this minireview, we summarize the identification and analysis of the KAT6 complexes and discuss the regulatory mechanisms governing their enzymatic activities and substrate specificities. We further focus on the roles of KAT6 HATs in regulating cell proliferation and stem cell maintenance and review recent insights that aid in understanding their involvement in human diseases.
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20
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The BRPF2/BRD1-MOZ complex is involved in retinoic acid-induced differentiation of embryonic stem cells. Exp Cell Res 2016; 346:30-9. [PMID: 27256846 DOI: 10.1016/j.yexcr.2016.05.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 05/24/2016] [Accepted: 05/27/2016] [Indexed: 12/13/2022]
Abstract
The scaffold protein BRPF2 (also called BRD1), a key component of histone acetyltransferase complexes, plays an important role in embryonic development, but its function in the differentiation of embryonic stem cells (ESCs) remains unknown. In the present study, we investigated whether BRPF2 is involved in mouse ESC differentiation. BRPF2 depletion resulted in abnormal formation of embryoid bodies, downregulation of differentiation-associated genes, and persistent maintenance of alkaline phosphatase activity even after retinoic acid-induced differentiation, indicating impaired differentiation of BRPF2-depleted ESCs. We also found reduced global acetylation of histone H3 lysine 14 (H3K14) in BRPF2-depleted ESCs, irrespective of differentiation status. Further, co-immunoprecipitation analysis revealed a physical association between BRPF2 and the histone acetyltransferase MOZ in differentiated ESCs, suggesting the role of BRPF2-MOZ complexes in ESC differentiation. Together, these results suggest that BRPF2-MOZ complexes play an important role in the differentiation of ESCs via H3K14 acetylation.
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21
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Todd MAM, Huh MS, Picketts DJ. The sub-nucleolar localization of PHF6 defines its role in rDNA transcription and early processing events. Eur J Hum Genet 2016; 24:1453-9. [PMID: 27165002 PMCID: PMC5027685 DOI: 10.1038/ejhg.2016.40] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/30/2016] [Accepted: 04/12/2016] [Indexed: 12/20/2022] Open
Abstract
Ribosomal RNA synthesis occurs in the nucleolus and is a tightly regulated process that is targeted in some developmental diseases and hyperactivated in multiple cancers. Subcellular localization and immunoprecipitation coupled mass spectrometry demonstrated that a proportion of plant homeodomain (PHD) finger protein 6 (PHF6) protein is localized within the nucleolus and interacts with proteins involved in ribosomal processing. PHF6 sequence variants cause Börjeson–Forssman–Lehmann syndrome (BFLS, MIM#301900) and are also associated with a female-specific phenotype overlapping with Coffin–Siris syndrome (MIM#135900), T-cell acute lymphoblastic leukemia (MIM#613065), and acute myeloid leukemia (MIM#601626); however, very little is known about its cellular function, including its nucleolar role. HEK 293T cells were treated with RNase A, DNase I, actinomycin D, or 5,6-dichloro-β-D-ribofuranosylbenzimadole, followed by immunocytochemistry to determine PHF6 sub-nucleolar localization. We observed RNA-dependent localization of PHF6 to the sub-nucleolar fibrillar center (FC) and dense fibrillar component (DFC), at whose interface rRNA transcription occurs. Subsequent ChIP-qPCR analysis revealed strong enrichment of PHF6 across the entire rDNA-coding sequence but not along the intergenic spacer (IGS) region. When rRNA levels were quantified in a PHF6 gain-of-function model, we observed an overall decrease in rRNA transcription, accompanied by a modest increase in repressive promoter-associated RNA (pRNA) and a significant increase in the expression levels of the non-coding IGS36RNA and IGS39RNA transcripts. Collectively, our results demonstrate a role for PHF6 in carefully mediating the overall levels of ribosome biogenesis within a cell.
