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Fan T, Jiang L, Zhou X, Chi H, Zeng X. Deciphering the dual roles of PHD finger proteins from oncogenic drivers to tumor suppressors. Front Cell Dev Biol 2024; 12:1403396. [PMID: 38813086 PMCID: PMC11133592 DOI: 10.3389/fcell.2024.1403396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
PHD (plant homeodomain) finger proteins emerge as central epigenetic readers and modulators in cancer biology, orchestrating a broad spectrum of cellular processes pivotal to oncogenesis and tumor suppression. This review delineates the dualistic roles of PHD fingers in cancer, highlighting their involvement in chromatin remodeling, gene expression regulation, and interactions with cellular signaling networks. PHD fingers' ability to interpret specific histone modifications underscores their influence on gene expression patterns, impacting crucial cancer-related processes such as cell proliferation, DNA repair, and apoptosis. The review delves into the oncogenic potential of certain PHD finger proteins, exemplified by PHF1 and PHF8, which promote tumor progression through epigenetic dysregulation and modulation of signaling pathways like Wnt and TGFβ. Conversely, it discusses the tumor-suppressive functions of PHD finger proteins, such as PHF2 and members of the ING family, which uphold genomic stability and inhibit tumor growth through their interactions with chromatin and transcriptional regulators. Additionally, the review explores the therapeutic potential of targeting PHD finger proteins in cancer treatment, considering their pivotal roles in regulating cancer stem cells and influencing the immune response to cancer therapy. Through a comprehensive synthesis of current insights, this review underscores the complex but promising landscape of PHD finger proteins in cancer biology, advocating for further research to unlock novel therapeutic avenues that leverage their unique cellular roles.
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Affiliation(s)
- Tingyu Fan
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Lai Jiang
- Clinical Medical College, Southwest Medical University, Luzhou, Sichuan, China
| | - Xuancheng Zhou
- Clinical Medical College, Southwest Medical University, Luzhou, Sichuan, China
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, Sichuan, China
| | - Xi Zeng
- Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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2
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Huang X, Chen Y, Xiao Q, Shang X, Liu Y. Chemical inhibitors targeting histone methylation readers. Pharmacol Ther 2024; 256:108614. [PMID: 38401773 DOI: 10.1016/j.pharmthera.2024.108614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Histone methylation reader domains are protein modules that recognize specific histone methylation marks, such as methylated or unmethylated lysine or arginine residues on histones. These reader proteins play crucial roles in the epigenetic regulation of gene expression, chromatin structure, and DNA damage repair. Dysregulation of these proteins has been linked to various diseases, including cancer, neurodegenerative diseases, and developmental disorders. Therefore, targeting these proteins with chemical inhibitors has emerged as an attractive approach for therapeutic intervention, and significant progress has been made in this area. In this review, we will summarize the development of inhibitors targeting histone methylation readers, including MBT domains, chromodomains, Tudor domains, PWWP domains, PHD fingers, and WD40 repeat domains. For each domain, we will briefly discuss its identification and biological/biochemical functions, and then focus on the discovery of inhibitors tailored to target this domain, summarizing the property and potential application of most inhibitors. We will also discuss the structural basis for the potency and selectivity of these inhibitors, which will aid in further lead generation and optimization. Finally, we will also address the challenges and strategies involved in the development of these inhibitors. It should facilitate the rational design and development of novel chemical scaffolds and new targeting strategies for histone methylation reader domains with the help of this body of data.
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Affiliation(s)
- Xiaolei Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yichang Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Qin Xiao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Xinci Shang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yanli Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China.
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3
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Ortiz G, Longbotham JE, Qin SL, Zhang MY, Lee GM, Neitz RJ, Kelly MJS, Arkin MR, Fujimori DG. Identifying ligands for the PHD1 finger of KDM5A through high-throughput screening. RSC Chem Biol 2024; 5:209-215. [PMID: 38456036 PMCID: PMC10915964 DOI: 10.1039/d3cb00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/18/2023] [Indexed: 03/09/2024] Open
Abstract
PHD fingers are a type of chromatin reader that primarily recognize chromatin as a function of lysine methylation state. Dysregulated PHD fingers are implicated in various human diseases, including acute myeloid leukemia. Targeting PHD fingers with small molecules is considered challenging as their histone tail binding pockets are often shallow and surface-exposed. The KDM5A PHD1 finger regulates the catalytic activity of KDM5A, an epigenetic enzyme often misregulated in cancers. To identify ligands that disrupt the PHD1-histone peptide interaction, we conducted a high-throughput screen and validated hits by orthogonal methods. We further elucidated structure-activity relationships in two classes of compounds to identify features important for binding. Our investigation offers a starting point for further optimization of small molecule PHD1 ligands.
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Affiliation(s)
- Gloria Ortiz
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Sophia L Qin
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Meng Yao Zhang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
| | - Gregory M Lee
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - R Jeffrey Neitz
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Michelle R Arkin
- Small Molecule Discovery Center (SMDC), University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco CA 94158 USA
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco CA 94158 USA
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4
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Ortiz G, Kutateladze TG, Fujimori DG. Chemical tools targeting readers of lysine methylation. Curr Opin Chem Biol 2023; 74:102286. [PMID: 36948085 PMCID: PMC10264141 DOI: 10.1016/j.cbpa.2023.102286] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 02/01/2023] [Accepted: 02/20/2023] [Indexed: 03/22/2023]
Abstract
Reader domains that recognize methylated lysine and arginine residues on histones play a role in the recruitment, stabilization, and regulation of chromatin regulatory proteins. Targeting reader proteins with small molecule and peptidomimetic inhibitors has enabled the elucidation of the structure and function of specific domains and uncovered their role in diseases. Recent progress towards chemical probes that target readers of lysine methylation, including the Royal family and plant homeodomains (PHD), is discussed here. We highlight recently developed covalent cyclic peptide inhibitors of a plant homeodomain. Additionally, inhibitors targeting previously untargeted Tudor domains and chromodomains are discussed.
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Affiliation(s)
- Gloria Ortiz
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco, CA 94158, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
| | - Danica Galonic Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco San Francisco, CA 94158, USA.
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5
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Atypical histone targets of PHD fingers. J Biol Chem 2023; 299:104601. [PMID: 36907441 PMCID: PMC10124903 DOI: 10.1016/j.jbc.2023.104601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023] Open
Abstract
Plant homeodomain (PHD) fingers are structurally conserved zinc fingers that selectively bind unmodified or methylated at lysine 4 histone H3 tails. This binding stabilizes transcription factors and chromatin-modifying proteins at specific genomic sites, which is required for vital cellular processes, including gene expression and DNA repair. Several PHD fingers have recently been shown to recognize other regions of H3 or histone H4. In this review, we detail molecular mechanisms and structural features of the non-canonical histone recognition, discuss biological implications of the atypical interactions, highlight therapeutic potential of PHD fingers, and compare inhibition strategies.
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Qiu X, Kong L, Chen H, Lin Y, Tu S, Wang L, Chen Z, Zeng M, Xiao J, Yuan P, Qiu M, Wang Y, Ye W, Duan K, Dong S, Wang Y. The Phytophthora sojae nuclear effector PsAvh110 targets a host transcriptional complex to modulate plant immunity. THE PLANT CELL 2023; 35:574-597. [PMID: 36222564 PMCID: PMC9806631 DOI: 10.1093/plcell/koac300] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/18/2022] [Indexed: 05/27/2023]
Abstract
Plants have evolved sophisticated immune networks to restrict pathogen colonization. In response, pathogens deploy numerous virulent effectors to circumvent plant immune responses. However, the molecular mechanisms by which pathogen-derived effectors suppress plant defenses remain elusive. Here, we report that the nucleus-localized RxLR effector PsAvh110 from the pathogen Phytophthora sojae, causing soybean (Glycine max) stem and root rot, modulates the activity of a transcriptional complex to suppress plant immunity. Soybean like-heterochromatin protein 1-2 (GmLHP1-2) and plant homeodomain finger protein 6 (GmPHD6) form a transcriptional complex with transcriptional activity that positively regulates plant immunity against Phytophthora infection. To suppress plant immunity, the nuclear effector PsAvh110 disrupts the assembly of the GmLHP1-2/GmPHD6 complex via specifically binding to GmLHP1-2, thus blocking its transcriptional activity. We further show that PsAvh110 represses the expression of a subset of immune-associated genes, including BRI1-associated receptor kinase 1-3 (GmBAK1-3) and pathogenesis-related protein 1 (GmPR1), via G-rich elements in gene promoters. Importantly, PsAvh110 is a conserved effector in different Phytophthora species, suggesting that the PsAvh110 regulatory mechanism might be widely utilized in the genus to manipulate plant immunity. Thus, our study reveals a regulatory mechanism by which pathogen effectors target a transcriptional complex to reprogram transcription.
