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Yuan XN, Shao YC, Guan XQ, Liu Q, Chu MF, Yang ZL, Li H, Zhao S, Tian YH, Zhang JW, Wei L. METTL3 orchestrates glycolysis by stabilizing the c-Myc/WDR5 complex in triple-negative breast cancer. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119716. [PMID: 38547933 DOI: 10.1016/j.bbamcr.2024.119716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND The carcinogenic transcription factor c-Myc is the most aggressive oncogene, which drive malignant transformation and dissemination of triple-negative breast cancer (TNBC). Recruitment of many cofactors, especially WDR5, a protein that nucleates H3K4me chromatin modifying complexes, play a pivotal role in regulating c-Myc-dependent gene transcription, a critical process for c-Myc signaling to function in a variety of biological and pathological contexts. For this reason, interrupting the interaction between c-Myc and the transcription cofactor WDR5 may become the most promising new strategy for treating c-Myc driven TNBC. METHODS Immunoprecipitation and mass spectrometry (IP-MS) is used to screen proteins that bind c-Myc/WDR5 interactions. The interaction of METTL3 with c-Myc/WDR5 in breast cancer tissues and TNBC cells was detected by Co-IP and immunofluorescence. Subsequently, we further analyzed the influence of METTL3 expression on c-Myc/WDR5 protein expression and its interaction stability by Western blot and Co-IP. The correlation between METTL3 and c-Myc pathway was analyzed by ChIP-seq sequencing and METTL3 knockdown transcriptome data. The effect of METTL3 expression on c-Myc transcriptional activity was detected by ChIP-qPCR and Dual Luciferase Reporter. At the same time, the overexpression vector METTL3-MUT (m6A) was constructed, which mutated the methyltransferase active site (Aa395-398, DPPW/APPA), and further explored whether the interaction between METTL3 and c-Myc/WDR5 was independent of methyltransferase activity. In addition, we also detected the changes of METTL3 expression on TNBC's sensitivity to small molecule inhibitors such as JQ1 and OICR9429 by CCK8, Transwell and clonal formation assays. Finally, we further verified our conclusions in spontaneous tumor formation mouse MMTV-PyMT and nude mouse orthotopic transplantation tumor models. RESULTS METTL3 was found to bind mainly to c-Myc/WDR5 protein in the nucleus. It enhances the stability of c-Myc/WDR5 interaction through its methyltransferase independent mechanism, thereby enhancing the transcriptional activity of c-Myc on downstream glucose metabolism genes. Notably, the study also confirmed that METTL3 can directly participate in the transcription of glucose metabolism genes as a transcription factor, and knockdown METTL3 enhances the drug sensitivity of breast cancer cells to small molecule inhibitors JQ1 and OICR9429. The study was further confirmed by spontaneous tumor formation mouse MMTV-PyMT and nude mouse orthotopic transplantation tumor models. CONCLUSION METTL3 binds to the c-Myc/WDR5 protein complex and promotes glycolysis, which plays a powerful role in promoting TNBC progression. Our findings further broaden our understanding of the role and mechanism of action of METTL3, and may open up new therapeutic avenues for effective treatment of TNBC with high c-Myc expression.
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Affiliation(s)
- Xiao-Ning Yuan
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - You-Cheng Shao
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Xiao-Qing Guan
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Qin Liu
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Meng-Fei Chu
- Department of Human Anatomy, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Ze-Lin Yang
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Hui Li
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Sai Zhao
- Department of Human Anatomy, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China
| | - Yi-Hao Tian
- Department of Human Anatomy, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China.
| | - Jing-Wei Zhang
- Department of Breast and Thyroid Surgery, Zhongnan Hospital of Wuhan University, Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Cancer Clinical Study Center, Wuhan, Hubei 430071, PR China.
| | - Lei Wei
- Department of Pathology and Pathophysiology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, Hubei 430071, PR China.
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Dashti P, Lewallen EA, Gordon JAR, Montecino MA, Davie JR, Stein GS, van Leeuwen JPTM, van der Eerden BCJ, van Wijnen AJ. Epigenetic regulators controlling osteogenic lineage commitment and bone formation. Bone 2024; 181:117043. [PMID: 38341164 DOI: 10.1016/j.bone.2024.117043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/08/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Bone formation and homeostasis are controlled by environmental factors and endocrine regulatory cues that initiate intracellular signaling pathways capable of modulating gene expression in the nucleus. Bone-related gene expression is controlled by nucleosome-based chromatin architecture that limits the accessibility of lineage-specific gene regulatory DNA sequences and sequence-specific transcription factors. From a developmental perspective, bone-specific gene expression must be suppressed during the early stages of embryogenesis to prevent the premature mineralization of skeletal elements during fetal growth in utero. Hence, bone formation is initially inhibited by gene suppressive epigenetic regulators, while other epigenetic regulators actively support osteoblast differentiation. Prominent epigenetic regulators that stimulate or attenuate osteogenesis include lysine methyl transferases (e.g., EZH2, SMYD2, SUV420H2), lysine deacetylases (e.g., HDAC1, HDAC3, HDAC4, HDAC7, SIRT1, SIRT3), arginine methyl transferases (e.g., PRMT1, PRMT4/CARM1, PRMT5), dioxygenases (e.g., TET2), bromodomain proteins (e.g., BRD2, BRD4) and chromodomain proteins (e.g., CBX1, CBX2, CBX5). This narrative review provides a broad overview of the covalent modifications of DNA and histone proteins that involve hundreds of enzymes that add, read, or delete these epigenetic modifications that are relevant for self-renewal and differentiation of mesenchymal stem cells, skeletal stem cells and osteoblasts during osteogenesis.
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Affiliation(s)
- Parisa Dashti
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Orthopedic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Eric A Lewallen
- Department of Biological Sciences, Hampton University, Hampton, VA, USA
| | | | - Martin A Montecino
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad Andres Bello, Santiago, Chile; Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
| | - James R Davie
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada; CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, Manitoba R3E 0V9, Canada.
| | - Gary S Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | | | - Bram C J van der Eerden
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Andre J van Wijnen
- Department of Internal Medicine, Erasmus MC, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Biochemistry, University of Vermont, Burlington, VT, USA.
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Kim YJ, Jung KH. WD40-domain protein GORI is an integrative scaffold that is required for pollen tube growth in rice. PLANT SIGNALING & BEHAVIOR 2023; 18:2082678. [PMID: 35642508 PMCID: PMC9851197 DOI: 10.1080/15592324.2022.2082678] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The pollen tube plays a critical role in angiosperm plants by delivering sperm gametes for double fertilization. Although the molecular mechanisms underlying pollen tube germination and growth are crucial to crop plants, they are poorly understood. Here, we describe recent advancements in the understanding of the role of the WD40-domain protein in regulating pollen germination and discuss future directions to investigate its role in rice. GORI encodes a seven-WD40-motif protein that interacts with an AP180 N-terminal homology (ANTH)-domain protein, which modulates clathrin-mediated endocytosis (CME), and regulates Rac6 activity in the apical plasma membrane of elongating pollen tubes. Loss of function of GORI or Rac6 reduces pollen germination and tube growth, thereby resulting in male sterility in rice. In contrast, overexpression of Rac6 increases pollen tube elongation, with this effect being rescued by GORI overexpression. In the absence of ANTH, pollen germination was reduced, similar to the results observed after inhibitor treatment, indicating that pollen germination partially requires CME. Our findings demonstrated that the GORI protein is a positive regulator of pollen germination and tube growth, serving as a link between Rac6 activity regulation and ANTH-mediated endocytosis.
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Affiliation(s)
- Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, Pusan National University, Miryang, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
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Zhang X, Feng Q, Miao J, Zhu J, Zhou C, Fan D, Lu Y, Tian Q, Wang Y, Zhan Q, Wang ZQ, Wang A, Zhang L, Shangguan Y, Li W, Chen J, Weng Q, Huang T, Tang S, Si L, Huang X, Wang ZX, Han B. The WD40 domain-containing protein Ehd5 positively regulates flowering in rice (Oryza sativa). THE PLANT CELL 2023; 35:4002-4019. [PMID: 37648256 PMCID: PMC10615205 DOI: 10.1093/plcell/koad223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 09/01/2023]
Abstract
Heading date (flowering time), which greatly influences regional and seasonal adaptability in rice (Oryza sativa), is regulated by many genes in different photoperiod pathways. Here, we characterized a heading date gene, Early heading date 5 (Ehd5), using a modified bulked segregant analysis method. The ehd5 mutant showed late flowering under both short-day and long-day conditions, as well as reduced yield, compared to the wild type. Ehd5, which encodes a WD40 domain-containing protein, is induced by light and follows a circadian rhythm expression pattern. Transcriptome analysis revealed that Ehd5 acts upstream of the flowering genes Early heading date 1 (Ehd1), RICE FLOWERING LOCUS T 1 (RFT1), and Heading date 3a (Hd3a). Functional analysis showed that Ehd5 directly interacts with Rice outermost cell-specific gene 4 (Roc4) and Grain number, plant height, and heading date 8 (Ghd8), which might affect the formation of Ghd7-Ghd8 complexes, resulting in increased expression of Ehd1, Hd3a, and RFT1. In a nutshell, these results demonstrate that Ehd5 functions as a positive regulator of rice flowering and provide insight into the molecular mechanisms underlying heading date.
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Affiliation(s)
- Xuening Zhang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
- University of Chinese Academy of Sciences, Beijing 100049,China
| | - Qi Feng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Jiashun Miao
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Jingjie Zhu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Congcong Zhou
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Danlin Fan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Yiqi Lu
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Qilin Tian
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Yongchun Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Qilin Zhan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Zi-Qun Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Ahong Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Lei Zhang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Yingying Shangguan
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Wenjun Li
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Jiaying Chen
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Qijun Weng
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Tao Huang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Shican Tang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Lizhen Si
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234,China
| | - Zi-Xuan Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233,China
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Han QL, Zhang XL, Ren PX, Mei LH, Lin WH, Wang L, Cao Y, Li K, Bai F. Discovery, evaluation and mechanism study of WDR5-targeted small molecular inhibitors for neuroblastoma. Acta Pharmacol Sin 2023; 44:877-887. [PMID: 36207403 PMCID: PMC10043273 DOI: 10.1038/s41401-022-00999-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022] Open
Abstract
Neuroblastoma is the most common and deadliest tumor in infancy. WDR5 (WD Repeat Domain 5), a critical factor supporting an N-myc transcriptional complex via its WBM site and interacting with chromosome via its WIN site, promotes the progression of neuroblastoma, thus making it a potential anti-neuroblastoma drug target. So far, a few WIN site inhibitors have been reported, and the WBM site disruptors are rare to see. In this study we conducted virtual screening to identify candidate hit compounds targeting the WBM site of WDR5. As a result, 60 compounds were selected as candidate WBM site inhibitors. Cell proliferation assay demonstrated 6 structurally distinct WBM site inhibitors, numbering as compounds 4, 7, 11, 13, 19 and 22, which potently suppressed 3 neuroblastoma cell lines (MYCN-amplified IMR32 and LAN5 cell lines, and MYCN-unamplified SK-N-AS cell line). Among them, compound 19 suppressed the proliferation of IMR32 and LAN5 cells with EC50 values of 12.34 and 14.89 μM, respectively, and exerted a moderate inhibition on SK-N-AS cells, without affecting HEK293T cells at 20 μM. Analysis of high-resolution crystal complex structure of compound 19 against WDR5 revealed that it competitively occupied the hydrophobic pocket where V264 was located, which might disrupt the interaction of MYC with WDR5 and further MYC-medicated gene transcription. By performing RNA-seq analysis we demonstrated the differences in molecular action mechanisms of the compound 19 and a WIN site inhibitor OICR-9429. Most interestingly, we established the particularly high synergy rate by combining WBM site inhibitor 19 and the WIN site inhibitor OICR-9429, providing a novel therapeutic avenue for neuroblastoma.