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Affiliation(s)
- Matthew A M Todd
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Michael S Huh
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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22
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Yan K, You L, Degerny C, Ghorbani M, Liu X, Chen L, Li L, Miao D, Yang XJ. The Chromatin Regulator BRPF3 Preferentially Activates the HBO1 Acetyltransferase but Is Dispensable for Mouse Development and Survival. J Biol Chem 2015; 291:2647-63. [PMID: 26677226 DOI: 10.1074/jbc.m115.703041] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 12/12/2022] Open
Abstract
To interpret epigenetic information, chromatin readers utilize various protein domains for recognition of DNA and histone modifications. Some readers possess multidomains for modification recognition and are thus multivalent. Bromodomain- and plant homeodomain-linked finger-containing protein 3 (BRPF3) is such a chromatin reader, containing two plant homeodomain-linked fingers, one bromodomain and a PWWP domain. However, its molecular and biological functions remain to be investigated. Here, we report that endogenous BRPF3 preferentially forms a tetrameric complex with HBO1 (also known as KAT7) and two other subunits but not with related acetyltransferases such as MOZ, MORF, TIP60, and MOF (also known as KAT6A, KAT6B, KAT5, and KAT8, respectively). We have also characterized a mutant mouse strain with a lacZ reporter inserted at the Brpf3 locus. Systematic analysis of β-galactosidase activity revealed dynamic spatiotemporal expression of Brpf3 during mouse embryogenesis and high expression in the adult brain and testis. Brpf3 disruption, however, resulted in no obvious gross phenotypes. This is in stark contrast to Brpf1 and Brpf2, whose loss causes lethality at E9.5 and E15.5, respectively. In Brpf3-null mice and embryonic fibroblasts, RT-quantitative PCR uncovered no changes in levels of Brpf1 and Brpf2 transcripts, confirming no compensation from them. These results indicate that BRPF3 forms a functional tetrameric complex with HBO1 but is not required for mouse development and survival, thereby distinguishing BRPF3 from its paralogs, BRPF1 and BRPF2.
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Affiliation(s)
- Kezhi Yan
- From the Rosalind and Morris Goodman Cancer Research Center, Departments of Biochemistry and Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Linya You
- From the Rosalind and Morris Goodman Cancer Research Center, Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Cindy Degerny
- From the Rosalind and Morris Goodman Cancer Research Center
| | - Mohammad Ghorbani
- From the Rosalind and Morris Goodman Cancer Research Center, Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Xin Liu
- From the Rosalind and Morris Goodman Cancer Research Center
| | - Lulu Chen
- the State Key Laboratory of Reproductive Medicine, Research Center for Bone and Stem Cells, Department of Human Anatomy, Nanjing Medical University, Nanjing 210029, China, and
| | - Lin Li
- From the Rosalind and Morris Goodman Cancer Research Center, Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Dengshun Miao
- the State Key Laboratory of Reproductive Medicine, Research Center for Bone and Stem Cells, Department of Human Anatomy, Nanjing Medical University, Nanjing 210029, China, and
| | - Xiang-Jiao Yang
- From the Rosalind and Morris Goodman Cancer Research Center, Departments of Biochemistry and Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada, the McGill University Health Center, Montreal, Quebec H3A 1A3, Canada
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23
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Klein BJ, Muthurajan UM, Lalonde ME, Gibson MD, Andrews FH, Hepler M, Machida S, Yan K, Kurumizaka H, Poirier MG, Côté J, Luger K, Kutateladze TG. Bivalent interaction of the PZP domain of BRPF1 with the nucleosome impacts chromatin dynamics and acetylation. Nucleic Acids Res 2015; 44:472-84. [PMID: 26626149 PMCID: PMC4705663 DOI: 10.1093/nar/gkv1321] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/11/2015] [Indexed: 01/09/2023] Open
Abstract
BRPF1 (bromodomain PHD finger 1) is a core subunit of the MOZ histone acetyltransferase (HAT) complex, critical for normal developmental programs and implicated in acute leukemias. BRPF1 contains a unique assembly of zinc fingers, termed a PZP domain, the physiological role of which remains unclear. Here, we elucidate the structure-function relationship of this novel epigenetic reader and detail the biological and mechanistic consequences of its interaction with nucleosomes. PZP has a globular architecture and forms a 2:1 stoichiometry complex with the nucleosome, bivalently interacting with histone H3 and DNA. This binding impacts the nucleosome dynamics, shifting the DNA unwrapping/rewrapping equilibrium toward the unwrapped state and increasing DNA accessibility. We demonstrate that the DNA-binding function of the BRPF1 PZP domain is required for the MOZ-BRPF1-ING5-hEaf6 HAT complex to be recruited to chromatin and to acetylate nucleosomal histones. Our findings reveal a novel link between chromatin dynamics and MOZ-mediated acetylation.