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Affiliation(s)
- Xufang Qiu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Kong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Han Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Yachun Lin
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Siqun Tu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiyuan Chen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Mengzhu Zeng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Junhua Xiao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Peiguo Yuan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA
| | - Min Qiu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaixuan Duan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Suomeng Dong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
- The Key Laboratory of Integrated Management of Crop Diseases and Pests (Ministry of Education), College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Biological Interaction and Crop Health, Nanjing Agricultural University, Nanjing 210095, China
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7
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Franco-Echevarría E, Rutherford TJ, Fiedler M, Dean C, Bienz M. Plant vernalization proteins contain unusual PHD superdomains without histone H3 binding activity. J Biol Chem 2022; 298:102540. [PMID: 36174674 PMCID: PMC9640981 DOI: 10.1016/j.jbc.2022.102540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022] Open
Abstract
PHD fingers are modular domains in chromatin-associated proteins that decode the methylation status of histone H3 tails. A PHD finger signature is found in plant vernalization (VEL) proteins, which function as accessory factors of the Polycomb system to control flowering in Arabidopsis through an epigenetic silencing mechanism. It has been proposed that VEL PHD fingers bind to methylated histone H3 tails to facilitate association of the Polycomb silencing machinery with target genes. Here, we use structural analysis by X-ray crystallography to show that the VEL PHD finger forms the central module of a larger compact tripartite superdomain that also contains a zinc finger and a four-helix bundle. This PHD superdomain fold is only found in one other family, the OBERON proteins, which have multiple functions in Arabidopsis meristems to control plant growth. The putative histone-binding surface of OBERON proteins exhibits the characteristic three-pronged pocket of histone-binding PHD fingers and binds to methylated histone H3 tails. However, that of VEL PHD fingers lacks this architecture and exhibits unusually high positive surface charge. This VEL PHD superdomain neither binds to unmodified nor variously modified histone H3 tails, as demonstrated by isothermal calorimetry and NMR spectroscopy. Instead, the VEL PHD superdomain interacts with negatively charged polymers. Our evidence argues for evolution of a divergent function for the PHD superdomain in vernalization that does not involve histone tail decoding.
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Affiliation(s)
| | | | - Marc Fiedler
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Caroline Dean
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom; John Innes Centre, Norwich Research Park, Norwich, United Kingdom.
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.
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Gül N, Yıldız A. An in silico study of how histone tail conformation affects the binding affinity of ING family proteins. PeerJ 2022; 10:e14029. [PMID: 36199288 PMCID: PMC9528904 DOI: 10.7717/peerj.14029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/16/2022] [Indexed: 01/19/2023] Open
Abstract
Background Due to its intrinsically disordered nature, the histone tail is conformationally heterogenic. Therefore, it provides specific binding sites for different binding proteins or factors through reversible post-translational modifications (PTMs). For instance, experimental studies stated that the ING family binds with the histone tail that has methylation on the lysine in position 4. However, numerous complexes featuring a methylated fourth lysine residue of the histone tail can be found in the UniProt database. So the question arose if other factors like the conformation of the histone tail affect the binding affinity. Methods The crystal structure of the PHD finger domain from the proteins ING1, ING2, ING4, and ING5 are docked to four histone H3 tails with two different conformations using Haddock 2.4 and ClusPro. The best four models for each combination are selected and a two-sample t-test is performed to compare the binding affinities of helical conformations vs. linear conformations using Prodigy. The protein-protein interactions are examined using LigPlot. Results The linear histone conformations in predicted INGs-histone H3 complexes exhibit statistically significant higher binding affinity than their helical counterparts (confidence level of 99%). The outputs of predicted models generated by the molecular docking programs Haddock 2.4 and ClusPro are comparable, and the obtained protein-protein interaction patterns are consistent with experimentally confirmed binding patterns. Conclusion The results show that the conformation of the histone tail is significantly affecting the binding affinity of the docking protein. Herewith, this in silico study demonstrated in detail the binding preference of the ING protein family to histone H3 tail. Further research on the effect of certain PTMs on the final tail conformation and the interaction between those factors seem to be promising for a better understanding of epigenetics.
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Affiliation(s)
- Nadir Gül
- Faculty of Natural Sciences, Turkish-German University, Istanbul, Turkey
| | - Ahmet Yıldız
- Faculty of Engineering, Turkish-German University, Istanbul, Turkey
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Ezhova TA. Paradoxes of Plant Epigenetics. Russ J Dev Biol 2021. [DOI: 10.1134/s1062360421060047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Plants have a unique ability to adapt ontogenesis to changing environmental conditions and the influence of stress factors. This ability is based on the existence of two specific features of epigenetic regulation in plants, which seem to be mutually exclusive at first glance. On the one hand, plants are capable of partial epigenetic reprogramming of the genome, which can lead to adaptation of physiology and metabolism to changed environmental conditions as well as to changes in ontogenesis programs. On the other hand, plants can show amazing stability of epigenetic modifications and the ability to transmit them to vegetative and sexual generations. The combination of these inextricably linked epigenetic features not only ensures survival in the conditions of a sessile lifestyle but also underlies a surprisingly wide morphological diversity of plants, which can lead to the appearance of morphs within one population and the existence of interpopulation morphological differences. The review discusses the molecular genetic mechanisms that cause a paradoxical combination of the stability and lability properties of epigenetic modifications and underlie the polyvariance of ontogenesis. We also consider the existing approaches for studying the role of epigenetic regulation in the manifestation of polyvariance of ontogenesis and discuss their limitations and prospects.
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10
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Sundaresan S, Philosoph-Hadas S, Ma C, Jiang CZ, Riov J, Kochanek B, Salim S, Reid MS, Meir S. Role of the KNOTTED1-LIKE HOMEOBOX protein (KD1) in regulating abscission of tomato flower pedicels at early and late stages of the process. PHYSIOLOGIA PLANTARUM 2021; 173:2103-2118. [PMID: 34545591 DOI: 10.1111/ppl.13560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/06/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
The KNOTTED1-LIKE HOMEOBOX PROTEIN1 (KD1) gene is highly expressed in flower and leaf abscission zones (AZs), and KD1 was reported to regulate tomato flower pedicel abscission via alteration of the auxin gradient and response in the flower AZ (FAZ). The present work was aimed to further examine how KD1 regulates signaling factors and regulatory genes involved in pedicel abscission, by using silenced KD1 lines and performing a large-scale transcriptome profiling of the FAZ before and after flower removal, using a customized AZ-specific microarray. The results highlighted a differential expression of regulatory genes in the FAZ of KD1-silenced plants compared to the wild-type. In the TAPG4::antisense KD1-silenced plants, KD1 gene expression decreased before flower removal, resulting in altered expression of regulatory genes, such as epigenetic modifiers, transcription factors, posttranslational regulators, and antioxidative defense factors occurring at zero time and before affecting auxin levels in the FAZ detected at 4 h after flower removal. The expression of additional regulatory genes was altered in the FAZ of KD1-silenced plants at 4-20 h after flower removal, thereby leading to an inhibited abscission phenotype, and downregulation of genes involved in abscission execution and defense processes. Our data suggest that KD1 is a master regulator of the abscission process, which promotes abscission of tomato flower pedicels. This suggestion is based on the inhibitory effect of KD1 silencing on flower pedicel abscission that operates via alteration of various regulatory pathways, which delay the competence acquisition of the FAZ cells to respond to ethylene signaling.
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Affiliation(s)
- Srivignesh Sundaresan
- Department of Postharvest Science, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZiyon, Israel
- Department of Horticulture, Neelakudi Campus, School of Life Sciences, Central University of Tamil Nadu (CUTN), Thiruvarur, India
| | - Sonia Philosoph-Hadas
- Department of Postharvest Science, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZiyon, Israel
| | - Chao Ma
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China
| | - Cai-Zhong Jiang
- Crops Pathology and Genetic Research Unit, USDA-ARS, Davis, California, USA
- Department of Plant Sciences, University of California at Davis, Davis, California, USA
| | - Joseph Riov
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Betina Kochanek
- Department of Postharvest Science, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZiyon, Israel
| | - Shoshana Salim
- Department of Postharvest Science, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZiyon, Israel
| | - Michael S Reid
- Department of Plant Sciences, University of California at Davis, Davis, California, USA
| | - Shimon Meir
- Department of Postharvest Science, Agricultural Research Organization (ARO), Volcani Institute, Rishon LeZiyon, Israel
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Ngwa CJ, Farrukh A, Pradel G. Zinc finger proteins of Plasmodium falciparum. Cell Microbiol 2021; 23:e13387. [PMID: 34418264 DOI: 10.1111/cmi.13387] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/19/2021] [Accepted: 07/24/2021] [Indexed: 01/14/2023]
Abstract
Zinc finger proteins (ZFPs) are a large diverse family of proteins with one or more zinc finger domains in which zinc is important in stabilising the domain. ZFPs can interact with DNA, RNA, lipids or even other proteins and therefore contribute to diverse cellular processes including transcriptional regulation, ubiquitin-mediated protein degradation, mRNA decay and stability. In this review, we provide the first comprehensive classification of ZFPs of the malaria parasite Plasmodium falciparum and provide a state of knowledge on the main ZFPs in the parasite, which include the C2H2, CCCH, RING finger and the PHD finger proteins. TAKE AWAYS: The Plasmodium falciparum genome encodes 170 putative Zinc finger proteins (ZFPs). The C2H2, CCCH, RING finger and PHD finger subfamilies of ZFPs are most represented. Known ZFP functions include the regulation of mRNA metabolism and proteostasis.