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Affiliation(s)
- Qi-Lei Han
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Xiang-Lei Zhang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Peng-Xuan Ren
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Information Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Liang-He Mei
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Wei-Hong Lin
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Lin Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Information Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yu Cao
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
- School of Information Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Kai Li
- Department of Pediatric Surgery, Children's Hospital of Fudan University, Shanghai, 201102, China.
| | - Fang Bai
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
- School of Information Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
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Qiao G, Xing J, Luo X, Zhang C, Yi J. Integrated bioinformatics analysis and screening of hub genes in polycystic ovary syndrome. Endocrine 2022; 78:615-627. [PMID: 36068422 DOI: 10.1007/s12020-022-03181-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/23/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE Polycystic ovary syndrome (PCOS) is one of the most common endocrine and metabolic disorders, posing a serious threat to the health of women. Herein, we aimed to explore new biomarkers and potential therapeutic targets for PCOS by employing integrated bioinformatics tools. METHODS Three gene expression profile datasets (GSE138518, GSE155489, GSE106724) were obtained from the Gene Expression Omnibus database and the differentially expressed genes in PCOS and normal groups with an adjusted p-value < 0.05 and a |log fold change (FC) | > 1.2 were first identified using the DESeq package. The weighted correlation network analysis (WGCNA) R package was used to identify clusters of highly correlated genes or modules associated with PCOS. Protein-protein interaction (PPI) network analysis and visualization of genes in the key module were performed using the STRINGdb database and the NetworkX package (edge > 5), respectively. The genes overlapping among the key module genes and PCOS-associated genes were further analyzed. Ligand molecules with strong binding energy < -10 kJ/mol to GNB3 were screened in the drug library using MTiOpenScreen. AutoDock, ChimeraX, and BIOVIA Discovery Studio Visualizer were further used to elucidate the mechanism of ligand interaction with GNB3. Finally, the relationship between GNB3 and PCOS was verified using experimental models in vivo and in vitro. RESULTS Of the 11 modules identified by WGCNA, the black module had the highest correlation with PCOS (correlation = 0.96, P = 0.00016). The PPI network of 351 related genes revealed that VCL, GNB3, MYH11, LMNA, MLLT4, EZH2, PAK3, and CHRM1 have important roles in PCOS. The hub gene GNB3 was identified by taking the intersection of PCOS-related gene sets. MTiOpenScreen revealed that five compounds interacted with GNB3. Of these five, compound 1 had the strongest binding ability and can bind amino acids in the WD40 motif of GNB3, which in turn affects the function of the G protein-coupled receptor β subunit. GNB3 was also significantly downregulated in PCOS models. CONCLUSION We identified the hub gene GNB3 as the most important regulatory gene in PCOS. We suggest that compound 1 can target the WD40 motif of GNB3 to affect related functions and must be considered as a lead compound for drug development. This study will provide new insights into the development of PCOS-related drugs.
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Affiliation(s)
- Gan Qiao
- Department of Pharmacology, School of Pharmacy, Nucleic Acid Medicine of Luzhou Key Laboratory, Central Nervous System Drug Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jinshan Xing
- Department of Neurosurgery, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xin Luo
- Department of Pharmacology, School of Pharmacy, Nucleic Acid Medicine of Luzhou Key Laboratory, Central Nervous System Drug Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Chunxiang Zhang
- Nucleic Acid Medicine of Luzhou Key Laboratory, Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, Sichuan, China.
| | - Jingyan Yi
- Department of Medical Cell Biology and Genetics, School of Basic Medical Sciences, Nucleic Acid Medicine of Luzhou Key Laboratory, Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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7
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Ka M, Kim HG, Kim WY. WDR5-HOTTIP Histone Modifying Complex Regulates Neural Migration and Dendrite Polarity of Pyramidal Neurons via Reelin Signaling. Mol Neurobiol 2022; 59:5104-5120. [PMID: 35672601 PMCID: PMC9378496 DOI: 10.1007/s12035-022-02905-4] [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: 03/11/2022] [Accepted: 05/26/2022] [Indexed: 11/26/2022]
Abstract
WD-repeat domain 5 (WDR5), a core component of histone methyltransferase complexes, is associated with Kabuki syndrome and Kleefstra syndrome that feature intellectual disability and neurodevelopmental delay. Despite its critical status in gene regulation and neurological disorders, the role of WDR5 in neural development is unknown. Here we show that WDR5 is required for normal neuronal placement and dendrite polarization in the developing cerebral cortex. WDR5 knockdown led to defects in both entry into the bipolar transition of pyramidal neurons within the intermediate zone and radial migration into cortical layers. Moreover, WDR5 deficiency disrupted apical and basal polarity of cortical dendrites. Aberrant dendritic spines and synapses accompanied the dendrite polarity phenotype. WDR5 deficiency reduced expression of reelin signaling receptors, ApoER and VdldR, which were associated with abnormal H3K4 methylation and H4 acetylation on their promoter regions. Finally, an lncRNA, HOTTIP, was found to be a partner of WDR5 to regulate dendritic polarity and reelin signaling via histone modification. Our results demonstrate a novel role for WDR5 in neuronal development and provide mechanistic insights into the neuropathology associated with histone methyltransferase dysfunction.
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Affiliation(s)
- Minhan Ka
- Department of Advanced Toxicology Research, Korea Institute of Toxicology, KRICT, Daejeon, 34114, Republic of Korea
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamid Bin Khalifa University, Doha, Qatar
| | - Woo-Yang Kim
- Department of Biological Sciences, Kent State University, Kent, OH, 44242, USA.
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Imran A, Moyer BS, Kalina D, Duncan TM, Moody KJ, Wolfe AJ, Cosgrove MS, Movileanu L. Convergent Alterations of a Protein Hub Produce Divergent Effects within a Binding Site. ACS Chem Biol 2022; 17:1586-1597. [PMID: 35613319 PMCID: PMC9207812 DOI: 10.1021/acschembio.2c00273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Progress in tumor
sequencing and cancer databases has created an
enormous amount of information that scientists struggle to sift through.
While several research groups have created computational methods to
analyze these databases, much work still remains in distinguishing
key implications of pathogenic mutations. Here, we describe an approach
to identify and evaluate somatic cancer mutations of WD40 repeat protein
5 (WDR5), a chromatin-associated protein hub. This multitasking protein
maintains the functional integrity of large multi-subunit enzymatic
complexes of the six human SET1 methyltransferases. Remarkably, the
somatic cancer mutations of WDR5 preferentially distribute within
and around an essential cavity, which hosts the WDR5 interaction (Win)
binding site. Hence, we assessed the real-time binding kinetics of
the interactions of key clustered WDR5 mutants with the Win motif
peptide ligands of the SET1 family members (SET1Win). Our
measurements highlight that this subset of mutants exhibits divergent
perturbations in the kinetics and strength of interactions not only
relative to those of the native WDR5 but also among various SET1Win ligands. These outcomes could form a fundamental basis
for future drug discovery and other developments in medical biotechnology.
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Affiliation(s)
- Ali Imran
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
| | - Brandon S. Moyer
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
| | - Dan Kalina
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
| | - Thomas M. Duncan
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Kelsey J. Moody
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Aaron J. Wolfe
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Ichor Life Sciences, Inc., 2651 US Route 11, LaFayette, New York 13084, United States
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, 1 Forestry Dr., Syracuse, New York 13210, United States
- Lewis School of Health Sciences, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, 4249 Weiskotten Hall, 766 Irving Avenue, Syracuse, New York 13210, United States
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, United States
- Department of Biomedical and Chemical Engineering, Syracuse University, 329 Link Hall, Syracuse, New York 13244, United States
- The BioInspired Institute, Syracuse University, Syracuse, New York 13244, United States
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9
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Mayse LA, Imran A, Larimi MG, Cosgrove MS, Wolfe AJ, Movileanu L. Disentangling the recognition complexity of a protein hub using a nanopore. Nat Commun 2022; 13:978. [PMID: 35190547 PMCID: PMC8861093 DOI: 10.1038/s41467-022-28465-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 01/25/2022] [Indexed: 11/12/2022] Open
Abstract
WD40 repeat proteins are frequently involved in processing cell signaling and scaffolding large multi-subunit machineries. Despite their significance in physiological and disease-like conditions, their reversible interactions with other proteins remain modestly examined. Here, we show the development and validation of a protein nanopore for the detection and quantification of WD40 repeat protein 5 (WDR5), a chromatin-associated hub involved in epigenetic regulation of histone methylation. Our nanopore sensor is equipped with a 14-residue Win motif of mixed lineage leukemia 4 methyltransferase (MLL4Win), a WDR5 ligand. Our approach reveals a broad dynamic range of MLL4Win-WDR5 interactions and three distant subpopulations of binding events, representing three modes of protein recognition. The three binding events are confirmed as specific interactions using a weakly binding WDR5 derivative and various environmental contexts. These outcomes demonstrate the substantial sensitivity of our nanopore sensor, which can be utilized in protein analytics. Nanopores are powerful tools for sampling protein-peptide interactions. Here, the authors convert a protein-based nanopore into a sensitive biosensor to characterize the complex binding of WDR5 protein to a 14-residue ligand.
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10
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Tan M, Li S, Juillard F, Chitas R, Custódio TF, Xue H, Szymula A, Sun Q, Liu B, Álvarez ÁL, Chen S, Huang J, Simas JP, McVey CE, Kaye KM. MLL1 is regulated by KSHV LANA and is important for virus latency. Nucleic Acids Res 2021; 49:12895-12911. [PMID: 34850113 PMCID: PMC8682764 DOI: 10.1093/nar/gkab1094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/29/2021] [Accepted: 10/20/2021] [Indexed: 01/19/2023] Open
Abstract
Mixed lineage leukemia 1 (MLL1) is a histone methyltransferase. Kaposi's sarcoma-associated herpesvirus (KSHV) is a leading cause of malignancy in AIDS. KSHV latently infects tumor cells and its genome is decorated with epigenetic marks. Here, we show that KSHV latency-associated nuclear antigen (LANA) recruits MLL1 to viral DNA where it establishes H3K4me3 modifications at the extensive KSHV terminal repeat elements during primary infection. LANA interacts with MLL1 complex members, including WDR5, integrates into the MLL1 complex, and regulates MLL1 activity. We describe the 1.5-Å crystal structure of N-terminal LANA peptide complexed with MLL1 complex member WDR5, which reveals a potential regulatory mechanism. Disruption of MLL1 expression rendered KSHV latency establishment highly deficient. This deficiency was rescued by MLL1 but not by catalytically inactive MLL1. Therefore, MLL1 is LANA regulable and exerts a central role in virus infection. These results suggest broad potential for MLL1 regulation, including by non-host factors.