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Affiliation(s)
- Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Uma M Muthurajan
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Marie-Eve Lalonde
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, CHU de Québec Research Center-Oncology Axis, Quebec City, Québec G1R 2J6, Canada
| | - Matthew D Gibson
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Forest H Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Maggie Hepler
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Shinichi Machida
- Graduate School of Advanced Science & Engineering, Waseda University, Tokyo 162-8480, Japan
| | - Kezhi Yan
- Goodman Cancer Research Center & Department of Medicine, McGill University, Montreal, Québec H3A 1A1, Canada
| | - Hitoshi Kurumizaka
- Graduate School of Advanced Science & Engineering, Waseda University, Tokyo 162-8480, Japan
| | - Michael G Poirier
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, CHU de Québec Research Center-Oncology Axis, Quebec City, Québec G1R 2J6, Canada
| | - Karolin Luger
- Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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24
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PHF6 Degrees of Separation: The Multifaceted Roles of a Chromatin Adaptor Protein. Genes (Basel) 2015; 6:325-52. [PMID: 26103525 PMCID: PMC4488667 DOI: 10.3390/genes6020325] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/12/2015] [Accepted: 06/16/2015] [Indexed: 12/13/2022] Open
Abstract
The importance of chromatin regulation to human disease is highlighted by the growing number of mutations identified in genes encoding chromatin remodeling proteins. While such mutations were first identified in severe developmental disorders, or in specific cancers, several genes have been implicated in both, including the plant homeodomain finger protein 6 (PHF6) gene. Indeed, germline mutations in PHF6 are the cause of the Börjeson–Forssman–Lehmann X-linked intellectual disability syndrome (BFLS), while somatic PHF6 mutations have been identified in T-cell acute lymphoblastic leukemia (T-ALL) and acute myeloid leukemia (AML). Studies from different groups over the last few years have made a significant impact towards a functional understanding of PHF6 protein function. In this review, we summarize the current knowledge of PHF6 with particular emphasis on how it interfaces with a distinct set of interacting partners and its functional roles in the nucleoplasm and nucleolus. Overall, PHF6 is emerging as a key chromatin adaptor protein critical to the regulation of neurogenesis and hematopoiesis.
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25
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Yang XJ. MOZ and MORF acetyltransferases: Molecular interaction, animal development and human disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1818-26. [PMID: 25920810 DOI: 10.1016/j.bbamcr.2015.04.014] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 04/17/2015] [Accepted: 04/22/2015] [Indexed: 01/16/2023]
Abstract
Lysine residues are subject to many forms of covalent modification and one such modification is acetylation of the ε-amino group. Initially identified on histone proteins in the 1960s, lysine acetylation is now considered as an important form of post-translational modification that rivals phosphorylation. However, only about a dozen of human lysine acetyltransferases have been identified. Among them are MOZ (monocytic leukemia zinc finger protein; a.k.a. MYST3 and KAT6A) and its paralog MORF (a.k.a. MYST4 and KAT6B). Although there is a distantly related protein in Drosophila and sea urchin, these two enzymes are vertebrate-specific. They form tetrameric complexes with BRPF1 (bromodomain- and PHD finger-containing protein 1) and two small non-catalytic subunits. These two acetyltransferases and BRPF1 play key roles in various developmental processes; for example, they are important for development of hematopoietic and neural stem cells. The human KAT6A and KAT6B genes are recurrently mutated in leukemia, non-hematologic malignancies, and multiple developmental disorders displaying intellectual disability and various other abnormalities. In addition, the BRPF1 gene is mutated in childhood leukemia and adult medulloblastoma. Therefore, these two acetyltransferases and their partner BRPF1 are important in animal development and human disease.
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Affiliation(s)
- Xiang-Jiao Yang
- The Rosalind & Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec H3A 1A3, Canada; Department of Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada; McGill University Health Center, Montreal, Quebec H3A 1A3, Canada.