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Affiliation(s)
- Che Julius Ngwa
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Afia Farrukh
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, Aachen, Germany
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Zheng S, Bi Y, Chen H, Gong B, Jia S, Li H. Molecular basis for bipartite recognition of histone H3 by the PZP domain of PHF14. Nucleic Acids Res 2021; 49:8961-8973. [PMID: 34365506 PMCID: PMC8421203 DOI: 10.1093/nar/gkab670] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 07/13/2021] [Accepted: 07/23/2021] [Indexed: 11/14/2022] Open
Abstract
Histone recognition constitutes a key epigenetic mechanism in gene regulation and cell fate decision. PHF14 is a conserved multi-PHD finger protein that has been implicated in organ development, tissue homeostasis, and tumorigenesis. Here we show that PHF14 reads unmodified histone H3(1–34) through an integrated PHD1-ZnK-PHD2 cassette (PHF14PZP). Our binding, structural and HDX-MS analyses revealed a feature of bipartite recognition, in which PHF14PZP utilizes two distinct surfaces for concurrent yet separable engagement of segments H3-Nter (e.g. 1–15) and H3-middle (e.g. 14–34) of H3(1–34). Structural studies revealed a novel histone H3 binding mode by PHD1 of PHF14PZP, in which a PHF14-unique insertion loop but not the core β-strands of a PHD finger dominates H3K4 readout. Binding studies showed that H3-PHF14PZP engagement is sensitive to modifications occurring to H3 R2, T3, K4, R8 and K23 but not K9 and K27, suggesting multiple layers of modification switch. Collectively, our work calls attention to PHF14 as a ‘ground’ state (unmodified) H3(1–34) reader that can be negatively regulated by active marks, thus providing molecular insights into a repressive function of PHF14 and its derepression.
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Affiliation(s)
- Shuangping Zheng
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yucong Bi
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Haining Chen
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bo Gong
- Key Laboratory of Biomembrane and Membrane Engineering, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shunji Jia
- Key Laboratory of Biomembrane and Membrane Engineering, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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13
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Qian F, Zhao QY, Zhang TN, Li YL, Su YN, Li L, Sui JH, Chen S, He XJ. A histone H3K27me3 reader cooperates with a family of PHD finger-containing proteins to regulate flowering time in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:787-802. [PMID: 33433058 DOI: 10.1111/jipb.13067] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 01/10/2021] [Indexed: 05/29/2023]
Abstract
Trimethylated histone H3 lysine 27 (H3K27me3) is a repressive histone marker that regulates a variety of developmental processes, including those that determine flowering time. However, relatively little is known about the mechanism of how H3K27me3 is recognized to regulate transcription. Here, we identified BAH domain-containing transcriptional regulator 1 (BDT1) as an H3K27me3 reader. BDT1 is responsible for preventing flowering by suppressing the expression of flowering genes. Mutation of the H3K27me3 recognition sites in the BAH domain disrupted the binding of BDT1 to H3K27me3, leading to de-repression of H3K27me3-enriched flowering genes and an early-flowering phenotype. We also found that BDT1 interacts with a family of PHD finger-containing proteins, which we named PHD1-6, and with CPL2, a Pol II carboxyl terminal domain (CTD) phosphatase responsible for transcriptional repression. Pull-down assays showed that the PHD finger-containing proteins can enhance the binding of BDT1 to the H3K27me3 peptide. Mutations in all of the PHD genes caused increased expression of flowering genes and an early-flowering phenotype. This study suggests that the binding of BDT1 to the H3K27me3 peptide, which is enhanced by PHD proteins, is critical for preventing early flowering.
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Affiliation(s)
- Feng Qian
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Qiu-Yuan Zhao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Tie-Nan Zhang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yu-Lu Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jian-Hua Sui
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
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14
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Abstract
Methylation at DNA, RNA and protein levels plays critical roles in many cellular processes and is associated with diverse differentiation events, physiological activities and human diseases. To aid in the diagnostic and therapeutic design for cancer treatment utilising methylation, this review provides a boutique yet comprehensive overview on methylation at different levels including the mechanisms, cross-talking and clinical implications with a particular focus on cancers. We conclude that DNA methylation is the sole type of methylation that has been largely translated into clinics and used for, mostly, early diagnosis. Translating the onco-therapeutic and prognostic values of RNA and protein methylations into clinical use deserves intensive efforts. Simultaneous examination of methylations at multiple levels or together with other forms of molecular markers represents an interesting research direction with profound clinical translational potential.
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15
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Zhang YZ, Yuan J, Zhang L, Chen C, Wang Y, Zhang G, Peng L, Xie SS, Jiang J, Zhu JK, Du J, Duan CG. Coupling of H3K27me3 recognition with transcriptional repression through the BAH-PHD-CPL2 complex in Arabidopsis. Nat Commun 2020; 11:6212. [PMID: 33277495 PMCID: PMC7718874 DOI: 10.1038/s41467-020-20089-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/12/2020] [Indexed: 01/07/2023] Open
Abstract
Histone 3 Lys 27 trimethylation (H3K27me3)-mediated epigenetic silencing plays a critical role in multiple biological processes. However, the H3K27me3 recognition and transcriptional repression mechanisms are only partially understood. Here, we report a mechanism for H3K27me3 recognition and transcriptional repression. Our structural and biochemical data showed that the BAH domain protein AIPP3 and the PHD proteins AIPP2 and PAIPP2 cooperate to read H3K27me3 and unmodified H3K4 histone marks, respectively, in Arabidopsis. The BAH-PHD bivalent histone reader complex silences a substantial subset of H3K27me3-enriched loci, including a number of development and stress response-related genes such as the RNA silencing effector gene ARGONAUTE 5 (AGO5). We found that the BAH-PHD module associates with CPL2, a plant-specific Pol II carboxyl terminal domain (CTD) phosphatase, to form the BAH-PHD-CPL2 complex (BPC) for transcriptional repression. The BPC complex represses transcription through CPL2-mediated CTD dephosphorylation, thereby causing inhibition of Pol II release from the transcriptional start site. Our work reveals a mechanism coupling H3K27me3 recognition with transcriptional repression through the alteration of Pol II phosphorylation states, thereby contributing to our understanding of the mechanism of H3K27me3-dependent silencing.
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Affiliation(s)
- Yi-Zhe Zhang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jianlong Yuan
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Lingrui Zhang
- grid.169077.e0000 0004 1937 2197Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Chunxiang Chen
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Yuhua Wang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Guiping Zhang
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Li Peng
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China
| | - Si-Si Xie
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Jing Jiang
- grid.256922.80000 0000 9139 560XState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Jian-Kang Zhu
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.169077.e0000 0004 1937 2197Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907 USA
| | - Jiamu Du
- grid.263817.9Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, 518055 Shenzhen, China
| | - Cheng-Guo Duan
- grid.9227.e0000000119573309Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 201602 Shanghai, China ,grid.256922.80000 0000 9139 560XState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
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16
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Structure and function of Pygo in organ development dependent and independent Wnt signalling. Biochem Soc Trans 2020; 48:1781-1794. [PMID: 32677664 DOI: 10.1042/bst20200393] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 11/17/2022]
Abstract
Pygo is a nuclear protein containing two conserved domains, NHD and PHD, which play important roles in embryonic development and carcinogenesis. Pygo was first identified as a core component of the Wnt/β-catenin signalling pathway. However, it has also been reported that the function of Pygo is not always Wnt/β-catenin signalling dependent. In this review, we summarise the functions of both domains of Pygo and show that their functions are synergetic. The PHD domain mainly combines with transcription co-factors, including histone 3 and Bcl9/9l. The NHD domain mainly recruits histone methyltransferase/acetyltransferase (HMT/HAT) to modify lysine 4 of the histone 3 tail (H3K4) and interacts with Chip/LIM-domain DNA-binding proteins (ChiLS) to form enhanceosomes to regulate transcriptional activity. Furthermore, we summarised chromatin modification differences of Pygo in Drosophila (dPygo) and vertebrates, and found that Pygo displayes a chromatin silencing function in Drosophila, while in vertebates, Pygo has a chromatin-activating function due to the two substitution of two amino acid residues. Next, we confirmed the relationship between Pygo and Bcl9/9l and found that Pygo-Bcl/9l are specifically partnered both in the nucleus and in the cytoplasm. Finally, we discuss whether transcriptional activity of Pygo is Wnt/β-catenin dependent during embryonic development. Available information indications that the transcriptional activity of Pygo in embryonic development is either Wnt/β-catenin dependent or independent in both tissue-specific and cell-specific-modes.