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Affiliation(s)
- Min Tan
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shijun Li
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Franceline Juillard
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Rute Chitas
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Tânia F Custódio
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Han Xue
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 200031 Shanghai, China
| | - Agnieszka Szymula
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Qiming Sun
- Departments of Biochemistry and Cardiology, Second Affiliated Hospital Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Bing Liu
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ángel L Álvarez
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - She Chen
- Proteomics Center, National Institute of Biological Sciences, Beijing 102206, China
| | - Jing Huang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine 200125 Shanghai, China
| | - J Pedro Simas
- Instituto de Medicina Molecular, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal.,Católica Biomedical Research, Católica Medical School, Universidade Católica Portuguesa, Palma de Cima, 1649-023 Lisboa, Portugal
| | - Colin E McVey
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras 2780-157, Portugal
| | - Kenneth M Kaye
- Departments of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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11
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Kim DK, Redon CE, Aladjem MI, Kim HK, Jang SM. Molecular double clips within RepID WD40 domain control chromatin binding and CRL4-substrate assembly. Biochem Biophys Res Commun 2021; 567:208-214. [PMID: 34171797 PMCID: PMC9969741 DOI: 10.1016/j.bbrc.2021.06.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/11/2021] [Accepted: 06/13/2021] [Indexed: 01/07/2023]
Abstract
The cell cycle is modulated by ubiquitin ligases, including CRL4, which facilitate degradation of the chromatin-bound substrates involved in DNA replication and chromosome segregation. One of the members of the CRL4 complex, RepID (DCAF14/PHIP), recognizes kinetochore-localizing BUB3, known as the CRL4 substrate, and recruits CRL4 to the chromatin/chromosome using the WD40 domain. Here, we show that the RepID WD40 domain provides different platforms to CRL4 and BUB3. Deletion of the H-box or exon 8 located in the RepID WD40 domain compromises the interaction between RepID and CRL4, whereas BUB3 interacts with the exon 1-2 region. Moreover, deletion mutants of other exons in the WD40 domain lost chromatin binding affinity. Structure prediction revealed that the RepID WD40 domain has two beta-propeller folds, linked by loops, which are possibly crucial for chromatin binding. These findings provide mechanistic insights into the space occupancy of the RepID WD40 domain to form a complex with CRL4, BUB3, or chromatin.
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Affiliation(s)
- Dong-Kyu Kim
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Christophe E. Redon
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892-4255, USA
| | - Mirit I. Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892-4255, USA
| | - Hyong Kyu Kim
- Department of Medicine and Microbiology, College of Medicine, Chungbuk National University, Cheongju, 361-763, Republic of Korea
| | - Sang-Min Jang
- Department of Biochemistry, Chungbuk National University, Cheongju, 28644, Republic of Korea; Developmental Therapeutics Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892-4255, USA.
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12
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Seok HY, Bae H, Kim T, Mehdi SMM, Nguyen LV, Lee SY, Moon YH. Non-TZF Protein AtC3H59/ZFWD3 Is Involved in Seed Germination, Seedling Development, and Seed Development, Interacting with PPPDE Family Protein Desi1 in Arabidopsis. Int J Mol Sci 2021; 22:ijms22094738. [PMID: 33947021 PMCID: PMC8124945 DOI: 10.3390/ijms22094738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 11/16/2022] Open
Abstract
Despite increasing reports on the function of CCCH zinc finger proteins in plant development and stress response, the functions and molecular aspects of many non-tandem CCCH zinc finger (non-TZF) proteins remain uncharacterized. AtC3H59/ZFWD3 is an Arabidopsis non-TZF protein and belongs to the ZFWD subfamily harboring a CCCH zinc finger motif and a WD40 domain. In this study, we characterized the biological and molecular functions of AtC3H59, which is subcellularly localized in the nucleus. The seeds of AtC3H59-overexpressing transgenic plants (OXs) germinated faster than those of wild type (WT), whereas atc3h59 mutant seeds germinated slower than WT seeds. AtC3H59 OX seedlings were larger and heavier than WT seedlings, whereas atc3h59 mutant seedlings were smaller and lighter than WT seedlings. Moreover, AtC3H59 OX seedlings had longer primary root length than WT seedlings, whereas atc3h59 mutant seedlings had shorter primary root length than WT seedlings, owing to altered cell division activity in the root meristem. During seed development, AtC3H59 OXs formed larger and heavier seeds than WT. Using yeast two-hybrid screening, we isolated Desi1, a PPPDE family protein, as an interacting partner of AtC3H59. AtC3H59 and Desi1 interacted via their WD40 domain and C-terminal region, respectively, in the nucleus. Taken together, our results indicate that AtC3H59 has pleiotropic effects on seed germination, seedling development, and seed development, and interacts with Desi1 in the nucleus via its entire WD40 domain. To our knowledge, this is the first report to describe the biological functions of the ZFWD protein and Desi1 in Arabidopsis.
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Affiliation(s)
- Hye-Yeon Seok
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea; (H.-Y.S.); (H.B.)
| | - Hyungjoon Bae
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea; (H.-Y.S.); (H.B.)
| | - Taehyoung Kim
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (T.K.); (S.M.M.M.); (L.V.N.)
| | - Syed Muhammad Muntazir Mehdi
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (T.K.); (S.M.M.M.); (L.V.N.)
| | - Linh Vu Nguyen
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (T.K.); (S.M.M.M.); (L.V.N.)
| | - Sun-Young Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
| | - Yong-Hwan Moon
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea; (H.-Y.S.); (H.B.)
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea; (T.K.); (S.M.M.M.); (L.V.N.)
- Department of Molecular Biology, Pusan National University, Busan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2592
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13
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Kim YJ, Kim MH, Hong WJ, Moon S, Kim EJ, Silva J, Lee J, Lee S, Kim ST, Park SK, Jung KH. GORI, encoding the WD40 domain protein, is required for pollen tube germination and elongation in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1645-1664. [PMID: 33345419 DOI: 10.1111/tpj.15139] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 10/30/2020] [Accepted: 11/13/2020] [Indexed: 05/05/2023]
Abstract
Successful delivery of sperm cells to the embryo sac in higher plants is mediated by pollen tube growth. The molecular mechanisms underlying pollen germination and tube growth in crop plants remain rather unclear, although these mechanisms are crucial to plant reproduction and seed formation. By screening pollen-specific gene mutants in rice (Oryza sativa), we identified a T-DNA insertional mutant of Germinating modulator of rice pollen (GORI) that showed a one-to-one segregation ratio for wild type (WT) to heterozygous. GORI encodes a seven-WD40-motif protein that is homologous to JINGUBANG/REN4 in Arabidopsis. GORI is specifically expressed in rice pollen, and its protein is localized in the nucleus, cytosol and plasma membrane. Furthermore, a homozygous mutant, gori-2, created through CRISPR-Cas9 clearly exhibited male sterility with disruption of pollen tube germination and elongation. The germinated pollen tube of gori-2 exhibited decreased actin filaments and altered pectin distribution. Transcriptome analysis revealed that 852 pollen-specific genes were downregulated in gori-2 compared with the WT, and Gene Ontology enrichment analysis indicated that these genes are strongly associated with cell wall modification and clathrin coat assembly. Based on the molecular features of GORI, phenotypical observation of the gori mutant and its interaction with endocytic proteins and Rac GTPase, we propose that GORI plays key roles in forming endo-/exocytosis complexes that could mediate pollen tube growth in rice.
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Affiliation(s)
- Yu-Jin Kim
- Department of Life Science and Environmental Biochemistry, Pusan National University, Miryang, 50463, Republic of Korea
| | - Myung-Hee Kim
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Woo-Jong Hong
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Sunok Moon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Eui-Jung Kim
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Jeniffer Silva
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Jinwon Lee
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 50463, Republic of Korea
| | - Soon Ki Park
- School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea
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14
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Cao J, Fan T, Li Y, Du Z, Chen L, Wang Y, Wang X, Shen J, Huang X, Xiong B, Cao D. Phage-Display Based Discovery and Characterization of Peptide Ligands against WDR5. Molecules 2021; 26:1225. [PMID: 33668971 PMCID: PMC7956166 DOI: 10.3390/molecules26051225] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 02/17/2021] [Accepted: 02/21/2021] [Indexed: 11/16/2022] Open
Abstract
WD40 is a ubiquitous domain presented in at least 361 human proteins and acts as scaffold to form protein complexes. Among them, WDR5 protein is an important mediator in several protein complexes to exert its functions in histone modification and chromatin remodeling. Therefore, it was considered as a promising epigenetic target involving in anti-cancer drug development. In view of the protein-protein interaction nature of WDR5, we initialized a campaign to discover new peptide-mimic inhibitors of WDR5. In current study, we utilized the phage display technique and screened with a disulfide-based cyclic peptide phage library. Five rounds of biopanning were performed and isolated clones were sequenced. By analyzing the sequences, total five peptides were synthesized for binding assay. The four peptides are shown to have the moderate binding affinity. Finally, the detailed binding interactions were revealed by solving a WDR5-peptide cocrystal structure.
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Affiliation(s)
- Jiawen Cao
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Tiantian Fan
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yanlian Li
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhiyan Du
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lin Chen
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Ying Wang
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xin Wang
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jingkang Shen
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xun Huang
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Division of Anti-Tumor Pharmacology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Bing Xiong
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Danyan Cao
- Department of College of Pharmacy, University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; (J.C.); (T.F.); (Y.L.); (Z.D.); (L.C.); (Y.W.); (X.W.); (J.S.); (X.H.)
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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15
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Gao W, Jia Z, Tian Y, Yang P, Sun H, Wang C, Ding Y, Zhang M, Zhang Y, Yang D, Tian Z, Zhou J, Ruan Z, Wu Y, Ni B. HBx Protein Contributes to Liver Carcinogenesis by H3K4me3 Modification Through Stabilizing WD Repeat Domain 5 Protein. Hepatology 2020; 71:1678-1695. [PMID: 31544250 DOI: 10.1002/hep.30947] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 09/09/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Cancer is typically considered as a genetic and epigenetic disease. Although numerous studies have indicated that an aberrant structure, function, or expression level of epigenetic enzymes contribute to many tumor types, precisely how the epigenetic mechanisms are involved in the hepatitis B virus (HBV)-induced hepatocellular carcinoma (HCC) remains unknown. APPROACH AND RESULTS In this study, we found that the WD repeat domain 5 protein (WDR5)-a core subunit of histone H3 lysine 4 methyltransferase complexes, which catalyze the generation of histone H3 lysine 4 trimethylation (H3K4me3) modification-is highly expressed in HBV-related HCC and promotes HCC development. WDR5 plays a critical role in HBV-driven cell proliferation and tumor growth in mice, and the WDR5-0103 small-molecule inhibitor of WDR5 activity compromises HBV- and hepatitis B x protein (HBx)-driven tumor proliferation. The aberrantly high WDR5 protein level was found to involve HBx through its stabilization of the WDR5 protein by inhibiting the interaction between the damage-specific DNA-binding protein 1/cullin-4 and WDR5, causing decreased ubiquitination of the WDR5 protein. HBx was found to colocalize with WDR5 on chromatin genome wide and promotes genome-wide H3K4me3 modification by means of WDR5. Furthermore, the recruitment of HBx to promoters of target genes relied on its interaction with WDR5 through its α-helix domain. WDR5 was also found to promote HBV transcription through H3K4 modification of covalently closed circular DNA minichromosome, and WDR5-0103 was able to inhibit HBV transcription. Finally, the in vitro and in vivo data further proved that HBx exerted its tumor-promoting function in a WDR5-dependent manner. CONCLUSIONS Our data reveals that WDR5 is a key epigenetic determinant of HBV-induced tumorigenesis and that the HBx-WDR5-H3K4me3 axis may be a potential therapeutic target in HBV-induced liver pathogenesis.