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26
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Katoh M. Functional proteomics of the epigenetic regulators ASXL1, ASXL2 and ASXL3: a convergence of proteomics and epigenetics for translational medicine. Expert Rev Proteomics 2015; 12:317-28. [PMID: 25835095 DOI: 10.1586/14789450.2015.1033409] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
ASXL1, ASXL2 and ASXL3 are epigenetic scaffolds for BAP1, EZH2, NCOA1, nuclear receptors and WTIP. Here, functional proteomics of the ASXL family members are reviewed with emphasis on mutation spectra, the ASXM2 domain and the plant homeodomain (PHD) finger. Copy number gains of ASXL1 occur in chromosome 20q11.2 duplication syndrome and cervical cancer. Truncation mutations of ASXLs occur in autism, Bohring-Opitz and related syndromes, hematological malignancies and solid tumors, such as prostate cancer, breast cancer and high-grade glioma, which are gain- or loss-of-function mutations. The ASXM2 domain is a binding module for androgen receptor and estrogen receptor α, while the PHD finger is a ligand of WTIP LIM domains and a putative chromatin-binding module. Phylogenetic analyses of 139 human PHD fingers revealed that ASXL PHD fingers cluster with those of BPTF, DIDO, ING1, KDM5A (JARID1A), KMT2E (MLL5), PHF2, PHF8 and PHF23. The cell context-dependent epigenetic code of ASXLs should be deciphered to develop therapeutics for human diseases.
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Affiliation(s)
- Masaru Katoh
- Department of Omics Network, National Cancer Center - Japan, 5-1-1 Tsukiji Chuo Ward, Tokyo 104-0045, Japan
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Lubula MY, Eckenroth BE, Carlson S, Poplawski A, Chruszcz M, Glass KC. Structural insights into recognition of acetylated histone ligands by the BRPF1 bromodomain. FEBS Lett 2014; 588:3844-54. [PMID: 25281266 DOI: 10.1016/j.febslet.2014.09.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 09/16/2014] [Accepted: 09/16/2014] [Indexed: 01/10/2023]
Abstract
Bromodomain-PHD finger protein 1 (BRPF1) is part of the MOZ HAT complex and contains a unique combination of domains typically found in chromatin-associated factors, which include plant homeodomain (PHD) fingers, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. Bromodomains are conserved structural motifs generally known to recognize acetylated histones, and the BRPF1 bromodomain preferentially selects for H2AK5ac, H4K12ac and H3K14ac. We solved the X-ray crystal structures of the BRPF1 bromodomain in complex with the H2AK5ac and H4K12ac histone peptides. Site-directed mutagenesis on residues in the BRPF1 bromodomain-binding pocket was carried out to investigate the contribution of specific amino acids on ligand binding. Our results provide critical insights into the molecular mechanism of ligand binding by the BRPF1 bromodomain, and reveal that ordered water molecules are an essential component driving ligand recognition.
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Affiliation(s)
- Mulu Y Lubula
- Department of Pharmaceutical Science, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA
| | - Brian E Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Samuel Carlson
- Department of Pharmaceutical Science, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA
| | - Amanda Poplawski
- Department of Pharmaceutical Science, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Karen C Glass
- Department of Pharmaceutical Science, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA.
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28
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Qin S, Min J. Structure and function of the nucleosome-binding PWWP domain. Trends Biochem Sci 2014; 39:536-47. [PMID: 25277115 DOI: 10.1016/j.tibs.2014.09.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/26/2014] [Accepted: 09/08/2014] [Indexed: 12/11/2022]
Abstract
PWWP domain-containing proteins are often involved in chromatin-associated biological processes, such as transcriptional regulation and DNA repair, and recent studies have shown that the PWWP domain specifies chromatin localization. Mutations in the PWWP domain, a 100-150 amino acid motif, have been linked to various human diseases, emphasizing its importance. Structural studies reveal that PWWP domains possess a conserved aromatic cage for histone methyl-lysine recognition, and synergistically bind both histone and DNA, which contributes to their nucleosome-binding ability and chromatin localization. Furthermore, the PWWP domain often cooperates with other histone and DNA 'reader' or 'modifier' domains to evoke crosstalk between various epigenetic marks. Here, we discuss these recent advances in understanding the structure and function of the PWWP domain.
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Affiliation(s)
- Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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29
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Carlson S, Glass KC. The MOZ histone acetyltransferase in epigenetic signaling and disease. J Cell Physiol 2014; 229:1571-4. [PMID: 24633655 DOI: 10.1002/jcp.24617] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 03/12/2014] [Indexed: 01/18/2023]
Abstract
The monocytic leukemic zinc finger (MOZ) histone acetyltransferase (HAT) plays a role in acute myeloid leukemia (AML). It functions as a quaternary complex with the bromodomain PHD finger protein 1 (BRPF1), the human Esa1-associated factor 6 homolog (hEAF6), and the inhibitor of growth 5 (ING5). Each of these subunits contain chromatin reader domains that recognize specific post-translational modifications (PTMs) on histone tails, and this recognition directs the MOZ HAT complex to specific chromatin substrates. The structure and function of these epigenetic reader modules has now been elucidated, and a model describing how the cooperative action of these domains regulates HAT activity in response to the epigenetic landscape is proposed. The emerging role of epigenetic reader domains in disease, and their therapeutic potential for many types of cancer is also highlighted.
