1
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Huang X, Chen Y, Xiao Q, Shang X, Liu Y. Chemical inhibitors targeting histone methylation readers. Pharmacol Ther 2024; 256:108614. [PMID: 38401773 DOI: 10.1016/j.pharmthera.2024.108614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Histone methylation reader domains are protein modules that recognize specific histone methylation marks, such as methylated or unmethylated lysine or arginine residues on histones. These reader proteins play crucial roles in the epigenetic regulation of gene expression, chromatin structure, and DNA damage repair. Dysregulation of these proteins has been linked to various diseases, including cancer, neurodegenerative diseases, and developmental disorders. Therefore, targeting these proteins with chemical inhibitors has emerged as an attractive approach for therapeutic intervention, and significant progress has been made in this area. In this review, we will summarize the development of inhibitors targeting histone methylation readers, including MBT domains, chromodomains, Tudor domains, PWWP domains, PHD fingers, and WD40 repeat domains. For each domain, we will briefly discuss its identification and biological/biochemical functions, and then focus on the discovery of inhibitors tailored to target this domain, summarizing the property and potential application of most inhibitors. We will also discuss the structural basis for the potency and selectivity of these inhibitors, which will aid in further lead generation and optimization. Finally, we will also address the challenges and strategies involved in the development of these inhibitors. It should facilitate the rational design and development of novel chemical scaffolds and new targeting strategies for histone methylation reader domains with the help of this body of data.
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Affiliation(s)
- Xiaolei Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yichang Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Qin Xiao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Xinci Shang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yanli Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China.
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2
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Sun H, Zhang H. Lysine Methylation-Dependent Proteolysis by the Malignant Brain Tumor (MBT) Domain Proteins. Int J Mol Sci 2024; 25:2248. [PMID: 38396925 PMCID: PMC10889763 DOI: 10.3390/ijms25042248] [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: 12/14/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Lysine methylation is a major post-translational protein modification that occurs in both histones and non-histone proteins. Emerging studies show that the methylated lysine residues in non-histone proteins provide a proteolytic signal for ubiquitin-dependent proteolysis. The SET7 (SETD7) methyltransferase specifically transfers a methyl group from S-Adenosyl methionine to a specific lysine residue located in a methylation degron motif of a protein substrate to mark the methylated protein for ubiquitin-dependent proteolysis. LSD1 (Kdm1a) serves as a demethylase to dynamically remove the methyl group from the modified protein. The methylated lysine residue is specifically recognized by L3MBTL3, a methyl-lysine reader that contains the malignant brain tumor domain, to target the methylated proteins for proteolysis by the CRL4DCAF5 ubiquitin ligase complex. The methylated lysine residues are also recognized by PHF20L1 to protect the methylated proteins from proteolysis. The lysine methylation-mediated proteolysis regulates embryonic development, maintains pluripotency and self-renewal of embryonic stem cells and other stem cells such as neural stem cells and hematopoietic stem cells, and controls other biological processes. Dysregulation of the lysine methylation-dependent proteolysis is associated with various diseases, including cancers. Characterization of lysine methylation should reveal novel insights into how development and related diseases are regulated.