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Affiliation(s)
- Weiwu Gao
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing, China
- Key Laboratory of High Altitude Medicine, PLA, Chongqing, China
- Institute of Immunology of PLA, Third Military Medical University, Chongqing, China
| | - Zhengcai Jia
- Department of Neurosurgery, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Yi Tian
- Institute of Immunology of PLA, Third Military Medical University, Chongqing, China
| | | | - Hui Sun
- Department of Rheumatology and Immunology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Chenhui Wang
- Institute of Immunology of PLA, Third Military Medical University, Chongqing, China
| | - Yi Ding
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD
- Allen Institute for Brain Science, Seattle, WA
| | - Mengjie Zhang
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University, Chongqing, China
| | - Yi Zhang
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University, Chongqing, China
| | - Di Yang
- Institute of Immunology of PLA, Third Military Medical University, Chongqing, China
| | - Zhiqiang Tian
- Institute of Immunology of PLA, Third Military Medical University, Chongqing, China
| | - Jian Zhou
- Institute of Immunology of PLA, Third Military Medical University, Chongqing, China
| | - Zhihua Ruan
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Yuzhang Wu
- Institute of Immunology of PLA, Third Military Medical University, Chongqing, China
| | - Bing Ni
- Department of Pathophysiology, College of High Altitude Military Medicine, Third Military Medical University, Chongqing, China
- Key Laboratory of Extreme Environmental Medicine, Ministry of Education of China, Chongqing, China
- Key Laboratory of High Altitude Medicine, PLA, Chongqing, China
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16
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Yu Y, Jia W, Lyu Y, Su D, Bai M, Shen J, Qiao J, Han T, Liu W, Chen J, Chen W, Ye D, Guo X, Zhu S, Xi J, Zhu R, Wan X, Gao S, Zhu J, Kang J. Pwp1 regulates telomere length by stabilizing shelterin complex and maintaining histone H4K20 trimethylation. Cell Discov 2019; 5:47. [PMID: 31754456 PMCID: PMC6868014 DOI: 10.1038/s41421-019-0116-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 07/24/2019] [Indexed: 01/02/2023] Open
Abstract
Telomere maintenance is critical for chromosome stability. Here we report that periodic tryptophan protein 1 (PWP1) is involved in regulating telomere length homeostasis. Pwp1 appears to be essential for mouse development and embryonic stem cell (ESC) survival, as homozygous Pwp1-knockout mice and ESCs have never been obtained. Heterozygous Pwp1-knockout mice had shorter telomeres and decreased reproductive capacity. Pwp1 depletion induced rapid telomere shortening accompanied by reduced shelterin complex and increased DNA damage in telomeric regions. Mechanistically, PWP1 bound and stabilized the shelterin complex via its WD40 domains and regulated the overall level of H4K20me3. The rescue of telomere length in Pwp1-deficient cells by PWP1 overexpression depended on SUV4-20H2 co-expression and increased H4K20me3. Therefore, our study revealed a novel protein involved in telomere homeostasis in both mouse and human cells. This knowledge will improve our understanding of how chromatin structure and histone modifications are involved in maintaining telomere integrity.
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Affiliation(s)
- Yangyang Yu
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Wenwen Jia
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China.,2Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200123 China
| | - Yao Lyu
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Dingwen Su
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Mingliang Bai
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Junwei Shen
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Jing Qiao
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Tong Han
- 3Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 201204 P. R. China
| | - Wenqiang Liu
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Jiayu Chen
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Wen Chen
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Dan Ye
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Xudong Guo
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Songcheng Zhu
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Jiajie Xi
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Ruixin Zhu
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Xiaoping Wan
- 3Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 201204 P. R. China
| | - Shaorong Gao
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China
| | - Jiyue Zhu
- 4Department of Pharmaceutical Sciences, College of Pharmacy, Washington State University, Spokane, WA 99210 USA
| | - Jiuhong Kang
- 1Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science; School of Life Sciences and Technology, Tongji University, Shanghai, 200092 China.,2Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200123 China
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Phospho-peptide binding domains in S. cerevisiae model organism. Biochimie 2019; 163:117-127. [PMID: 31194995 DOI: 10.1016/j.biochi.2019.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 06/06/2019] [Indexed: 02/07/2023]
Abstract
Protein phosphorylation is one of the main mechanisms by which signals are transmitted in eukaryotic cells, and it plays a crucial regulatory role in almost all cellular processes. In yeast, more than half of the proteins are phosphorylated in at least one site, and over 20,000 phosphopeptides have been experimentally verified. However, the functional consequences of these phosphorylation events for most of the identified phosphosites are unknown. A family of protein interaction domains selectively recognises phosphorylated motifs to recruit regulatory proteins and activate signalling pathways. Nine classes of dedicated modules are coded by the yeast genome: 14-3-3, FHA, WD40, BRCT, WW, PBD, and SH2. The recognition specificity relies on a few residues on the target protein and has coevolved with kinase specificity. In the present study, we review the current knowledge concerning yeast phospho-binding domains and their networks. We emphasise the relevance of both positive and negative amino acid selection to orchestrate the highly regulated outcomes of inter- and intra-molecular interactions. Finally, we hypothesise that only a small fraction of yeast phosphorylation events leads to the creation of a docking site on the target molecule, while many have a direct effect on the protein or, as has been proposed, have no function at all.
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Fonseca S, Rubio V. Arabidopsis CRL4 Complexes: Surveying Chromatin States and Gene Expression. FRONTIERS IN PLANT SCIENCE 2019; 10:1095. [PMID: 31608079 PMCID: PMC6761389 DOI: 10.3389/fpls.2019.01095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/09/2019] [Indexed: 05/10/2023]
Abstract
CULLIN4 (CUL4) RING ligase (CRL4) complexes contain a CUL4 scaffold protein, associated to RBX1 and to DDB1 proteins and have traditionally been associated to protein degradation events. Through DDB1, these complexes can associate with numerous DCAF proteins, which directly interact with specific targets promoting their ubiquitination and subsequent degradation by the proteasome. A characteristic feature of the majority of DCAF proteins that associate with DDB1 is the presence of the DWD motif. DWD-containing proteins sum up to 85 in the plant model species Arabidopsis. In the last decade, numerous Arabidopsis DWD proteins have been studied and their molecular functions uncovered. Independently of whether their association with CRL4 has been confirmed or not, DWD proteins are often found as components of additional multimeric protein complexes that play key roles in essential nuclear events. For most of them, the significance of their complex partnership is still unexplored. Here, we summarize recent findings involving both confirmed and putative CRL4-associated DCAF proteins in regulating nuclei architecture remodelling, DNA damage repair, histone post-translational modification, mRNA processing and export, and ribosome biogenesis, that definitely have an impact in gene expression and de novo protein synthesis. We hypothesized that, by maintaining accurate levels of regulatory proteins through targeted degradation and transcriptional control, CRL4 complexes help to surveil nuclear processes essential for plant development and survival.
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Ye X, Zhang R, Lian F, Zhang W, Lu W, Han J, Zhang N, Jin J, Luo C, Chen K, Ye F, Ding H. The identification of novel small-molecule inhibitors targeting WDR5-MLL1 interaction through fluorescence polarization based high-throughput screening. Bioorg Med Chem Lett 2018; 29:638-645. [PMID: 30626558 DOI: 10.1016/j.bmcl.2018.12.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/21/2018] [Accepted: 12/15/2018] [Indexed: 01/27/2023]
Abstract
The protein-protein interaction between WDR5 (WD40 repeat protein 5) and MLL1 (mixed-lineage leukemia 1) is important for maintaining optimal H3K4 methyltransferase activity of MLL1. Dysregulation of MLL1 catalytic function is relevant to mixed-lineage leukemia, and targeting WDR5-MLL1 interaction could be a promising therapeutic strategy for leukemia harboring MLL1 fusion proteins. To date, several peptidomimetic and non-peptidomimetic small-molecule inhibitors targeting WDR5-MLL1 interaction have been reported, yet the discovery walk of new drugs inhibiting MLL1 methytransferase activity is still in its infancy. It's urgent to find other small-molecule WDR5-MLL1 inhibitors with novel scaffolds. In this study, through fluorescence polarization (FP)-based high throughput screening, several small-molecule inhibitors with potent inhibitory activities in vitro against WDR5-MLL1 interaction were discovered. Nuclear Magnetic Resonance (NMR) assays were carried out to confirm the direct binding between hit compounds and WDR5. Subsequent similarity-based analog searching of the 4 hits led to several inhibitors with better activity, among them, DC_M5_2 displayed highest inhibitory activity with IC50 values of 9.63 ± 1.46 µM. Furthermore, a molecular docking study was performed and disclosed the binding modes and interaction mechanisms between two most potent inhibitors and WDR5.
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Affiliation(s)
- Xiaoqing Ye
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Rukang Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Fulin Lian
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weiyao Zhang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wenchao Lu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jie Han
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Naixia Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jia Jin
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kaixian Chen
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
| | - Fei Ye
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Hong Ding
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China.
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20
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Neilsen BK, Chakraborty B, McCall JL, Frodyma DE, Sleightholm RL, Fisher KW, Lewis RE. WDR5 supports colon cancer cells by promoting methylation of H3K4 and suppressing DNA damage. BMC Cancer 2018; 18:673. [PMID: 29925347 PMCID: PMC6011590 DOI: 10.1186/s12885-018-4580-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 06/08/2018] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND KMT2/MLL proteins are commonly overexpressed or mutated in cancer and have been shown to support cancer maintenance. These proteins are responsible for methylating histone 3 at lysine 4 and promoting transcription and DNA synthesis; however, they are inactive outside of a multi-protein complex that requires WDR5. WDR5 has been implicated in cancer for its role in the COMPASS complex and its interaction with Myc; however, the role of WDR5 in colon cancer has not yet been elucidated. METHODS WDR5 expression was evaluated using RT-qPCR and western blot analysis. Cell viability and colony forming assays were utilized to evaluate the effects of WDR5 depletion or inhibition in colon cancer cells. Downstream effects of WDR5 depletion and inhibition were observed by western blot. RESULTS WDR5 is overexpressed in colon tumors and colon cancer cell lines at the mRNA and protein level. WDR5 depletion reduces cell viability in HCT116, LoVo, RKO, HCT15, SW480, SW620, and T84 colon cancer cells. Inhibition of the WDR5:KMT2/MLL interaction using OICR-9429 reduces cell viability in the same panel of cell lines albeit not to the same extent as RNAi-mediated WDR5 depletion. WDR5 depletion reduced H3K4Me3 and increased phosphorylation of H2AX in HCT116, SW620, and RKO colon cancer cells; however, OICR-9429 treatment did not recapitulate these effects in all cell lines potentially explaining the reduced toxicity of OICR-9429 treatment as compared to WDR5 depletion. WDR5 depletion also sensitized colon cancer cells to radiation-induced DNA damage. CONCLUSIONS These data demonstrate a clear role for WDR5 in colon cancer and future studies should examine its potential to serve as a therapeutic target in cancer. Additional studies are needed to fully elucidate if the requirement for WDR5 is independent of or consistent with its role within the COMPASS complex. OICR-9429 treatment was particularly toxic to SW620 and T84 colon cancer cells, two cell lines without mutations in WDR5 and KMT2/MLL proteins suggesting COMPASS complex inhibition may be particularly effective in tumors lacking KMT2 mutations. Additionally, the ability of WDR5 depletion to amplify the toxic effects of radiation presents the possibility of targeting WDR5 to sensitize cells to DNA-damaging therapies.