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Affiliation(s)
- Samuel Carlson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, Vermont
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30
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Ju J, Wang Y, Liu R, Zhang Y, Xu Z, Wang Y, Wu Y, Liu M, Cerruti L, Zou F, Ma C, Fang M, Tan R, Jane SM, Zhao Q. Human fetal globin gene expression is regulated by LYAR. Nucleic Acids Res 2014; 42:9740-52. [PMID: 25092918 PMCID: PMC4150809 DOI: 10.1093/nar/gku718] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human globin gene expression during development is modulated by transcription factors in a stage-dependent manner. However, the mechanisms controlling the process are still largely unknown. In this study, we found that a nuclear protein, LYAR (human homologue of mouse Ly-1 antibody reactive clone) directly interacted with the methyltransferase PRMT5 which triggers the histone H4 Arg3 symmetric dimethylation (H4R3me2s) mark. We found that PRMT5 binding on the proximal γ-promoter was LYAR-dependent. The LYAR DNA-binding motif (GGTTAT) was identified by performing CASTing (cyclic amplification and selection of targets) experiments. Results of EMSA and ChIP assays confirmed that LYAR bound to a DNA region corresponding to the 5′-untranslated region of the γ-globin gene. We also found that LYAR repressed human fetal globin gene expression in both K562 cells and primary human adult erythroid progenitor cells. Thus, these data indicate that LYAR acts as a novel transcription factor that binds the γ-globin gene, and is essential for silencing the γ-globin gene.
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Affiliation(s)
- Junyi Ju
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ying Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ronghua Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yichong Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Zhen Xu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yadong Wang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Yupeng Wu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ming Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Loretta Cerruti
- Department of Medicine, Monash University Central Clinical School, Prahran, VIC 3181, Australia
| | - Fengwei Zou
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Chi Ma
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Ming Fang
- Institute of Life Sciences, Southeast University, Nanjing 210096, China
| | - Renxiang Tan
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
| | - Stephen M Jane
- Department of Medicine, Monash University Central Clinical School, Prahran, VIC 3181, Australia
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
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Abstract
Histone modifiers like acetyltransferases, methyltransferases, and demethylases are critical regulators of most DNA-based nuclear processes, de facto controlling cell cycle progression and cell fate. These enzymes perform very precise post-translational modifications on specific histone residues, which in turn are recognized by different effector modules/proteins. We now have a better understanding of how these enzymes exhibit such specificity. As they often reside in multisubunit complexes, they use associated factors to target their substrates within chromatin structure and select specific histone mark-bearing nucleosomes. In this review, we cover the current understanding of how histone modifiers select their histone targets. We also explain how different experimental approaches can lead to conflicting results about the histone specificity and function of these enzymes.
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Affiliation(s)
- Marie-Eve Lalonde
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Quebec City, Quebec G1R 2J6, Canada
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Quebec City, Quebec G1R 2J6, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Quebec City, Quebec G1R 2J6, Canada
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32
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You L, Chen L, Penney J, Miao D, Yang XJ. Expression atlas of the multivalent epigenetic regulator Brpf1 and its requirement for survival of mouse embryos. Epigenetics 2014; 9:860-72. [PMID: 24646517 DOI: 10.4161/epi.28530] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Bromodomain- and PHD finger-containing protein 1 (BRPF1) is a unique epigenetic regulator that contains multiple structural domains for recognizing different chromatin modifications. In addition, it possesses sequence motifs for forming multiple complexes with three different histone acetyltransferases, MOZ, MORF, and HBO1. Within these complexes, BRPF1 serves as a scaffold for bridging subunit interaction, stimulating acetyltransferase activity, governing substrate specificity and stimulating gene expression. To investigate how these molecular interactions are extrapolated to biological functions of BRPF1, we utilized a mouse strain containing a knock-in reporter and analyzed the spatiotemporal expression from embryos to adults. The analysis revealed dynamic expression in the extraembryonic, embryonic, and fetal tissues, suggesting important roles of Brpf1 in prenatal development. In support of this, inactivation of the mouse Brpf1 gene causes lethality around embryonic day 9.5. After birth, high expression is present in the testis and specific regions of the brain. The 4-dimensional expression atlas of mouse Brpf1 should serve as a valuable guide for analyzing its interaction with Moz, Morf, and Hbo1 in vivo, as well as for investigating whether Brpf1 functions independently of these three enzymatic epigenetic regulators.