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Lu JY, Xiong SX, Yin W, Teng XD, Lou Y, Zhu J, Zhang C, Gu JN, Wilson ZA, Yang ZN. MS1, a direct target of MS188, regulates the expression of key sporophytic pollen coat protein genes in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4877-4889. [PMID: 32374882 PMCID: PMC7410184 DOI: 10.1093/jxb/eraa219] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/29/2020] [Indexed: 05/04/2023]
Abstract
Sporophytic pollen coat proteins (sPCPs) derived from the anther tapetum are deposited into pollen wall cavities and function in pollen-stigma interactions, pollen hydration, and environmental protection. In Arabidopsis, 13 highly abundant proteins have been identified in pollen coat, including seven major glycine-rich proteins GRP14, 16, 17, 18, 19, 20, and GRP-oleosin; two caleosin-related family proteins (AT1G23240 and AT1G23250); three lipase proteins EXL4, EXL5 and EXL6, and ATA27/BGLU20. Here, we show that GRP14, 17, 18, 19, and EXL4 and EXL6 fused with green fluorescent protein (GFP) are translated in the tapetum and then accumulate in the anther locule following tapetum degeneration. The expression of these sPCPs is dependent on two essential tapetum transcription factors, MALE STERILE188 (MS188) and MALE STERILITY 1 (MS1). The majority of sPCP genes are up-regulated within 30 h after MS1 induction and could be restored by MS1 expression driven by the MS188 promoter in ms188, indicating that MS1 is sufficient to activate their expression; however, additional MS1 downstream factors appear to be required for high-level sPCP expression. Our ChIP, in vivo transactivation assay, and EMSA data indicate that MS188 directly activates MS1. Together, these results reveal a regulatory cascade whereby outer pollen wall formation is regulated by MS188 followed by synthesis of sPCPs controlled by MS1.
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Affiliation(s)
- Jie-Yang Lu
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shuang-Xi Xiong
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Wenzhe Yin
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
- Correspondence: or
| | - Xiao-Dong Teng
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yue Lou
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jun Zhu
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Cheng Zhang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jing-Nan Gu
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zoe A Wilson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK
- Correspondence: or
| | - Zhong-Nan Yang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
- Correspondence: or
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18
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Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194567. [PMID: 32360393 PMCID: PMC7294231 DOI: 10.1016/j.bbagrm.2020.194567] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/24/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The precise regulation of gene transcription is required to establish and maintain cell type-specific gene expression programs during multicellular development. In addition to transcription factors, chromatin, and its chemical modification, play a central role in regulating gene expression. In vertebrates, DNA is pervasively methylated at CG dinucleotides, a modification that is repressive to transcription. However, approximately 70% of vertebrate gene promoters are associated with DNA elements called CpG islands (CGIs) that are refractory to DNA methylation. CGIs integrate the activity of a range of chromatin-regulating factors that can post-translationally modify histones and modulate gene expression. This is exemplified by the trimethylation of histone H3 at lysine 4 (H3K4me3), which is enriched at CGI-associated gene promoters and correlates with transcriptional activity. Through studying H3K4me3 at CGIs it has become clear that CGIs shape the distribution of H3K4me3 and, in turn, H3K4me3 influences the chromatin landscape at CGIs. Here we will discuss our understanding of the emerging relationship between CGIs, H3K4me3, and gene expression.
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19
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Miura K, Renhu N, Suzaki T. The PHD finger of Arabidopsis SIZ1 recognizes trimethylated histone H3K4 mediating SIZ1 function and abiotic stress response. Commun Biol 2020; 3:23. [PMID: 31925312 PMCID: PMC6954211 DOI: 10.1038/s42003-019-0746-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 12/19/2019] [Indexed: 11/23/2022] Open
Abstract
Arabidopsis SIZ1 encodes a SUMO E3 ligase to regulate abiotic and biotic stress responses. Among SIZ1 or mammalian PIAS orthologs, plant SIZ1 proteins contain the plant homeodomain (PHD) finger, a C4HC3 zinc finger. Here, we investigated the importance of PHD of Arabidopsis SIZ1. The ProSIZ1::SIZ1(ΔPHD):GFP was unable to complement growth retardation, ABA hypersensitivity, and the cold-sensitive phenotype of the siz1 mutant, but ProSIZ1::SIZ1:GFP could. Substitution of C162S in the PHD finger was unable to complement the siz1 mutation. Tri-methylated histone H3K4 (H3K4me3) was recognized by PHD, not by PHD(C162S). WRKY70 was up-regulated in the siz1-2 mutant and H3K4me3 accumulated at high levels in the WRKY70 promoter. PHD interacts with ATX, which mediates methylation of histone, probably leading to suppression of ATX’s function. These results suggest that the PHD finger of SIZ1 is important for recognition of the histone code and is required for SIZ1 function and transcriptional suppression. Kenji Miura et al. investigate the role of the plant homeodomain (PHD) finger of the Arabidopsis SIZ1 protein. They show that the PHD finger is involved in hormone response and temperature sensitivity, and plays an important role in H3K4 methylation, thereby affecting recognition of histone code and transcriptional suppression.
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Affiliation(s)
- Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan. .,Tsukuba-Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, 305-8572, Japan.
| | - Na Renhu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Takuya Suzaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.,Tsukuba-Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, 305-8572, Japan
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20
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Alam I, Liu CC, Ge HL, Batool K, Yang YQ, Lu YH. Genome wide survey, evolution and expression analysis of PHD finger genes reveal their diverse roles during the development and abiotic stress responses in Brassica rapa L. BMC Genomics 2019; 20:773. [PMID: 31651238 PMCID: PMC6814106 DOI: 10.1186/s12864-019-6080-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 09/04/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Plant homeodomain (PHD) finger proteins are widely present in all eukaryotes and play important roles in chromatin remodeling and transcriptional regulation. The PHD finger can specifically bind a number of histone modifications as an "epigenome reader", and mediate the activation or repression of underlying genes. Many PHD finger genes have been characterized in animals, but only few studies were conducted on plant PHD finger genes to this day. Brassica rapa (AA, 2n = 20) is an economically important vegetal, oilseed and fodder crop, and also a good model crop for functional and evolutionary studies of important gene families among Brassica species due to its close relationship to Arabidopsis thaliana. RESULTS We identified a total of 145 putative PHD finger proteins containing 233 PHD domains from the current version of B. rapa genome database. Gene ontology analysis showed that 67.7% of them were predicted to be located in nucleus, and 91.3% were predicted to be involved in protein binding activity. Phylogenetic, gene structure, and additional domain analyses clustered them into different groups and subgroups, reflecting their diverse functional roles during plant growth and development. Chromosomal location analysis showed that they were unevenly distributed on the 10 B. rapa chromosomes. Expression analysis from RNA-Seq data showed that 55.7% of them were constitutively expressed in all the tested tissues or organs with relatively higher expression levels reflecting their important housekeeping roles in plant growth and development, while several other members were identified as preferentially expressed in specific tissues or organs. Expression analysis of a subset of 18 B. rapa PHD finger genes under drought and salt stresses showed that all these tested members were responsive to the two abiotic stress treatments. CONCLUSIONS Our results reveal that the PHD finger genes play diverse roles in plant growth and development, and can serve as a source of candidate genes for genetic engineering and improvement of Brassica crops against abiotic stresses. This study provides valuable information and lays the foundation for further functional determination of PHD finger genes across the Brassica species.
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Affiliation(s)
- Intikhab Alam
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Cui-Cui Liu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong-Liu Ge
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Khadija Batool
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yan-Qing Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yun-Hai Lu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
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Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL. Nat Commun 2018; 9:2425. [PMID: 29930355 PMCID: PMC6013494 DOI: 10.1038/s41467-018-04836-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 05/24/2018] [Indexed: 02/06/2023] Open
Abstract
The ability of a cell to dynamically switch its chromatin between different functional states constitutes a key mechanism regulating gene expression. Histone mark “readers” display distinct binding specificity to different histone modifications and play critical roles in regulating chromatin states. Here, we show a plant-specific histone reader SHORT LIFE (SHL) capable of recognizing both H3K27me3 and H3K4me3 via its bromo-adjacent homology (BAH) and plant homeodomain (PHD) domains, respectively. Detailed biochemical and structural studies suggest a binding mechanism that is mutually exclusive for either H3K4me3 or H3K27me3. Furthermore, we show a genome-wide co-localization of SHL with H3K27me3 and H3K4me3, and that BAH-H3K27me3 and PHD-H3K4me3 interactions are important for SHL-mediated floral repression. Together, our study establishes BAH-PHD cassette as a dual histone methyl-lysine binding module that is distinct from others in recognizing both active and repressive histone marks. Histone mark reader proteins bind to particular histone modifications and regulate chromatin state. Here, Qian et al. show that the SHORT LIFE reader has a unique ability to recognize both activating and repressive histone marks and that these interactions enable SHORT LIFE to repress flowering in plants.