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Affiliation(s)
- Beth K Neilsen
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Binita Chakraborty
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Present address: Department of Pharmacology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jamie L McCall
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Present address: Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, 26506, USA
| | - Danielle E Frodyma
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Richard L Sleightholm
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kurt W Fisher
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Robert E Lewis
- Eppley Institute, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin. Cells 2018; 7:cells7030017. [PMID: 29498679 PMCID: PMC5870349 DOI: 10.3390/cells7030017] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 02/07/2023] Open
Abstract
Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex. Here we discuss recent findings that try to elucidate the important question of how KMT2 complexes are recruited to specific sites on chromatin. This is embedded into short overviews of the biological functions of KMT2 complexes and the consequences of H3K4 methylation.
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22
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Moonlighting with WDR5: A Cellular Multitasker. J Clin Med 2018; 7:jcm7020021. [PMID: 29385767 PMCID: PMC5852437 DOI: 10.3390/jcm7020021] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/16/2018] [Accepted: 01/18/2018] [Indexed: 11/17/2022] Open
Abstract
WDR5 is a highly conserved WD40 repeat-containing protein that is essential for proper regulation of multiple cellular processes. WDR5 is best characterized as a core scaffolding component of histone methyltransferase complexes, but emerging evidence demonstrates that it does much more, ranging from expanded functions in the nucleus through to controlling the integrity of cell division. The purpose of this review is to describe the current molecular understandings of WDR5, discuss how it participates in diverse cellular processes, and highlight drug discovery efforts around WDR5 that may form the basis of new anti-cancer therapies.
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23
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WDR5 high expression and its effect on tumorigenesis in leukemia. Oncotarget 2018; 7:37740-37754. [PMID: 27192115 PMCID: PMC5122345 DOI: 10.18632/oncotarget.9312] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/27/2016] [Indexed: 01/21/2023] Open
Abstract
WD repeat domain 5 (WDR5) plays an important role in various biological functions through the epigenetic regulation of gene transcription. However, the oncogenic effect of WDR5 in leukemia remains largely unknown. Here, we found WDR5 expression is increased in leukemia patients. High expression of WDR5 is associated with high risk leukemia; Patients with WDR5 and MLL1 high expression have poor complete remission rate. We further identified the global genomic binding of WDR5 in leukemic cells and found the genomic co-localization of WDR5 binding with H3K4me3 enrichment. Moreover, WDR5 knockdown by shRNA suppresses cell proliferation, induces apoptosis, inhibits the expression of WDR5 targets, and blocks the H3K4me3 enrichment on the promoter of its targets. We also observed the positive correlation of WDR5 expression with these targets in the cohort study of leukemia patients. Our data reveal that WDR5 may have oncogenic effect and WDR5-mediated H3K4 methylation plays an important role in leukemogenesis.
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24
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Teske KA, Hadden MK. Methyllysine binding domains: Structural insight and small molecule probe development. Eur J Med Chem 2017; 136:14-35. [DOI: 10.1016/j.ejmech.2017.04.047] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 04/14/2017] [Accepted: 04/19/2017] [Indexed: 12/19/2022]
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25
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An allosteric PRC2 inhibitor targeting the H3K27me3 binding pocket of EED. Nat Chem Biol 2017; 13:381-388. [PMID: 28135235 DOI: 10.1038/nchembio.2304] [Citation(s) in RCA: 226] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/23/2016] [Indexed: 12/15/2022]
Abstract
Polycomb repressive complex 2 (PRC2) consists of three core subunits, EZH2, EED and SUZ12, and plays pivotal roles in transcriptional regulation. The catalytic subunit EZH2 methylates histone H3 lysine 27 (H3K27), and its activity is further enhanced by the binding of EED to trimethylated H3K27 (H3K27me3). Small-molecule inhibitors that compete with the cofactor S-adenosylmethionine (SAM) have been reported. Here we report the discovery of EED226, a potent and selective PRC2 inhibitor that directly binds to the H3K27me3 binding pocket of EED. EED226 induces a conformational change upon binding EED, leading to loss of PRC2 activity. EED226 shows similar activity to SAM-competitive inhibitors in blocking H3K27 methylation of PRC2 target genes and inducing regression of human lymphoma xenograft tumors. Interestingly, EED226 also effectively inhibits PRC2 containing a mutant EZH2 protein resistant to SAM-competitive inhibitors. Together, we show that EED226 inhibits PRC2 activity via an allosteric mechanism and offers an opportunity for treatment of PRC2-dependent cancers.
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26
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Abstract
Protein arginine methyltransferase 5 (PRMT5) plays multiple roles in cellular processes at different stages of the cell cycle in a tissue specific manner. PRMT5 in complex with MEP50/p44/WDR77 associates with a plethora of partner proteins to symmetrically dimethylate arginine residues on target proteins in both the nucleus and the cytoplasm. Overexpression of PRMT5 has been observed in several cancers, making it an attractive drug target. The structure of the 453 kDa heterooctameric PRMT5:MEP50 complex bound to an S-adenosylmethionine analog and a substrate peptide provides valuable insights into this intriguing target.
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Affiliation(s)
- Stephen Antonysamy
- Structural Biology, Discovery Chemistry Research and Technologies, Eli Lilly and Company, Lilly Biotechnology Center, 10290 Campus Point Drive, San Diego, CA, 92121, USA.
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27
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He T, Surdez D, Rantala JK, Haapa-Paananen S, Ban J, Kauer M, Tomazou E, Fey V, Alonso J, Kovar H, Delattre O, Iljin K. High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability. Gene 2016; 596:137-146. [PMID: 27760381 DOI: 10.1016/j.gene.2016.10.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 09/21/2016] [Accepted: 10/14/2016] [Indexed: 12/31/2022]
Abstract
A translocation leading to the formation of an oncogenic EWS-ETS fusion protein defines Ewing sarcoma. The most frequent gene fusion, present in 85 percent of Ewing sarcomas, is EWS-FLI1. Here, a high-throughput RNA interference screen was performed to identify genes whose function is critical for EWS-FLI1 driven cell viability. In total, 6781 genes were targeted by siRNA molecules and the screen was performed both in presence and absence of doxycycline-inducible expression of the EWS-FLI1 shRNA in A673/TR/shEF Ewing sarcoma cells. The Leucine rich repeats and WD repeat Domain containing 1 (LRWD1) targeting siRNA pool was the strongest hit reducing cell viability only in EWS-FLI1 expressing Ewing sarcoma cells. LRWD1 had been previously described as a testis specific gene with only limited information on its function. Analysis of LRWD1 mRNA levels in patient samples indicated that high expression associated with poor overall survival in Ewing sarcoma. Gene ontology analysis of LRWD1 co-expressed genes in Ewing tumors revealed association with DNA replication and analysis of differentially expressed genes in LRWD1 depleted Ewing sarcoma cells indicated a role in connective tissue development and cellular morphogenesis. Moreover, EWS-FLI1 repressed genes with repressive H3K27me3 chromatin marks were highly enriched among LRWD1 target genes in A673/TR/shEF Ewing sarcoma cells, suggesting that LRWD1 contributes to EWS-FLI1 driven transcriptional regulation. Taken together, we have identified LRWD1 as a novel regulator of EWS-FLI1 driven cell viability in A673/TR/shEF Ewing sarcoma cells, shown association between high LRWD1 mRNA expression and aggressive disease and identified processes by which LRWD1 may promote oncogenesis in Ewing sarcoma.
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Affiliation(s)
- Tao He
- VTT Technical Research Centre of Finland, Turku, Finland
| | - Didier Surdez
- Institut Curie, Unité de génétique somatique, Paris, France; Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France; INSERM U830, Institut Curie Research Center, Paris, France
| | | | | | - Jozef Ban
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Maximilian Kauer
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Eleni Tomazou
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Vidal Fey
- VTT Technical Research Centre of Finland, Turku, Finland
| | - Javier Alonso
- Unidad de Tumores Sólidos Infantiles, Área de Genética Humana, Instituto de Investigación de Enfermedades Raras, Instituto de Salud Carlos III, Madrid, Spain
| | - Heinrich Kovar
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria; Department of Pediatrics, Medical University, Vienna, Austria
| | - Olivier Delattre
- Institut Curie, Unité de génétique somatique, Paris, France; Genetics and Biology of Cancers Unit, Institut Curie, PSL Research University, Paris, France; INSERM U830, Institut Curie Research Center, Paris, France; Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, Paris, France
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28
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Hauri S, Comoglio F, Seimiya M, Gerstung M, Glatter T, Hansen K, Aebersold R, Paro R, Gstaiger M, Beisel C. A High-Density Map for Navigating the Human Polycomb Complexome. Cell Rep 2016; 17:583-595. [PMID: 27705803 DOI: 10.1016/j.celrep.2016.08.096] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/23/2016] [Accepted: 08/30/2016] [Indexed: 12/20/2022] Open
Abstract
Polycomb group (PcG) proteins are major determinants of gene silencing and epigenetic memory in higher eukaryotes. Here, we systematically mapped the human PcG complexome using a robust affinity purification mass spectrometry approach. Our high-density protein interaction network uncovered a diverse range of PcG complexes. Moreover, our analysis identified PcG interactors linking them to the PcG system, thus providing insight into the molecular function of PcG complexes and mechanisms of recruitment to target genes. We identified two human PRC2 complexes and two PR-DUB deubiquitination complexes, which contain the O-linked N-acetylglucosamine transferase OGT1 and several transcription factors. Finally, genome-wide profiling of PR-DUB components indicated that the human PR-DUB and PRC1 complexes bind distinct sets of target genes, suggesting differential impact on cellular processes in mammals.
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Affiliation(s)
- Simon Hauri
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; Competence Center Personalized Medicine UZH/ETH, 8044 Zürich, Switzerland
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Makiko Seimiya
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Moritz Gerstung
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Timo Glatter
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Klaus Hansen
- Biotech Research and Innovation Centre (BRIC) and Centre for Epigenetics, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; Faculty of Science, University of Zürich, 8057 Zürich, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland; Competence Center Personalized Medicine UZH/ETH, 8044 Zürich, Switzerland.
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland.