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Affiliation(s)
- Linya You
- The Rosalind & Morris Goodman Cancer Research Center; Montreal, QC Canada; Department of Medicine; McGill University; Montreal, QC Canada
| | - Lulu Chen
- The State Key Laboratory of Reproductive Medicine; The Research Center for Bone and Stem Cells; Department of Human Anatomy; Nanjing Medical University; Nanjing, China
| | - Janice Penney
- The Rosalind & Morris Goodman Cancer Research Center; Montreal, QC Canada
| | - Dengshun Miao
- The State Key Laboratory of Reproductive Medicine; The Research Center for Bone and Stem Cells; Department of Human Anatomy; Nanjing Medical University; Nanjing, China
| | - Xiang-Jiao Yang
- The Rosalind & Morris Goodman Cancer Research Center; Montreal, QC Canada; Department of Medicine; McGill University; Montreal, QC Canada; Department of Biochemistry; McGill University; Montreal, QC Canada; McGill University Health Center; Montreal, QC Canada
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33
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Liu Z, Li F, Ruan K, Zhang J, Mei Y, Wu J, Shi Y. Structural and functional insights into the human Börjeson-Forssman-Lehmann syndrome-associated protein PHF6. J Biol Chem 2014; 289:10069-83. [PMID: 24554700 DOI: 10.1074/jbc.m113.535351] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The plant homeodomain finger 6 (PHF6) was originally identified as the gene mutated in the X-linked mental retardation disorder Börjeson-Forssman-Lehmann syndrome. Mutations in the PHF6 gene have also been associated with T-cell acute lymphoblastic leukemia and acute myeloid leukemia. Approximately half of the disease-associated mutations are distributed in the second conserved extended plant homeodomain (ePHD2) of PHF6, indicating the functional importance of the ePHD2 domain. Here, we report the high resolution crystal structure of the ePHD2 domain of PHF6, which contains an N-terminal pre-PHD (C2HC zinc finger), a long linker, and an atypical PHD finger. PHF6-ePHD2 appears to fold as a novel integrated structural module. Structural analysis of PHF6-ePHD2 reveals pathological implication of PHF6 gene mutations in Börjeson-Forssman-Lehmann syndrome, T-cell acute lymphoblastic leukemia, and acute myeloid leukemia. The binding experiments show that PHF6-ePHD2 can bind dsDNA but not histones. We also demonstrate PHF6 protein directly interacts with the nucleosome remodeling and deacetylation complex component RBBP4. Via this interaction, PHF6 exerts its transcriptional repression activity. Taken together, these data support the hypothesis that PHF6 may function as a transcriptional repressor using its ePHD domains binding to the promoter region of its repressed gene, and this process was regulated by the nucleosome remodeling and deacetylation complex that was recruited to the genomic target site by NoLS region of PHF6.
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Affiliation(s)
- Zhonghua Liu
- From the Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
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34
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Poplawski A, Hu K, Lee W, Natesan S, Peng D, Carlson S, Shi X, Balaz S, Markley JL, Glass KC. Molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain. J Mol Biol 2013; 426:1661-76. [PMID: 24333487 DOI: 10.1016/j.jmb.2013.12.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 11/27/2013] [Accepted: 12/05/2013] [Indexed: 10/25/2022]
Abstract
The monocytic leukemic zinc finger (MOZ) histone acetyltransferase (HAT) acetylates free histones H3, H4, H2A, and H2B in vitro and is associated with up-regulation of gene transcription. The MOZ HAT functions as a quaternary complex with the bromodomain-PHD finger protein 1 (BRPF1), inhibitor of growth 5 (ING5), and hEaf6 subunits. BRPF1 links the MOZ catalytic subunit to the ING5 and hEaf6 subunits, thereby promoting MOZ HAT activity. Human BRPF1 contains multiple effector domains with known roles in gene transcription, as well as chromatin binding and remodeling. However, the biological function of the BRPF1 bromodomain remains unknown. Our findings reveal novel interactions of the BRPF1 bromodomain with multiple acetyllysine residues on the N-terminus of histones and show that it preferentially selects for H2AK5ac, H4K12ac, and H3K14ac. We used chemical shift perturbation data from NMR titration experiments to map the BRPF1 bromodomain ligand binding pocket and identified key residues responsible for coordination of the post-translationally modified histones. Extensive molecular dynamics simulations were used to generate structural models of bromodomain-histone ligand complexes, to analyze hydrogen bonding and other interactions, and to calculate the binding free energies. Our results outline the molecular mechanism driving binding specificity of the BRPF1 bromodomain for discrete acetyllysine residues on the N-terminal histone tails. Together, these data provide insights into how histone recognition by the bromodomain directs the biological function of BRPF1, ultimately targeting the MOZ HAT complex to chromatin substrates.