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22
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Three-component hetero-domino cyclization and copper-catalyzed double A3-coupling reaction of ethane-1,2-diamines, formaldehyde, and alkynes to afford 1,3-dipropargylimidazolidines. Chem Heterocycl Compd (N Y) 2018. [DOI: 10.1007/s10593-018-2273-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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23
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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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24
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Structure and mechanism of plant histone mark readers. SCIENCE CHINA-LIFE SCIENCES 2017; 61:170-177. [PMID: 29019143 DOI: 10.1007/s11427-017-9163-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 08/11/2017] [Indexed: 10/18/2022]
Abstract
In eukaryotes, epigenetic-based mechanisms are involved in almost all the important biological processes. Amongst different epigenetic regulation pathways, the dynamic covalent modifications on histones are the most extensively investigated and characterized types. The covalent modifications on histone can be "read" by specific protein domains and then subsequently trigger downstream signaling events. Plants generally possess epigenetic regulation systems similar to animals and fungi, but also exhibit some plant-specific features. Similar to animals and fungi, plants require distinct protein domains to specifically "read" modified histones in both modification-specific and sequence-specific manners. In this review, we will focus on recent progress of the structural studies on the recognition of the epigenetic marks on histones by plant reader proteins, and further summarize the general and exceptional features of plant histone mark readers.
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Kinetic and high-throughput profiling of epigenetic interactions by 3D-carbene chip-based surface plasmon resonance imaging technology. Proc Natl Acad Sci U S A 2017; 114:E7245-E7254. [PMID: 28808021 DOI: 10.1073/pnas.1704155114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Chemical modifications on histones and DNA/RNA constitute a fundamental mechanism for epigenetic regulation. These modifications often function as docking marks to recruit or stabilize cognate "reader" proteins. So far, a platform for quantitative and high-throughput profiling of the epigenetic interactome is urgently needed but still lacking. Here, we report a 3D-carbene chip-based surface plasmon resonance imaging (SPRi) technology for this purpose. The 3D-carbene chip is suitable for immobilizing versatile biomolecules (e.g., peptides, antibody, DNA/RNA) and features low nonspecific binding, random yet function-retaining immobilization, and robustness for reuses. We systematically profiled binding kinetics of 1,000 histone "reader-mark" pairs on a single 3D-carbene chip and validated two recognition events by calorimetric and structural studies. Notably, a discovery on H3K4me3 recognition by the DNA mismatch repair protein MSH6 in Capsella rubella suggests a mechanism of H3K4me3-mediated DNA damage repair in plant.
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26
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Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains. Biochem J 2017; 474:1633-1651. [PMID: 28341809 PMCID: PMC5415848 DOI: 10.1042/bcj20161053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 12/20/2022]
Abstract
The plant homeodomain (PHD) fingers are among the largest family of epigenetic domains, first characterized as readers of methylated H3K4. Readout of histone post-translational modifications by PHDs has been the subject of intense investigation; however, less is known about the recognition of secondary structure features within the histone tail itself. We solved the crystal structure of the PHD finger of the bromodomain adjacent to zinc finger 2A [BAZ2A, also known as TIP5 (TTF-I/interacting protein 5)] in complex with unmodified N-terminal histone H3 tail. The peptide is bound in a helical folded-back conformation after K4, induced by an acidic patch on the protein surface that prevents peptide binding in an extended conformation. Structural bioinformatics analyses identify a conserved Asp/Glu residue that we name ‘acidic wall’, found to be mutually exclusive with the conserved Trp for K4Me recognition. Neutralization or inversion of the charges at the acidic wall patch in BAZ2A, and homologous BAZ2B, weakened H3 binding. We identify simple mutations on H3 that strikingly enhance or reduce binding, as a result of their stabilization or destabilization of H3 helicity. Our work unravels the structural basis for binding of the helical H3 tail by PHD fingers and suggests that molecular recognition of secondary structure motifs within histone tails could represent an additional layer of regulation in epigenetic processes.
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27
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Xiong X, Panchenko T, Yang S, Zhao S, Yan P, Zhang W, Xie W, Li Y, Zhao Y, Allis CD, Li H. Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2. Nat Chem Biol 2016; 12:1111-1118. [PMID: 27775714 DOI: 10.1038/nchembio.2218] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 09/14/2016] [Indexed: 02/05/2023]
Abstract
Recognition of histone covalent modifications by 'reader' modules constitutes a major mechanism for epigenetic regulation. A recent upsurge of newly discovered histone lysine acylations, such as crotonylation (Kcr), butyrylation (Kbu), and propionylation (Kpr), greatly expands the coding potential of histone lysine modifications. Here we demonstrate that the histone acetylation-binding double PHD finger (DPF) domains of human MOZ (also known as KAT6A) and DPF2 (also known as BAF45d) accommodate a wide range of histone lysine acylations with the strongest preference for Kcr. Crystal structures of the DPF domain of MOZ in complex with H3K14cr, H3K14bu, and H3K14pr peptides reveal that these non-acetyl acylations are anchored in a hydrophobic 'dead-end' pocket with selectivity for crotonylation arising from intimate encapsulation and an amide-sensing hydrogen bonding network. Immunofluorescence and chromatin immunoprecipitation (ChIP)-quantitative PCR (qPCR) showed that MOZ and H3K14cr colocalize in a DPF-dependent manner. Our studies call attention to a new regulatory mechanism centered on histone crotonylation readout by DPF family members.
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Affiliation(s)
- Xiaozhe Xiong
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Tatyana Panchenko
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York, USA
| | - Shuang Yang
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Shuai Zhao
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Peiqiang Yan
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenhao Zhang
- School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Wei Xie
- School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.,Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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28
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Zhang X, Zhao D, Xiong X, He Z, Li H. Multifaceted Histone H3 Methylation and Phosphorylation Readout by the Plant Homeodomain Finger of Human Nuclear Antigen Sp100C. J Biol Chem 2016; 291:12786-12798. [PMID: 27129259 PMCID: PMC4933467 DOI: 10.1074/jbc.m116.721159] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 04/06/2016] [Indexed: 02/05/2023] Open
Abstract
The decoding of histone post-translational modifications by chromatin-binding modules ("readers") constitutes one major mechanism of epigenetic regulation. Nuclear antigen Sp100 (SPECKLED, 100 kDa), a constitutive component of the promyelocytic leukemia nuclear bodies, plays key roles in intrinsic immunity and transcriptional repression. Sp100C, a splicing isoform specifically up-regulated upon interferon stimulation, harbors a unique tandem plant homeodomain (PHD) finger and bromodomain at its C terminus. Combining structural, quantitative binding, and cellular co-localization studies, we characterized Sp100C PHD finger as an unmethylated histone H3 Lys(4) (H3K4me0) reader that tolerates histone H3 Thr(3) phosphorylation (H3T3ph), histone H3 Lys(9) trimethylation (H3K9me3), and histone H3 Ser(10) phosphorylation (H3S10ph), hallmarks associated with the mitotic chromosome. In contrast, whereas H3K4me0 reader activity is conserved in Sp140, an Sp100C paralog, the multivalent tolerance of H3T3ph, H3K9me3, and H3S10ph was lost for Sp140. The complex structure determined at 2.1 Å revealed a highly coordinated lysine ϵ-amine recognition sphere formed by an extended N-terminal motif for H3K4me0 readout. Interestingly, reader pocket rigidification by disulfide bond formation enhanced H3K4me0 binding by Sp100C. An additional complex structure solved at 2.7 Å revealed that H3T3ph is recognized by the arginine residue, Arg(713), that is unique to the PHD finger of Sp100C. Consistent with a restrictive cellular role of Sp100C, these results establish a direct chromatin targeting function of Sp100C that may regulate transcriptional gene silencing and promyelocytic leukemia nuclear body-mediated intrinsic immunity in response to interferon stimulation.
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Affiliation(s)
- Xiaojie Zhang
- From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and
| | - Dan Zhao
- From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and
| | - Xiaozhe Xiong
- From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and
| | - Zhimin He
- From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and
| | - Haitao Li
- From the Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084 and; the Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.