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29
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Kikani CK, Wu X, Paul L, Sabic H, Shen Z, Shakya A, Keefe A, Villanueva C, Kardon G, Graves B, Tantin D, Rutter J. Pask integrates hormonal signaling with histone modification via Wdr5 phosphorylation to drive myogenesis. eLife 2016; 5. [PMID: 27661449 PMCID: PMC5035144 DOI: 10.7554/elife.17985] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/08/2016] [Indexed: 01/08/2023] Open
Abstract
PAS domain containing protein kinase (Pask) is an evolutionarily conserved protein kinase implicated in energy homeostasis and metabolic regulation across eukaryotic species. We now describe an unexpected role of Pask in promoting the differentiation of myogenic progenitor cells, embryonic stem cells and adipogenic progenitor cells. This function of Pask is dependent upon its ability to phosphorylate Wdr5, a member of several protein complexes including those that catalyze histone H3 Lysine 4 trimethylation (H3K4me3) during transcriptional activation. Our findings suggest that, during myoblast differentiation, Pask stimulates the conversion of repressive H3K4me1 to activating H3K4me3 marks on the promoter of the differentiation gene myogenin (Myog) via Wdr5 phosphorylation. This enhances accessibility of the MyoD transcription factor and enables transcriptional activation of the Myog promoter to initiate muscle differentiation. Thus, as an upstream kinase of Wdr5, Pask integrates signaling cues with the transcriptional network to regulate the differentiation of progenitor cells. DOI:http://dx.doi.org/10.7554/eLife.17985.001
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Affiliation(s)
- Chintan K Kikani
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Xiaoying Wu
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Litty Paul
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Hana Sabic
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Zuolian Shen
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Arvind Shakya
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Alexandra Keefe
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Claudio Villanueva
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
| | - Gabrielle Kardon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Barbara Graves
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, United States.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, United States.,Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States.,Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, United States
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30
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Qin X, Huang Q, Xiao H, Zhang Q, Ni C, Xu Y, Liu G, Yang D, Zhu Y, Hu J. The rice DUF1620-containing and WD40-like repeat protein is required for the assembly of the restoration of fertility complex. THE NEW PHYTOLOGIST 2016; 210:934-945. [PMID: 26781807 DOI: 10.1111/nph.13824] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 11/22/2015] [Indexed: 06/05/2023]
Abstract
Cytoplasmic male sterility (CMS) and restoration of fertility (Rf) are widely distributed in plant species utilized by humans. RF5 and GRP162 are subunits of the restoration of fertility complex (RFC) in Hong-Lian rice. Despite the fact that the RFC is 400-500 kDa in size, the other proteins or factors in the complex still remain unknown. Here, we identified RFC subunit 3, which encodes a DUF1620-containing and WD40-like repeat protein (RFC3) that is present in all tissues but highly expressed in leaves. We established that RFC3 interacts with both RF5 and GRP162 in vitro and in vivo, and is transported into the mitochondria as a membrane protein. Furthermore, CMS RNA (atp6-orfH79) and CMS cytotoxic protein (ORFH79) accumulate when RFC3 is silenced in restorer lines. We presented the analysis with blue-native polyacrylamide gel electrophoresis, indicating that RFC is disrupted in the RNAi line. We concluded that RCF3 is indispensable as a scaffold protein for the assembly of the RFC complex. We unveil a new molecular player of the RFC in the Rf pathway in rice and propose the model of RFC based on these data.
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Affiliation(s)
- Xiaojian Qin
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Qi Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Haijun Xiao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Qiannan Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Chenzi Ni
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Yanghong Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
| | - Gai Liu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Daichang Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
- Engineering Research Center for Plant Biotechnology and Germplasm, Utilization, Ministry of Education, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, Wuhan University, Wuhan, Hubei, 430072, China
| | - Yingguo Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
- Engineering Research Center for Plant Biotechnology and Germplasm, Utilization, Ministry of Education, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, Wuhan University, Wuhan, Hubei, 430072, China
| | - Jun Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, China
- Engineering Research Center for Plant Biotechnology and Germplasm, Utilization, Ministry of Education, Key Laboratory for Research and Utilization of Heterosis in Indica Rice, the Ministry of Agriculture, The Yangtze River Valley Hybrid Rice Collaboration & Innovation Center, Wuhan University, Wuhan, Hubei, 430072, China
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31
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Förderer A, Zhou Y, Turck F. The age of multiplexity: recruitment and interactions of Polycomb complexes in plants. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:169-78. [PMID: 26826786 DOI: 10.1016/j.pbi.2015.11.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/23/2015] [Accepted: 11/28/2015] [Indexed: 05/08/2023]
Abstract
Polycomb group (PcG) proteins form distinct complexes that modify chromatin by histone H3 methylation and H2A mono-ubiquitination leading to chromatin compaction and epigenetic repression of target genes. A network of PcG protein complexes, associated partners and antagonistically acting chromatin modifiers is essential to regulate developmental transitions and cell fate in all multicellular eukaryotes. In this review, we discuss insights on the subfunctionalization of PcG complexes and their modes of recruitment to target sites based on data from the model organism Arabidopsis thaliana.
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Affiliation(s)
- Alexander Förderer
- Max Planck Institute for Plant Breeding Research, Department Plant Developmental Biology, Carl von Linne Weg 10, 50829 Köln, Germany
| | - Yue Zhou
- Max Planck Institute for Plant Breeding Research, Department Plant Developmental Biology, Carl von Linne Weg 10, 50829 Köln, Germany
| | - Franziska Turck
- Max Planck Institute for Plant Breeding Research, Department Plant Developmental Biology, Carl von Linne Weg 10, 50829 Köln, Germany.
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32
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Shen J, Jia W, Yu Y, Chen J, Cao X, Du Y, Zhang X, Zhu S, Chen W, Xi J, Wei T, Wang G, Yuan D, Duan T, Jiang C, Kang J. Pwp1 is required for the differentiation potential of mouse embryonic stem cells through regulating Stat3 signaling. Stem Cells 2015; 33:661-73. [PMID: 25335925 DOI: 10.1002/stem.1876] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 08/19/2014] [Accepted: 09/04/2014] [Indexed: 11/08/2022]
Abstract
Leukemia inhibitory factor/Stat3 signaling is critical for maintaining the self-renewal and differentiation potential of mouse embryonic stem cells (mESCs). However, the upstream effectors of this pathway have not been clearly defined. Here, we show that periodic tryptophan protein 1 (Pwp1), a WD-40 repeat-containing protein associated with histone H4 modification, is required for the exit of mESCs from the pluripotent state into all lineages. Knockdown (KD) of Pwp1 does not affect mESC proliferation, self-renewal, or apoptosis. However, KD of Pwp1 impairs the differentiation potential of mESCs both in vitro and in vivo. PWP1 chromatin immunoprecipitation-seq results revealed that the PWP1-occupied regions were marked with significant levels of H4K20me3. Moreover, Pwp1 binds to sites in the upstream region of Stat3. KD of Pwp1 decreases the level of H4K20me3 in the upstream region of Stat3 gene and upregulates the expression of Stat3. Furthermore, Pwp1 KD mESCs recover their differentiation potential through suppressing the expression of Stat3 or inhibiting the tyrosine phosphorylation of STAT3. Together, our results suggest that Pwp1 plays important roles in the differentiation potential of mESCs.
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Affiliation(s)
- Junwei Shen
- Shanghai Key Laboratory of Signaling and Disease Research, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, Shanghai, People's Republic of China
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33
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Gordon JAR, Stein JL, Westendorf JJ, van Wijnen AJ. Chromatin modifiers and histone modifications in bone formation, regeneration, and therapeutic intervention for bone-related disease. Bone 2015; 81:739-745. [PMID: 25836763 PMCID: PMC4591092 DOI: 10.1016/j.bone.2015.03.011] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/13/2015] [Indexed: 02/07/2023]
Abstract
Post-translational modifications of chromatin such as DNA methylation and different types of histone acetylation, methylation and phosphorylation are well-appreciated epigenetic mechanisms that confer information to progeny cells during lineage commitment. These distinct epigenetic modifications have defined roles in bone, development, tissue regeneration, cell commitment and differentiation, as well as disease etiologies. In this review, we discuss the role of these chromatin modifications and the enzymes regulating these marks (methyltransferases, demethylases, acetyltransferases, and deacetylases) in progenitor cells, osteoblasts and bone-related cells. In addition, the clinical relevance of deregulated histone modifications and enzymes as well as current and potential therapeutic interventions targeting chromatin modifiers are addressed.
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Affiliation(s)
| | - Janet L Stein
- Department of Biochemistry, University of Vermont, Burlington, VT, USA.
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34
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Hayashida N. Set1/MLL complex is indispensable for the transcriptional ability of heat shock transcription factor 2. Biochem Biophys Res Commun 2015; 467:805-12. [PMID: 26478434 DOI: 10.1016/j.bbrc.2015.10.061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 10/11/2015] [Indexed: 01/23/2023]
Abstract
Heat shock transcription factor 2 (HSF2) is one of four mammalian HSFs, and it is essential in neurogenesis and gametogenesis. However, other aspects of this transcription factor have not been thoroughly characterized. We recently demonstrated that HSF2 suppresses the aggregation caused by polyglutamine (polyQ) protein, and that the cell protective ability of HSF2 is mediated through the induction of the small HSP alphaB-crystallin (CRYAB). In the present study, we investigated the mechanism of HSF2-induced CRYAB expression. We demonstrated that HSF2 interacted with the core component of the Set1/MLL H3K4 histone methyltransferase complex, WDR5. Indeed, HSF2 up-regulated the H3K4me3, H3K14Ac, and H3K27Ac (active histone marks) of the CRYAB promoter. WDR5 bound to the HSF2 central domain (Domain X) in vitro and in vivo, and Cys278 of HSF2 was indispensable for HSF2-WDR5 interaction. HSF2 also interacted with the Set1/MLL complex. These results suggest that the interaction with the Set1/MLL complex via binding to WDR5 is critical for the transcriptional ability of HSF2.
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Affiliation(s)
- Naoki Hayashida
- Department of Biochemistry, Yamaguchi University School of Medicine, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan.
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35
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Thomas LR, Foshage AM, Weissmiller AM, Tansey WP. The MYC-WDR5 Nexus and Cancer. Cancer Res 2015; 75:4012-5. [PMID: 26383167 DOI: 10.1158/0008-5472.can-15-1216] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/10/2015] [Indexed: 02/05/2023]
Abstract
The MYC oncogenes encode a family of transcription factors that feature prominently in cancer. MYC proteins are overexpressed or deregulated in a majority of malignancies and drive tumorigenesis by inducing widespread transcriptional reprogramming that promotes cell proliferation, metabolism, and genomic instability. The ability of MYC to regulate transcription depends on its dimerization with MAX, which creates a DNA-binding domain that recognizes specific sequences in the regulatory elements of MYC target genes. Recently, we discovered that recognition of target genes by MYC also depends on its interaction with WDR5, a WD40-repeat protein that exists as part of several chromatin-regulatory complexes. Here, we discuss how interaction of MYC with WDR5 could create an avidity-based chromatin recognition mechanism that allows MYC to select its target genes in response to both genetic and epigenetic determinants. We rationalize how the MYC-WDR5 interaction provides plasticity in target gene selection by MYC and speculate on the biochemical and genomic contexts in which this interaction occurs. Finally, we discuss how properties of the MYC-WDR5 interface make it an attractive point for discovery of small-molecule inhibitors of MYC function in cancer cells.
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Affiliation(s)
- Lance R Thomas
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Audra M Foshage
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - April M Weissmiller
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.
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36
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Huang J, Cardamone MD, Johnson HE, Neault M, Chan M, Floyd ZE, Mallette FA, Perissi V. Exchange Factor TBL1 and Arginine Methyltransferase PRMT6 Cooperate in Protecting G Protein Pathway Suppressor 2 (GPS2) from Proteasomal Degradation. J Biol Chem 2015; 290:19044-54. [PMID: 26070566 DOI: 10.1074/jbc.m115.637660] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Indexed: 12/18/2022] Open
Abstract
G protein pathway suppressor 2 (GPS2) is a multifunctional protein involved in the regulation of a number of metabolic organs. First identified as part of the NCoR-SMRT corepressor complex, GPS2 is known to play an important role in the nucleus in the regulation of gene transcription and meiotic recombination. In addition, we recently reported a non-transcriptional role of GPS2 as an inhibitor of the proinflammatory TNFα pathway in the cytosol. Although this suggests that the control of GPS2 localization may be an important determinant of its molecular functions, a clear understanding of GPS2 differential targeting to specific cellular locations is still lacking. Here we show that a fine balance between protein stabilization and degradation tightly regulates GPS2 nuclear function. Our findings indicate that GPS2 is degraded upon polyubiquitination by the E3 ubiquitin ligase Siah2. Unexpectedly, interaction with the exchange factor TBL1 is required to protect GPS2 from degradation, with methylation of GPS2 by arginine methyltransferase PRMT6 regulating the interaction with TBL1 and inhibiting proteasome-dependent degradation. Overall, our findings indicate that regulation of GPS2 by posttranslational modifications provides an effective strategy for modulating its molecular function within the nuclear compartment.