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Affiliation(s)
- Amanda Poplawski
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA
| | - Kaifeng Hu
- National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Woonghee Lee
- National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Senthil Natesan
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA
| | - Danni Peng
- Department of Biochemistry and Molecular Biology, Division of Basic Science Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samuel Carlson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA
| | - Xiaobing Shi
- Department of Biochemistry and Molecular Biology, Division of Basic Science Research, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stefan Balaz
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA
| | - John L Markley
- National Magnetic Resonance Facility at Madison and Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Karen C Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA.
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35
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Klein BJ, Lalonde ME, Côté J, Yang XJ, Kutateladze TG. Crosstalk between epigenetic readers regulates the MOZ/MORF HAT complexes. Epigenetics 2013; 9:186-93. [PMID: 24169304 DOI: 10.4161/epi.26792] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The MOZ/MORF complexes represent an example of a chromatin-binding assembly whose recruitment to specific genomic regions and activity can be fine-tuned by posttranslational modifications of histones. Here we detail the structures and biological functions of epigenetic readers present in the four core subunits of the MOZ/MORF complexes, highlight the imperative role of combinatorial readout by the multiple readers, and discuss new research directions to advance our understanding of histone acetylation.
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Affiliation(s)
- Brianna J Klein
- Department of Pharmacology; University of Colorado School of Medicine; Aurora, CO USA
| | - Marie-Eve Lalonde
- Laval University Cancer Research Center; Hôtel-Dieu de Québec (CHUQ); Quebec City, QC Canada
| | - Jacques Côté
- Laval University Cancer Research Center; Hôtel-Dieu de Québec (CHUQ); Quebec City, QC Canada
| | - Xiang-Jiao Yang
- Rosalind and Morris Goodman Cancer Research Center; Departments of Medicine, Biochemistry, and Anatomy & Cell Biology; McGill University; Montréal, QC Canada
| | - Tatiana G Kutateladze
- Department of Pharmacology; University of Colorado School of Medicine; Aurora, CO USA
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36
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Lalonde ME, Avvakumov N, Glass KC, Joncas FH, Saksouk N, Holliday M, Paquet E, Yan K, Tong Q, Klein BJ, Tan S, Yang XJ, Kutateladze TG, Côté J. Exchange of associated factors directs a switch in HBO1 acetyltransferase histone tail specificity. Genes Dev 2013; 27:2009-24. [PMID: 24065767 PMCID: PMC3792477 DOI: 10.1101/gad.223396.113] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 08/23/2013] [Indexed: 12/13/2022]
Abstract
Histone acetyltransferases (HATs) assemble into multisubunit complexes in order to target distinct lysine residues on nucleosomal histones. Here, we characterize native HAT complexes assembled by the BRPF family of scaffold proteins. Their plant homeodomain (PHD)-Zn knuckle-PHD domain is essential for binding chromatin and is restricted to unmethylated H3K4, a specificity that is reversed by the associated ING subunit. Native BRPF1 complexes can contain either MOZ/MORF or HBO1 as catalytic acetyltransferase subunit. Interestingly, while the previously reported HBO1 complexes containing JADE scaffold proteins target histone H4, the HBO1-BRPF1 complex acetylates only H3 in chromatin. We mapped a small region to the N terminus of scaffold proteins responsible for histone tail selection on chromatin. Thus, alternate choice of subunits associated with HBO1 can switch its specificity between H4 and H3 tails. These results uncover a crucial new role for associated proteins within HAT complexes, previously thought to be intrinsic to the catalytic subunit.