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29
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Successful strategies in the discovery of small-molecule epigenetic modulators with anticancer potential. Future Med Chem 2015; 7:2243-61. [DOI: 10.4155/fmc.15.140] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
As a class, epigenetic enzymes have been identified as clear targets for cancer therapeutics based on their broad hyperactivity in solid and hematological malignancies. The search for effective inhibitors of histone writers and of histone erasers has been a focus of drug discovery efforts both in academic and pharmaceutical laboratories and has led to the identification of some promising leads. This review focuses on the discovery strategies and preclinical evaluation studies of a subset of the more advanced compounds that target histone writers or histone erasers. The specificity and anticancer potential of these small molecules is discussed within the context of their development pipeline.
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30
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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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31
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Mouriz A, López-González L, Jarillo JA, Piñeiro M. PHDs govern plant development. PLANT SIGNALING & BEHAVIOR 2015; 10:e993253. [PMID: 26156103 PMCID: PMC4622442 DOI: 10.4161/15592324.2014.993253] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 11/18/2014] [Indexed: 05/22/2023]
Abstract
Posttranslational modifications present in the amino-terminal tails of histones play a pivotal role in the chromatin-mediated regulation of gene expression patterns that control plant developmental transitions. Therefore, the function of protein domains that specifically recognize these histone covalent modifications and recruit chromatin remodeling complexes and the transcriptional machinery to modulate gene expression is essential for a proper control of plant development. Plant HomeoDomain (PHD) motifs act as effectors that can specifically bind a number of histone modifications and mediate the activation or repression of underlying genes. In this review we summarize recent findings that emphasize the crucial role of this versatile family of chromatin "reader" domains in the transcriptional regulation of plant developmental processes such as meiosis and postmeiotic events during pollen maturation, embryo meristem initiation and root development, germination as well as flowering time.
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Affiliation(s)
- Alfonso Mouriz
- Centro de Biotecnología y Genómica de Plantas; Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid; Madrid, Spain
| | - Leticia López-González
- Centro de Biotecnología y Genómica de Plantas; Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid; Madrid, Spain
| | - Jose A Jarillo
- Centro de Biotecnología y Genómica de Plantas; Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid; Madrid, Spain
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32
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López-Falcón B, Meyer-Nava S, Hernández-Rodríguez B, Campos A, Montero D, Rudiño E, Vázquez M, Zurita M, Valadez-Graham V. Characterization of the Drosophila group ortholog to the amino-terminus of the alpha-thalassemia and mental retardation X-Linked (ATRX) vertebrate protein. PLoS One 2014; 9:e113182. [PMID: 25437195 PMCID: PMC4249797 DOI: 10.1371/journal.pone.0113182] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/21/2014] [Indexed: 12/11/2022] Open
Abstract
The human ATRX gene encodes hATRX, a chromatin-remodeling protein harboring an helicase/ATPase and ADD domains. The ADD domain has two zinc fingers that bind to histone tails and mediate hATRX binding to chromatin. dAtrx, the putative ATRX homolog in Drosophila melanogaster, has a conserved helicase/ATPase domain but lacks the ADD domain. A bioinformatic search of the Drosophila genome using the human ADD sequence allowed us to identify the CG8290 annotated gene, which encodes three ADD harboring- isoforms generated by alternative splicing. This Drosophila ADD domain is highly similar in structure and in the amino acids which mediate the histone tail contacts to the ADD domain of hATRX as shown by 3D modeling. Very recently the CG8290 annotated gene has been named dadd1. We show through pull-down and CoIP assays that the products of the dadd1 gene interact physically with dAtrxL and HP1a and all of them mainly co-localize in the chromocenter, although euchromatic localization can also be observed through the chromosome arms. We confirm through ChIP analyses that these proteins are present in vivo in the same heterochromatic regions. The three isoforms are expressed throughout development. Flies carrying transheterozygous combinations of the dadd1 and atrx alleles are semi-viable and have different phenotypes including the appearance of melanotic masses. Interestingly, the dAdd1-b and c isoforms have extra domains, such as MADF, which suggest newly acquired functions of these proteins. These results strongly support that, in Drosophila, the atrx gene diverged and that the dadd1-encoded proteins participate with dAtrx in some cellular functions such as heterochromatin maintenance.
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Affiliation(s)
- Brenda López-Falcón
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Silvia Meyer-Nava
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Benjamín Hernández-Rodríguez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Adam Campos
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Daniel Montero
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Enrique Rudiño
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Martha Vázquez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (VVG); (MZ)
| | - Viviana Valadez-Graham
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail: (VVG); (MZ)
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33
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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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34
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Du J, Patel DJ. Structural biology-based insights into combinatorial readout and crosstalk among epigenetic marks. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:719-27. [PMID: 24747177 DOI: 10.1016/j.bbagrm.2014.04.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/20/2014] [Accepted: 04/11/2014] [Indexed: 12/11/2022]
Abstract
Epigenetic mechanisms control gene regulation by writing, reading and erasing specific epigenetic marks. Within the context of multi-disciplinary approaches applied to investigate epigenetic regulation in diverse systems, structural biology techniques have provided insights at the molecular level of key interactions between upstream regulators and downstream effectors. The early structural efforts focused on studies at the single domain-single mark level have been rapidly extended to research at the multiple domain-multiple mark level, thereby providing additional insights into connections within the complicated epigenetic regulatory network. This review focuses on recent results from structural studies on combinatorial readout and crosstalk among epigenetic marks. It starts with an overview of multiple readout of histone marks associated with both single and dual histone tails, as well as the potential crosstalk between them. Next, this review further expands on the simultaneous readout by epigenetic modules of histone and DNA marks, thereby establishing connections between histone lysine methylation and DNA methylation at the nucleosomal level. Finally, the review discusses the role of pre-existing epigenetic marks in directing the writing/erasing of certain epigenetic marks. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Jiamu Du
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China.
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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35
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Su X, Zhu G, Ding X, Lee SY, Dou Y, Zhu B, Wu W, Li H. Molecular basis underlying histone H3 lysine-arginine methylation pattern readout by Spin/Ssty repeats of Spindlin1. Genes Dev 2014; 28:622-36. [PMID: 24589551 PMCID: PMC3967050 DOI: 10.1101/gad.233239.113] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 01/30/2014] [Indexed: 01/22/2023]
Abstract
Histone modification patterns and their combinatorial readout have emerged as a fundamental mechanism for epigenetic regulation. Here we characterized Spindlin1 as a histone effector that senses a cis-tail histone H3 methylation pattern involving trimethyllysine 4 (H3K4me3) and asymmetric dimethylarginine 8 (H3R8me2a) marks. Spindlin1 consists of triple tudor-like Spin/Ssty repeats. Cocrystal structure determination established concurrent recognition of H3K4me3 and H3R8me2a by Spin/Ssty repeats 2 and 1, respectively. Both H3K4me3 and H3R8me2a are recognized using an "insertion cavity" recognition mode, contributing to a methylation state-specific layer of regulation. In vivo functional studies suggest that Spindlin1 activates Wnt/β-catenin signaling downstream from protein arginine methyltransferase 2 (PRMT2) and the MLL complex, which together are capable of generating a specific H3 "K4me3-R8me2a" pattern. Mutagenesis of Spindlin1 reader pockets impairs activation of Wnt target genes. Taken together, our work connects a histone "lysine-arginine" methylation pattern readout by Spindlin1-to-Wnt signaling at the transcriptional level.
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Affiliation(s)
- Xiaonan Su
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Guixin Zhu
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaozhe Ding
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shirley Y. Lee
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Bing Zhu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Wei Wu
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haitao Li
- Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
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36
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Wen H, Li Y, Xi Y, Jiang S, Stratton S, Peng D, Tanaka K, Ren Y, Xia Z, Wu J, Li B, Barton MC, Li W, Li H, Shi X. ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression. Nature 2014; 508:263-8. [PMID: 24590075 DOI: 10.1038/nature13045] [Citation(s) in RCA: 229] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 01/20/2014] [Indexed: 12/31/2022]
Abstract
Recognition of modified histones by 'reader' proteins plays a critical role in the regulation of chromatin. H3K36 trimethylation (H3K36me3) is deposited onto the nucleosomes in the transcribed regions after RNA polymerase II elongation. In yeast, this mark in turn recruits epigenetic regulators to reset the chromatin to a relatively repressive state, thus suppressing cryptic transcription. However, much less is known about the role of H3K36me3 in transcription regulation in mammals. This is further complicated by the transcription-coupled incorporation of the histone variant H3.3 in gene bodies. Here we show that the candidate tumour suppressor ZMYND11 specifically recognizes H3K36me3 on H3.3 (H3.3K36me3) and regulates RNA polymerase II elongation. Structural studies show that in addition to the trimethyl-lysine binding by an aromatic cage within the PWWP domain, the H3.3-dependent recognition is mediated by the encapsulation of the H3.3-specific 'Ser 31' residue in a composite pocket formed by the tandem bromo-PWWP domains of ZMYND11. Chromatin immunoprecipitation followed by sequencing shows a genome-wide co-localization of ZMYND11 with H3K36me3 and H3.3 in gene bodies, and its occupancy requires the pre-deposition of H3.3K36me3. Although ZMYND11 is associated with highly expressed genes, it functions as an unconventional transcription co-repressor by modulating RNA polymerase II at the elongation stage. ZMYND11 is critical for the repression of a transcriptional program that is essential for tumour cell growth; low expression levels of ZMYND11 in breast cancer patients correlate with worse prognosis. Consistently, overexpression of ZMYND11 suppresses cancer cell growth in vitro and tumour formation in mice. Together, this study identifies ZMYND11 as an H3.3-specific reader of H3K36me3 that links the histone-variant-mediated transcription elongation control to tumour suppression.