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Affiliation(s)
- Jiawen Huang
- From the Biochemistry Department, Boston University School of Medicine, Boston, Massachusetts 02118
| | - M Dafne Cardamone
- From the Biochemistry Department, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Holly E Johnson
- From the Biochemistry Department, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Mathieu Neault
- the Chromatin Structure and Cellular Senescence Research Unit, Centre de Recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Quebec H1T 2M4, Canada
| | - Michelle Chan
- From the Biochemistry Department, Boston University School of Medicine, Boston, Massachusetts 02118
| | - Z Elizabeth Floyd
- the Pennington Biomedical Research Center, Baton Rouge, Louisiana 70808, and
| | - Frédérick A Mallette
- the Chromatin Structure and Cellular Senescence Research Unit, Centre de Recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Quebec H1T 2M4, Canada, the Département de Médecine, Université de Montréal, Montréal, Quebec H1T 2M4, Canada
| | - Valentina Perissi
- From the Biochemistry Department, Boston University School of Medicine, Boston, Massachusetts 02118,
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37
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Mayes K, Qiu Z, Alhazmi A, Landry JW. ATP-dependent chromatin remodeling complexes as novel targets for cancer therapy. Adv Cancer Res 2015; 121:183-233. [PMID: 24889532 DOI: 10.1016/b978-0-12-800249-0.00005-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The progression to advanced stage cancer requires changes in many characteristics of a cell. These changes are usually initiated through spontaneous mutation. As a result of these mutations, gene expression is almost invariably altered allowing the cell to acquire tumor-promoting characteristics. These abnormal gene expression patterns are in part enabled by the posttranslational modification and remodeling of nucleosomes in chromatin. These chromatin modifications are established by a functionally diverse family of enzymes including histone and DNA-modifying complexes, histone deposition pathways, and chromatin remodeling complexes. Because the modifications these enzymes deposit are essential for maintaining tumor-promoting gene expression, they have recently attracted much interest as novel therapeutic targets. One class of enzyme that has not generated much interest is the chromatin remodeling complexes. In this review, we will present evidence from the literature that these enzymes have both causal and enabling roles in the transition to advanced stage cancers; as such, they should be seriously considered as high-value therapeutic targets. Previously published strategies for discovering small molecule regulators to these complexes are described. We close with thoughts on future research, the field should perform to further develop this potentially novel class of therapeutic target.
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Affiliation(s)
- Kimberly Mayes
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Zhijun Qiu
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Aiman Alhazmi
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Joseph W Landry
- Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.
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38
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Ucar D, Bayarsaihan D. Cell-specific gene promoters are marked by broader spans of H3K4me3 and are associated with robust gene expression patterns. Epigenomics 2015; 7:129-31. [DOI: 10.2217/epi.14.87] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Duygu Ucar
- Department of Bioinformatics & Computational Biology, The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Dashzeveg Bayarsaihan
- Department of Reconstructive Sciences, Institute for Systems Genomics & Center for Regenerative Medicine & Skeletal Development, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
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39
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Cohen ASA, Tuysuz B, Shen Y, Bhalla SK, Jones SJM, Gibson WT. A novel mutation in EED associated with overgrowth. J Hum Genet 2015; 60:339-42. [PMID: 25787343 DOI: 10.1038/jhg.2015.26] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/27/2015] [Accepted: 02/12/2015] [Indexed: 01/01/2023]
Abstract
In a patient suspected clinically to have Weaver syndrome, we ruled out mutations in EZH2 and NSD1, then identified a previously undescribed de novo mutation in EZH2's partner protein EED. Both proteins are members of the Polycomb Repressive Complex 2 that maintains gene silencing. On the basis of the similarities of the patient's phenotype to Weaver syndrome, which is caused by de novo mutations in EZH2, and on other lines of evidence including mouse Eed hypomorphs, we characterize this mutation as probably pathogenic for a Weaver-like overgrowth syndrome. This is the first report of overgrowth and related phenotypes associated with a constitutional mutation in human EED.
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Affiliation(s)
- Ana S A Cohen
- 1] Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada [2] Child and Family Research Institute, British Columbia Children's Hospital, Vancouver, BC, Canada
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Cerrahpasa Medical Faculty, Istanbul University, Istanbul, Turkey
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Sanjiv K Bhalla
- Department of Radiology, Surrey Memorial Hospital, Surrey, BC, Canada
| | - Steven J M Jones
- 1] Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada [2] Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada [3] Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - William T Gibson
- 1] Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada [2] Child and Family Research Institute, British Columbia Children's Hospital, Vancouver, BC, Canada
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40
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Guo J, Jin D. A genetic screen in Drosophila implicates Sex comb on midleg (Scm) in tissue overgrowth and mechanisms of Scm degradation by Wds. Mech Dev 2015; 136:1-7. [PMID: 25772304 DOI: 10.1016/j.mod.2015.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 11/30/2022]
Abstract
The sex comb on midleg (scm) gene encodes a transcriptional repressor and belongs to the Polycomb group (PcG) of genes, which regulates growth in Drosophila. Scm interacts with Polyhomeotic (a PcG protein) in vitro by recognizing its SPM domain. The homologous human protein, Sex comb on midleg-like 2 (Scml2), has been implicated in malignant brain tumors. Will die slowly (Wds) is another factor that regulates Drosophila development, and its homologous human protein, WD repeat domain 5(Wdr5), is part of the mixed lineage leukemia 1(MLL1) complex that promotes histone H3Lys4 methylation. Like Scml2, Wdr5 has been implicated in certain cancers; this protein plays an important role in leukemogenesis. In this study, we find that loss-of-function mutations in Scm result in non-autonomous tissue overgrowth in Drosophila, and determine that Scm is essential for ommatidium development and important for cell survival in Drosophila. Furthermore, our research suggests a relationship between Wds and Scm; Wds promotes Scm degradation through ubiquitination in vitro in Drosophila.
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Affiliation(s)
- Jiwei Guo
- College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Dan Jin
- College of Life Sciences, Nankai University, Tianjin 300071, China
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41
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Hoe M, Nicholas HR. Evidence of a MOF histone acetyltransferase-containing NSL complex in C. elegans. WORM 2014; 3:e982967. [PMID: 26430553 PMCID: PMC4588387 DOI: 10.4161/21624054.2014.982967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 10/28/2014] [Indexed: 11/19/2022]
Abstract
Regulation of chromatin is a key process in the developmental control of gene expression. Many multi-subunit protein complexes have been found to regulate chromatin through the modification of histone residues. One such complex is the MOF histone acetyltransferase-containing NSL complex. While the composition of the human and Drosophila NSL complexes has been determined and the functions of these complexes investigated, the existence of an equivalent complex in nematodes such as Caenorhabditis elegans has not yet been explored. Here we summarise evidence, from our own work and that of others, that homologues of NSL complex components are found in C. elegans. We review data suggesting that nematode proteins SUMV-1 and SUMV-2 are homologous to NSL2 and NSL3, respectively, and that SUMV-1 and SUMV-2 may form a complex with MYS-2, the worm homolog of MOF. We propose that these interactions suggest the existence of a nematode NSL-like complex and discuss the roles of this putative NSL complex in worms as well as exploring the possibility of crosstalk between NSL and COMPASS complexes via components that are common to both. We present the groundwork from which a full characterization of a nematode NSL complex may begin.
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Affiliation(s)
- Matthew Hoe
- School of Molecular Bioscience; University of Sydney ; Sydney, Australia
| | - Hannah R Nicholas
- School of Molecular Bioscience; University of Sydney ; Sydney, Australia
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42
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Vizán P, Beringer M, Ballaré C, Di Croce L. Role of PRC2-associated factors in stem cells and disease. FEBS J 2014; 282:1723-35. [PMID: 25271128 DOI: 10.1111/febs.13083] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 09/19/2014] [Accepted: 09/26/2014] [Indexed: 01/01/2023]
Abstract
The Polycomb group (PcG) of proteins form chromatin-binding complexes with histone-modifying activity. The two main PcG repressive complexes studied (PRC1 and PRC2) are generally associated with chromatin in its repressed state. PRC2 is responsible for methylation of histone H3 at lysine 27 (H3K27me3), an epigenetic mark that is linked with numerous biological processes, including development, adult homeostasis and cancer. The core canonical complex PRC2, which contains the EZH1/2, SUZ12 and EED proteins, may be extended and functionally manipulated through interactions with several other proteins. In this review, we focus on these PRC2-associated proteins. As PRC2 functions are diverse, the variability conferred by these sub-stoichiometrically associated members may help to understand specific changes in PRC2 activity, chromatin recruitment and distribution required for gene repression.
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Affiliation(s)
- Pedro Vizán
- Centre for Genomic Regulation, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
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Bujakowska KM, Zhang Q, Siemiatkowska AM, Liu Q, Place E, Falk MJ, Consugar M, Lancelot ME, Antonio A, Lonjou C, Carpentier W, Mohand-Saïd S, den Hollander AI, Cremers FPM, Leroy BP, Gai X, Sahel JA, van den Born LI, Collin RWJ, Zeitz C, Audo I, Pierce EA. Mutations in IFT172 cause isolated retinal degeneration and Bardet-Biedl syndrome. Hum Mol Genet 2014; 24:230-42. [PMID: 25168386 DOI: 10.1093/hmg/ddu441] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Primary cilia are sensory organelles present on most mammalian cells. The assembly and maintenance of primary cilia are facilitated by intraflagellar transport (IFT), a bidirectional protein trafficking along the cilium. Mutations in genes coding for IFT components have been associated with a group of diseases called ciliopathies. These genetic disorders can affect a variety of organs including the retina. Using whole exome sequencing in three families, we identified mutations in Intraflagellar Transport 172 Homolog [IFT172 (Chlamydomonas)] that underlie an isolated retinal degeneration and Bardet-Biedl syndrome. Extensive functional analyses of the identified mutations in cell culture, rat retina and in zebrafish demonstrated their hypomorphic or null nature. It has recently been reported that mutations in IFT172 cause a severe ciliopathy syndrome involving skeletal, renal, hepatic and retinal abnormalities (Jeune and Mainzer-Saldino syndromes). Here, we report for the first time that mutations in this gene can also lead to an isolated form of retinal degeneration. The functional data for the mutations can partially explain milder phenotypes; however, the involvement of modifying alleles in the IFT172-associated phenotypes cannot be excluded. These findings expand the spectrum of disease associated with mutations in IFT172 and suggest that mutations in genes originally reported to be associated with syndromic ciliopathies should also be considered in subjects with non-syndromic retinal dystrophy.