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Affiliation(s)
- Marie-Eve Lalonde
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
| | - Nikita Avvakumov
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
| | | | - France-Hélène Joncas
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
| | - Nehmé Saksouk
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
| | - Michael Holliday
- Molecular Biology Program, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Eric Paquet
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
| | - Kezhi Yan
- The Rosalind and Morris Goodman Cancer Research Center, Department of Biochemistry, McGill University, Montreal, Québec H3A 1A1, Canada
| | | | | | - Song Tan
- Center for Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania University, University Park, Pennsylvania 16802, USA
| | - Xiang-Jiao Yang
- The Rosalind and Morris Goodman Cancer Research Center, Department of Biochemistry, McGill University, Montreal, Québec H3A 1A1, Canada
- Department of Medicine, McGill University Health Center, Montreal, Québec H3A 1A1, Canada
| | - Tatiana G. Kutateladze
- Department of Pharmacology
- Molecular Biology Program, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Jacques Côté
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, Québec G1R 2J6, Canada
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37
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Functional and cancer genomics of ASXL family members. Br J Cancer 2013; 109:299-306. [PMID: 23736028 PMCID: PMC3721406 DOI: 10.1038/bjc.2013.281] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 05/08/2013] [Accepted: 05/10/2013] [Indexed: 12/22/2022] Open
Abstract
Additional sex combs-like (ASXL)1, ASXL2 and ASXL3 are human homologues of the Drosophila Asx gene that are involved in the regulation or recruitment of the Polycomb-group repressor complex (PRC) and trithorax-group (trxG) activator complex. ASXL proteins consist of ASXN, ASXH, ASXM1, ASXM2 and PHD domains. ASXL1 directly interacts with BAP1, KDM1A (LSD1), NCOA1 and nuclear hormone receptors (NHRs), such as retinoic acid receptors, oestrogen receptor and androgen receptor. ASXL family members are epigenetic scaffolding proteins that assemble epigenetic regulators and transcription factors to specific genomic loci with histone modifications. ASXL1 is involved in transcriptional repression through an interaction with PRC2 and also contributes to transcriptional regulation through interactions with BAP1 and/or NHR complexes. Germ-line mutations of human ASXL1 and ASXL3 occur in Bohring-Opitz and related syndromes. Amplification and overexpression of ASXL1 occur in cervical cancer. Truncation mutations of ASXL1 occur in colorectal cancers with microsatellite instability (MSI), malignant myeloid diseases, chronic lymphocytic leukaemia, head and neck squamous cell carcinoma, and liver, prostate and breast cancers; those of ASXL2 occur in prostate cancer, pancreatic cancer and breast cancer and those of ASXL3 are observed in melanoma. EPC1-ASXL2 gene fusion occurs in adult T-cell leukaemia/lymphoma. The prognosis of myeloid malignancies with misregulating truncation mutations of ASXL1 is poor. ASXL family members are assumed to be tumour suppressive or oncogenic in a context-dependent manner.
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38
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Crystal structure and functional characterization of the human RBM25 PWI domain and its flanking basic region. Biochem J 2013. [PMID: 23190262 PMCID: PMC3553564 DOI: 10.1042/bj20121382] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Human RBM25 (RNA-binding motif protein 25) is a novel splicing factor that contains a PWI domain, a newly identified RNA/DNA-binding domain, and regulates Bcl-x pre-mRNA alternative splicing. The flanking basic region has been suggested to serve as a co-operative partner of the PWI domain in the binding of nucleic acids, but the structure of this basic region is unknown. In the present paper, we report the crystal structure of the RBM25 PWI domain and its flanking basic region. The PWI domain is revealed to comprise a conserved four-helix bundle, and the flanking basic region forms two α-helices and associates with helix H4 of the PWI domain. These interactions promote directly the formation of an enlarged nucleic-acid-binding platform. Structure-guided mutagenesis reveals a positively charged nucleic-acid-binding surface in the RBM25 PWI domain that is entirely different from that in the SRm160 PWI domain. Furthermore, we show that the promotion of the pro-apoptotic Bcl-xS isoform expression by RBM25 is facilitated by the PWI domain in vivo. Thus the present study suggests that the PWI domain plays an important role in the regulation of Bcl-x pre-mRNA alternative splicing.
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