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Affiliation(s)
- Hong Wen
- 1] Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [2] Center for Cancer Epigenetics, Center for Genetics and Genomics, and Center for Stem Cell and Developmental Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [3]
| | - Yuanyuan Li
- 1] MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China [2] Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China [3]
| | - Yuanxin Xi
- 1] Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA [2]
| | - Shiming Jiang
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Sabrina Stratton
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Danni Peng
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Kaori Tanaka
- Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Yongfeng Ren
- 1] MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China [2] Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zheng Xia
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jun Wu
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Bing Li
- Department of Molecular Biology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Michelle C Barton
- 1] Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [2] Center for Cancer Epigenetics, Center for Genetics and Genomics, and Center for Stem Cell and Developmental Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [3] Genes and Development Graduate Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Teaxs 77030, USA
| | - Wei Li
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Haitao Li
- 1] MOE Key Laboratory of Protein Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China [2] Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaobing Shi
- 1] Department of Biochemistry and Molecular Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [2] Center for Cancer Epigenetics, Center for Genetics and Genomics, and Center for Stem Cell and Developmental Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA [3] Genes and Development Graduate Program, The University of Texas Graduate School of Biomedical Sciences, Houston, Teaxs 77030, USA
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Wee S, Dhanak D, Li H, Armstrong SA, Copeland RA, Sims R, Baylin SB, Liu XS, Schweizer L. Targeting epigenetic regulators for cancer therapy. Ann N Y Acad Sci 2014; 1309:30-6. [DOI: 10.1111/nyas.12356] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Susan Wee
- Bristol Myers Squibb Company; Princeton New Jersey
| | - Dash Dhanak
- Janssen Pharmaceuticals; Spring House Pennsylvania
| | - Haitao Li
- Tsinghua University; Beijing P.R. China
| | - Scott A. Armstrong
- Leukemia Center, Memorial Sloan-Kettering Cancer Center; New York New York
| | | | - Robert Sims
- Constellation Pharmaceuticals; Cambridge Massachusetts
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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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39
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Zucchelli C, Tamburri S, Quilici G, Palagano E, Berardi A, Saare M, Peterson P, Bachi A, Musco G. Structure of human Sp140 PHD finger: an atypical fold interacting with Pin1. FEBS J 2013; 281:216-31. [PMID: 24267382 DOI: 10.1111/febs.12588] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/24/2013] [Accepted: 10/25/2013] [Indexed: 12/30/2022]
Abstract
Sp140 is a nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. The presence of several chromatin related modules such as plant homeodomain (PHD), bromodomain and SAND domain suggests a role in chromatin-mediated regulation of gene expression; however, its real function is still elusive. Herein we present the solution structure of Sp140-PHD finger and investigate its role as epigenetic reader in vitro. Sp140-PHD presents an atypical PHD finger fold which does not bind to histone H3 tails but is recognized by peptidylprolyl isomerase Pin1. Pin1 specifically binds to a phosphopeptide corresponding to the L3 loop of Sp140-PHD and catalyzes cis-trans isomerization of a pThr-Pro bond. Moreover co-immunoprecipitation experiments demonstrate FLAG-Sp140 interaction with endogenous Pin1 in vivo. Overall these data include Sp140 in the list of the increasing number of Pin1 binders and expand the regulatory potential of PHD fingers as versatile structural platforms for diversified interactions.
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Affiliation(s)
- Chiara Zucchelli
- Dulbecco Telethon Institute, c/o Biomolecular NMR Laboratory, S. Raffaele Scientific Institute, Milano, Italy
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40
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Dreveny I, Deeves SE, Fulton J, Yue B, Messmer M, Bhattacharya A, Collins HM, Heery DM. The double PHD finger domain of MOZ/MYST3 induces α-helical structure of the histone H3 tail to facilitate acetylation and methylation sampling and modification. Nucleic Acids Res 2013; 42:822-35. [PMID: 24150941 PMCID: PMC3902925 DOI: 10.1093/nar/gkt931] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Histone tail modifications control many nuclear processes by dictating the dynamic exchange of regulatory proteins on chromatin. Here we report novel insights into histone H3 tail structure in complex with the double PHD finger (DPF) of the lysine acetyltransferase MOZ/MYST3/KAT6A. In addition to sampling H3 and H4 modification status, we show that the DPF cooperates with the MYST domain to promote H3K9 and H3K14 acetylation, although not if H3K4 is trimethylated. Four crystal structures of an extended DPF alone and in complex with unmodified or acetylated forms of the H3 tail reveal the molecular basis of crosstalk between H3K4me3 and H3K14ac. We show for the first time that MOZ DPF induces α-helical conformation of H3K4-T11, revealing a unique mode of H3 recognition. The helical structure facilitates sampling of H3K4 methylation status, and proffers H3K9 and other residues for modification. Additionally, we show that a conserved double glycine hinge flanking the H3 tail helix is required for a conformational change enabling docking of H3K14ac with the DPF. In summary, our data provide the first observations of extensive helical structure in a histone tail, revealing the inherent ability of the H3 tail to adopt alternate conformations in complex with chromatin regulators.
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Affiliation(s)
- Ingrid Dreveny
- Centre for Biomolecular Sciences, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, UK
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41
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A phylogenetic study of SPBP and RAI1: evolutionary conservation of chromatin binding modules. PLoS One 2013; 8:e78907. [PMID: 24205348 PMCID: PMC3799622 DOI: 10.1371/journal.pone.0078907] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 09/24/2013] [Indexed: 01/08/2023] Open
Abstract
Our genome is assembled into and array of highly dynamic nucleosome structures allowing spatial and temporal access to DNA. The nucleosomes are subject to a wide array of post-translational modifications, altering the DNA-histone interaction and serving as docking sites for proteins exhibiting effector or “reader” modules. The nuclear proteins SPBP and RAI1 are composed of several putative “reader” modules which may have ability to recognise a set of histone modification marks. Here we have performed a phylogenetic study of their putative reader modules, the C-terminal ePHD/ADD like domain, a novel nucleosome binding region and an AT-hook motif. Interactions studies in vitro and in yeast cells suggested that despite the extraordinary long loop region in their ePHD/ADD-like chromatin binding domains, the C-terminal region of both proteins seem to adopt a cross-braced topology of zinc finger interactions similar to other structurally determined ePHD/ADD structures. Both their ePHD/ADD-like domain and their novel nucleosome binding domain are highly conserved in vertebrate evolution, and construction of a phylogenetic tree displayed two well supported clusters representing SPBP and RAI1, respectively. Their genome and domain organisation suggest that SPBP and RAI1 have occurred from a gene duplication event. The phylogenetic tree suggests that this duplication has happened early in vertebrate evolution, since only one gene was identified in insects and lancelet. Finally, experimental data confirm that the conserved novel nucleosome binding region of RAI1 has the ability to bind the nucleosome core and histones. However, an adjacent conserved AT-hook motif as identified in SPBP is not present in RAI1, and deletion of the novel nucleosome binding region of RAI1 did not significantly affect its nuclear localisation.