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Affiliation(s)
- Kinga M Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA Institut National de la Santé et de la Recherche Médicale U968, Paris 75012, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, Institut de la Vision, Paris 75012, France Centre National de la Recherche Scientifique, UMR_7210, Paris 75012, France
| | - Qi Zhang
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | | | - Qin Liu
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - Emily Place
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - Marni J Falk
- Department of Pediatrics, Division of Human Genetics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mark Consugar
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - Marie-Elise Lancelot
- Institut National de la Santé et de la Recherche Médicale U968, Paris 75012, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, Institut de la Vision, Paris 75012, France Centre National de la Recherche Scientifique, UMR_7210, Paris 75012, France
| | - Aline Antonio
- Institut National de la Santé et de la Recherche Médicale U968, Paris 75012, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, Institut de la Vision, Paris 75012, France Centre National de la Recherche Scientifique, UMR_7210, Paris 75012, France
| | - Christine Lonjou
- Plateforme Post-génomique P3S, Hôpital Pitié Salpêtrière, Paris 75013, France
| | - Wassila Carpentier
- Plateforme Post-génomique P3S, Hôpital Pitié Salpêtrière, Paris 75013, France
| | - Saddek Mohand-Saïd
- Institut National de la Santé et de la Recherche Médicale U968, Paris 75012, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, Institut de la Vision, Paris 75012, France Centre National de la Recherche Scientifique, UMR_7210, Paris 75012, France Institut National de la Santé et de la Recherche Médicale and Direction de L'Hospitalisation et de L'Organisation des Soins Centre D'Investigation Clinique 1423, Centre Hospitalier National D'Ophtalmologie des Quinze-Vingts, Paris 75012, France
| | - Anneke I den Hollander
- Department of Human Genetics Radboud Institute for Molecular Life Sciences, and Department of Ophthalmology, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics Radboud Institute for Molecular Life Sciences, and
| | - Bart P Leroy
- Department of Ophthalmology and Center for Medical Genetics, Ghent University Hospital and Ghent University, Ghent 9000, Belgium Ophthalmic Genetics and Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, PA 19104, USA
| | - Xiaowu Gai
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
| | - José-Alain Sahel
- Institut National de la Santé et de la Recherche Médicale U968, Paris 75012, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, Institut de la Vision, Paris 75012, France Centre National de la Recherche Scientifique, UMR_7210, Paris 75012, France Institut National de la Santé et de la Recherche Médicale and Direction de L'Hospitalisation et de L'Organisation des Soins Centre D'Investigation Clinique 1423, Centre Hospitalier National D'Ophtalmologie des Quinze-Vingts, Paris 75012, France Fondation Ophtalmologique Adolphe de Rothschild, Paris 75019, France Academie des Sciences, Institut de France, Paris 75006, France University College London, Institute of Ophthalmology, London EC1V 9EL, UK and
| | | | - Rob W J Collin
- Department of Human Genetics Radboud Institute for Molecular Life Sciences, and
| | - Christina Zeitz
- Institut National de la Santé et de la Recherche Médicale U968, Paris 75012, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, Institut de la Vision, Paris 75012, France Centre National de la Recherche Scientifique, UMR_7210, Paris 75012, France
| | - Isabelle Audo
- Institut National de la Santé et de la Recherche Médicale U968, Paris 75012, France Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, Institut de la Vision, Paris 75012, France Centre National de la Recherche Scientifique, UMR_7210, Paris 75012, France Institut National de la Santé et de la Recherche Médicale and Direction de L'Hospitalisation et de L'Organisation des Soins Centre D'Investigation Clinique 1423, Centre Hospitalier National D'Ophtalmologie des Quinze-Vingts, Paris 75012, France University College London, Institute of Ophthalmology, London EC1V 9EL, UK and
| | - Eric A Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA
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Beck BB, Phillips JB, Bartram MP, Wegner J, Thoenes M, Pannes A, Sampson J, Heller R, Göbel H, Koerber F, Neugebauer A, Hedergott A, Nürnberg G, Nürnberg P, Thiele H, Altmüller J, Toliat MR, Staubach S, Boycott KM, Valente EM, Janecke AR, Eisenberger T, Bergmann C, Tebbe L, Wang Y, Wu Y, Fry AM, Westerfield M, Wolfrum U, Bolz HJ. Mutation of POC1B in a severe syndromic retinal ciliopathy. Hum Mutat 2014; 35:1153-62. [PMID: 25044745 DOI: 10.1002/humu.22618] [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] [Received: 05/28/2014] [Accepted: 07/12/2014] [Indexed: 12/20/2022]
Abstract
We describe a consanguineous Iraqi family with Leber congenital amaurosis (LCA), Joubert syndrome (JBTS), and polycystic kidney disease (PKD). Targeted next-generation sequencing for excluding mutations in known LCA and JBTS genes, homozygosity mapping, and whole-exome sequencing identified a homozygous missense variant, c.317G>C (p.Arg106Pro), in POC1B, a gene essential for ciliogenesis, basal body, and centrosome integrity. In silico modeling suggested a requirement of p.Arg106 for the formation of the third WD40 repeat and a protein interaction interface. In human and mouse retina, POC1B localized to the basal body and centriole adjacent to the connecting cilium of photoreceptors and in synapses of the outer plexiform layer. Knockdown of Poc1b in zebrafish caused cystic kidneys and retinal degeneration with shortened and reduced photoreceptor connecting cilia, compatible with the human syndromic ciliopathy. A recent study describes homozygosity for p.Arg106ProPOC1B in a family with nonsyndromic cone-rod dystrophy. The phenotype associated with homozygous p.Arg106ProPOC1B may thus be highly variable, analogous to homozygous p.Leu710Ser in WDR19 causing either isolated retinitis pigmentosa or Jeune syndrome. Our study indicates that POC1B is required for retinal integrity, and we propose POC1B mutations as a probable cause for JBTS with severe PKD.
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Affiliation(s)
- Bodo B Beck
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
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45
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Direct interaction between the WD40 repeat protein WDR-23 and SKN-1/Nrf inhibits binding to target DNA. Mol Cell Biol 2014; 34:3156-67. [PMID: 24912676 DOI: 10.1128/mcb.00114-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
SKN-1/Nrf transcription factors activate cytoprotective genes in response to reactive small molecules and strongly influence stress resistance, longevity, and development. The molecular mechanisms of SKN-1/Nrf regulation are poorly defined. We previously identified the WD40 repeat protein WDR-23 as a repressor of Caenorhabditis elegans SKN-1 that functions with a ubiquitin ligase to presumably target the factor for degradation. However, SKN-1 activity and nuclear accumulation are not always correlated, suggesting that there could be additional regulatory mechanisms. Here, we integrate forward genetics and biochemistry to gain insights into how WDR-23 interacts with and regulates SKN-1. We provide evidence that WDR-23 preferentially regulates one of three SKN-1 variants through a direct interaction that is required for normal stress resistance and development. Homology modeling predicts that WDR-23 folds into a β-propeller, and we identify the top of this structure and four motifs at the termini of SKN-1c as essential for the interaction. Two of these SKN-1 motifs are highly conserved in human Nrf1 and Nrf2 and two directly interact with target DNA. Lastly, we demonstrate that WDR-23 can block the ability of SKN-1c to interact with DNA sequences of target promoters identifying a new mechanism of regulation that is independent of the ubiquitin proteasome system, which can become occupied with damaged proteins during stress.
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Ali A, Veeranki SN, Tyagi S. A SET-domain-independent role of WRAD complex in cell-cycle regulatory function of mixed lineage leukemia. Nucleic Acids Res 2014; 42:7611-24. [PMID: 24880690 PMCID: PMC4081079 DOI: 10.1093/nar/gku458] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
MLL, the trithorax ortholog, is a well-characterized histone 3 lysine 4 methyltransferase that is crucial for proper regulation of the Hox genes during embryonic development. Chromosomal translocations, disrupting the Mll gene, lead to aggressive leukemia with poor prognosis. However, the functions of MLL in cellular processes like cell-cycle regulation are not well studied. Here we show that the MLL has a regulatory role during multiple phases of the cell cycle. RNAi-mediated knockdown reveals that MLL regulates S-phase progression and, proper segregation and cytokinesis during M phase. Using deletions and mutations, we narrow the cell-cycle regulatory role to the C subunit of MLL. Our analysis reveals that the transactivation domain and not the SET domain is important for the S-phase function of MLL. Surprisingly, disruption of MLL–WRAD interaction is sufficient to disrupt proper mitotic progression. These mitotic functions of WRAD are independent of SET domain of MLL and, therefore, define a new role of WRAD in subset of MLL functions. Finally, we address the overlapping and unique roles of the different SET family members in the cell cycle.
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Affiliation(s)
- Aamir Ali
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
| | - Sailaja Naga Veeranki
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Nampally, Hyderabad, India
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47
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Wagner T, Robaa D, Sippl W, Jung M. Mind the Methyl: Methyllysine Binding Proteins in Epigenetic Regulation. ChemMedChem 2014; 9:466-83. [DOI: 10.1002/cmdc.201300422] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Indexed: 11/07/2022]
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48
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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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49
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Kumar S, Jordan MC, Datla R, Cloutier S. The LuWD40-1 gene encoding WD repeat protein regulates growth and pollen viability in flax (Linum Usitatissimum L.). PLoS One 2013; 8:e69124. [PMID: 23935935 PMCID: PMC3728291 DOI: 10.1371/journal.pone.0069124] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 06/11/2013] [Indexed: 01/22/2023] Open
Abstract
As a crop, flax holds significant commercial value for its omega-3 rich oilseeds and stem fibres. Canada is the largest producer of linseed but there exists scope for significant yield improvements. Implementation of mechanisms such as male sterility can permit the development of hybrids to assist in achieving this goal. Temperature sensitive male sterility has been reported in flax but the leakiness of this system in field conditions limits the production of quality hybrid seeds. Here, we characterized a 2,588 bp transcript differentially expressed in male sterile lines of flax. The twelve intron gene predicted to encode a 368 amino acid protein has five WD40 repeats which, in silico, form a propeller structure with putative nucleic acid and histone binding capabilities. The LuWD40-1 protein localized to the nucleus and its expression increased during the transition and continued through the vegetative stages (seed, etiolated seedling, stem) while the transcript levels declined during reproductive development (ovary, anthers) and embryonic morphogenesis of male fertile plants. Knockout lines for LuWD40-1 in flax failed to develop shoots while overexpression lines showed delayed growth phenotype and were male sterile. The non-viable flowers failed to open and the pollen grains from these flowers were empty. Three independent transgenic lines overexpressing the LuWD40-1 gene had ∼80% non-viable pollen, reduced branching, delayed flowering and maturity compared to male fertile genotypes. The present study provides new insights into a male sterility mechanism present in flax.
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Affiliation(s)
- Santosh Kumar
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada
| | - Mark C. Jordan
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada
| | - Raju Datla
- National Research Council, Saskatoon, Saskatchewan, Canada
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada
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50
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Wang Y, Jiang F, Zhuo Z, Wu XH, Wu YD. A method for WD40 repeat detection and secondary structure prediction. PLoS One 2013; 8:e65705. [PMID: 23776530 PMCID: PMC3679165 DOI: 10.1371/journal.pone.0065705] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 05/02/2013] [Indexed: 11/19/2022] Open
Abstract
WD40-repeat proteins (WD40s), as one of the largest protein families in eukaryotes, play vital roles in assembling protein-protein/DNA/RNA complexes. WD40s fold into similar β-propeller structures despite diversified sequences. A program WDSP (WD40 repeat protein Structure Predictor) has been developed to accurately identify WD40 repeats and predict their secondary structures. The method is designed specifically for WD40 proteins by incorporating both local residue information and non-local family-specific structural features. It overcomes the problem of highly diversified protein sequences and variable loops. In addition, WDSP achieves a better prediction in identifying multiple WD40-domain proteins by taking the global combination of repeats into consideration. In secondary structure prediction, the average Q3 accuracy of WDSP in jack-knife test reaches 93.7%. A disease related protein LRRK2 was used as a representive example to demonstrate the structure prediction.
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Affiliation(s)
- Yang Wang
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
| | - Fan Jiang
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
| | - Zhu Zhuo
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
| | - Xian-Hui Wu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
- * E-mail: (XHW); (YDW)
| | - Yun-Dong Wu
- Lab of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, P. R. China
- College of Chemistry, Peking University, Beijing, P. R. China
- * E-mail: (XHW); (YDW)
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