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42
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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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Santiveri CM, García-Mayoral MF, Pérez-Cañadillas JM, Jiménez MA. NMR structure note: PHD domain from death inducer obliterator protein and its interaction with H3K4me3. JOURNAL OF BIOMOLECULAR NMR 2013; 56:183-190. [PMID: 23579637 DOI: 10.1007/s10858-013-9726-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 04/02/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Clara M Santiveri
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
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44
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Yang J, Lee S, Hang R, Kim SR, Lee YS, Cao X, Amasino R, An G. OsVIL2 functions with PRC2 to induce flowering by repressing OsLFL1 in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:566-78. [PMID: 23083333 DOI: 10.1111/tpj.12057] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 10/16/2012] [Indexed: 05/18/2023]
Abstract
Flowering is exquisitely regulated by both promotive and inhibitory factors. Molecular genetic studies with Arabidopsis have verified several epigenetic repressors that regulate flowering time. However, the roles of chromatin remodeling factors in developmental processes have not been well explored in Oryza sativa (rice). We identified a chromatin remodeling factor OsVIL2 (O. sativa VIN3-LIKE 2) that promotes flowering. OsVIL2 contains a plant homeodomain (PHD) finger, which is a conserved motif of histone binding proteins. Insertion mutations in OsVIL2 caused late flowering under both long and short days. In osvil2 mutants OsLFL1 expression was increased, but that of Ehd1, Hd3a and RFT1 was reduced. We demonstrated that OsVIL2 is bound to native histone H3 in vitro. Chromatin immunoprecipitation analyses showed that OsVIL2 was directly associated with OsLFL1 chromatin. We also observed that H3K27me3 was significantly enriched by OsLFL1 chromatin in the wild type, but that this enrichment was diminished in the osvil2 mutants. These results indicated that OsVIL2 epigenetically represses OsLFL1 expression. We showed that OsVIL2 physically interacts with OsEMF2b, a component of polycomb repression complex 2. As observed from osvil2, a null mutation of OsEMF2b caused late flowering by increasing OsLFL1 expression and decreasing Ehd1 expression. Thus, we conclude that OsVIL2 functions together with PRC2 to induce flowering by repressing OsLFL1.
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Affiliation(s)
- Jungil Yang
- Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea
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45
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Zhou Y, Tan B, Luo M, Li Y, Liu C, Chen C, Yu CW, Yang S, Dong S, Ruan J, Yuan L, Zhang Z, Zhao L, Li C, Chen H, Cui Y, Wu K, Huang S. HISTONE DEACETYLASE19 interacts with HSL1 and participates in the repression of seed maturation genes in Arabidopsis seedlings. THE PLANT CELL 2013; 25:134-48. [PMID: 23362207 PMCID: PMC3584530 DOI: 10.1105/tpc.112.096313] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Revised: 12/21/2012] [Accepted: 12/30/2012] [Indexed: 05/18/2023]
Abstract
The seed maturation genes are specifically and highly expressed during late embryogenesis. In this work, yeast two-hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays revealed that HISTONE DEACETYLASE19 (HDA19) interacted with the HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE2-LIKE1 (HSL1), and the zinc-finger CW [conserved Cys (C) and Trp (W) residues] domain of HSL1 was responsible for the interaction. Furthermore, we found that mutations in HDA19 resulted in the ectopic expression of seed maturation genes in seedlings, which was associated with increased levels of gene activation marks, such as Histone H3 acetylation (H3ac), Histone H4 acetylation (H4ac), and Histone H3 Lys 4 tri-methylation (H3K4me3), but decreased levels of the gene repression mark Histone H3 Lys 27 tri-methylation (H3K27me3) in the promoter and/or coding regions. In addition, elevated transcription of certain seed maturation genes was also found in the hsl1 mutant seedlings, which was also accompanied by the enrichment of gene activation marks but decreased levels of the gene repression mark. Chromatin immunoprecipitation assays showed that HDA19 could directly bind to the chromatin of the seed maturation genes. These results suggest that HDA19 and HSL1 may act together to repress seed maturation gene expression during germination. Further genetic analyses revealed that the homozygous hsl1 hda19 double mutants are embryonic lethal, suggesting that HDA19 and HSL1 may play a vital role during embryogenesis.
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Affiliation(s)
- Yi Zhou
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Bin Tan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Ming Luo
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yin Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chen Liu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chen Chen
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
| | - Chun-Wei Yu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Songguang Yang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Shuai Dong
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jiuxiao Ruan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Liangbin Yuan
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhou Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Linmao Zhao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Chenlong Li
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
| | - Huhui Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
| | - Keqiang Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- Address correspondences to
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He C, Li F, Zhang J, Wu J, Shi Y. The methyltransferase NSD3 has chromatin-binding motifs, PHD5-C5HCH, that are distinct from other NSD (nuclear receptor SET domain) family members in their histone H3 recognition. J Biol Chem 2012; 288:4692-703. [PMID: 23269674 DOI: 10.1074/jbc.m112.426148] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The NSD (nuclear receptor SET domain-containing) family members, consisting of NSD1, NSD2 (MMSET/WHSC1), and NSD3 (WHSC1L1), are SET domain-containing methyltransferases and aberrant expression of each member has been implicated in multiple diseases. They have specific mono- and dimethylase activities for H3K36, whereas play nonredundant roles during development. Aside from the well characterized catalytic SET domain, NSD proteins have multiple potential chromatin-binding motifs that are clinically relevant, including the fifth plant homeodomain (PHD5) and the adjacent Cys-His-rich domain (C5HCH) located at the C terminus. Herein, we report the crystal structures of the PHD5-C5HCH module of NSD3, in the free state and in complex with H3(1-7) (H3 residues 1-7), H3(1-15) (H3 residues 1-15), and H3(1-15)K9me3 (H3 residues 1-15 with trimethylation on K9) peptides. These structures reveal that the PHD5 and C5HCH domains fold into a novel integrated PHD-PHD-like structural module with H3 peptide bound only on the surface of PHD5 and provide the molecular basis for the recognition of unmodified H3K4 and trimethylated H3K9 by NSD3 PHD5. Structural studies and binding assays show that differences exist in histone binding specificity of the PHD5 domain between three members of the NSD family. For NSD2, the PHD5-C5HCH:H3 N terminus interaction is largely conserved, although with a stronger preference for unmethylated H3K9 (H3K9me0) than trimethylated H3K9 (H3K9me3), and NSD1 PHD5-C5HCH does not bind to H3 peptides. Our results shed light on how NSD proteins that mediate H3K36 methylation are localized to specific genomic sites and provide implications for the mechanism of functional diversity of NSD proteins.
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Affiliation(s)
- Chao He
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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47
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Wang J, Muntean AG, Wu L, Hess JL. A subset of mixed lineage leukemia proteins has plant homeodomain (PHD)-mediated E3 ligase activity. J Biol Chem 2012; 287:43410-6. [PMID: 23129768 DOI: 10.1074/jbc.m112.423855] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mixed lineage leukemia protein MLL1 contains four highly conserved plant homeodomain (PHD) fingers, which are invariably deleted in oncogenic MLL1 fusion proteins in human leukemia. Here we show that the second PHD finger (PHD2) of MLL1 is an E3 ubiquitin ligase in the presence of the E2-conjugating enzyme CDC34. This activity is conserved in the second PHD finger of MLL4, the closest homolog to MLL1 but not in MLL2 or MLL3. Mutation of PHD2 leads to MLL1 stabilization, as well as increased transactivation ability and MLL1 recruitment to the target gene loci, suggesting that PHD2 negatively regulates MLL1 activity.
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Affiliation(s)
- Jingya Wang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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48
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Spiliotopoulos D, Spitaleri A, Musco G. Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations and binding free energy calculations: AIRE-PHD1, a comparative study. PLoS One 2012; 7:e46902. [PMID: 23077531 PMCID: PMC3471955 DOI: 10.1371/journal.pone.0046902] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 09/06/2012] [Indexed: 01/13/2023] Open
Abstract
PHD fingers represent one of the largest families of epigenetic readers capable of decoding post-translationally modified or unmodified histone H3 tails. Because of their direct involvement in human pathologies they are increasingly considered as a potential therapeutic target. Several PHD/histone-peptide structures have been determined, however relatively little information is available on their dynamics. Studies aiming to characterize the dynamic and energetic determinants driving histone peptide recognition by epigenetic readers would strongly benefit from computational studies. Herein we focus on the dynamic and energetic characterization of the PHD finger subclass specialized in the recognition of histone H3 peptides unmodified in position K4 (H3K4me0). As a case study we focused on the first PHD finger of autoimmune regulator protein (AIRE-PHD1) in complex with H3K4me0. PCA analysis of the covariance matrix of free AIRE-PHD1 highlights the presence of a "flapping" movement, which is blocked in an open conformation upon binding to H3K4me0. Moreover, binding free energy calculations obtained through Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) methodology are in good qualitative agreement with experiments and allow dissection of the energetic terms associated with native and alanine mutants of AIRE-PHD1/H3K4me0 complexes. MM/PBSA calculations have also been applied to the energetic analysis of other PHD fingers recognizing H3K4me0. In this case we observe excellent correlation between computed and experimental binding free energies. Overall calculations show that H3K4me0 recognition by PHD fingers relies on compensation of the electrostatic and polar solvation energy terms and is stabilized by non-polar interactions.
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Affiliation(s)
- Dimitrios Spiliotopoulos
- Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular NMR Laboratory, Center for Translational Genomics and Bioinformatics, Milano, Italy
| | - Andrea Spitaleri
- Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular NMR Laboratory, Center for Translational Genomics and Bioinformatics, Milano, Italy
| | - Giovanna Musco
- Dulbecco Telethon Institute c/o S. Raffaele Scientific Institute, Biomolecular NMR Laboratory, Center for Translational Genomics and Bioinformatics, Milano, Italy
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