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Affiliation(s)
| | - Hui Zhang
- Department of Chemistry and Biochemistry, Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 South Maryland Parkway, P.O. Box 454003, Las Vegas, NV 89154-4003, USA;
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3
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Egger B. Neural Stem Cells and Brain Tumour Models in Drosophila. Neurogenetics 2023. [DOI: 10.1007/978-3-031-07793-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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4
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Yamamoto‐Matsuda H, Miyoshi K, Moritoh M, Yoshitane H, Fukada Y, Saito K, Yamanaka S, Siomi MC. Lint‐O
cooperates with L(3)mbt in target gene suppression to maintain homeostasis in fly ovary and brain. EMBO Rep 2022; 23:e53813. [PMID: 35993198 PMCID: PMC9535798 DOI: 10.15252/embr.202153813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022] Open
Abstract
Loss‐of‐function mutations in Drosophila lethal(3)malignant brain tumor [l(3)mbt] cause ectopic expression of germline genes and brain tumors. Loss of L(3)mbt function in ovarian somatic cells (OSCs) aberrantly activates germ‐specific piRNA amplification and leads to infertility. However, the underlying mechanism remains unclear. Here, ChIP‐seq for L(3)mbt in cultured OSCs and RNA‐seq before and after L(3)mbt depletion shows that L(3)mbt genomic binding is not necessarily linked to gene regulation and that L(3)mbt controls piRNA pathway genes in multiple ways. Lack of known L(3)mbt co‐repressors, such as Lint‐1, has little effect on the levels of piRNA amplifiers. Identification of L(3)mbt interactors in OSCs and subsequent analysis reveals CG2662 as a novel co‐regulator of L(3)mbt, termed “L(3)mbt interactor in OSCs” (Lint‐O). Most of the L(3)mbt‐bound piRNA amplifier genes are also bound by Lint‐O in a similar fashion. Loss of Lint‐O impacts the levels of piRNA amplifiers, similar to the lack of L(3)mbt. The lint‐O‐deficient flies exhibit female sterility and tumorous brains. Thus, L(3)mbt and its novel co‐suppressor Lint‐O cooperate in suppressing target genes to maintain homeostasis in the ovary and brain.
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Affiliation(s)
- Hitomi Yamamoto‐Matsuda
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Keita Miyoshi
- Department of Chromosome Science National Institute of Genetics, Research Organization of Information and Systems Shizuoka Japan
- Department of Genetics School of Life Science, SOKENDAI Shizuoka Japan
| | - Mai Moritoh
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Hikari Yoshitane
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Yoshitaka Fukada
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Kuniaki Saito
- Department of Chromosome Science National Institute of Genetics, Research Organization of Information and Systems Shizuoka Japan
- Department of Genetics School of Life Science, SOKENDAI Shizuoka Japan
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science The University of Tokyo Tokyo Japan
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5
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Oxidative Stress Is Associated with Overgrowth in Drosophila l(3)mbt Mutant Imaginal Discs. Cells 2022; 11:cells11162542. [PMID: 36010619 PMCID: PMC9406541 DOI: 10.3390/cells11162542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/04/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022] Open
Abstract
The loss-of-function conditions for an l(3)malignant brain tumour (l(3)mbt) in larvae reared at 29 °C results in malignant brain tumours and hyperplastic imaginal discs. Unlike the former that have been extensively characterised, little is known about the latter. Here we report the results of a study of the hyperplastic l(3)mbt mutant wing imaginal discs. We identify the l(3)mbt wing disc tumour transcriptome and find it to include genes involved in reactive oxygen species (ROS) metabolism. Furthermore, we show the presence of oxidative stress in l(3)mbt hyperplastic discs, even in apoptosis-blocked conditions, but not in l(3)mbt brain tumours. We also find that chemically blocking oxidative stress in l(3)mbt wing discs reduces the incidence of wing disc overgrowths. Our results reveal the involvement of oxidative stress in l(3)mbt wing discs hyperplastic growth.
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6
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Jiang L, Wang P, Su M, Yang L, Wang Q. Identification of mRNA Signature for Predicting Prognosis Risk of Rectal Adenocarcinoma. Front Genet 2022; 13:880945. [PMID: 35664306 PMCID: PMC9159392 DOI: 10.3389/fgene.2022.880945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The immune system plays a crucial role in rectal adenocarcinoma (READ). Immune-related genes may help predict READ prognoses. Methods: The Cancer Genome Atlas dataset and GSE56699 were used as the training and validation datasets, respectively, and differentially expressed genes (DEGs) were identified. The optimal DEG combination was determined, and the prognostic risk model was constructed. The correlation between optimal DEGs and immune infiltrating cells was evaluated. Results: Nine DEGs were selected for analysis. Moreover, ADAMDEC1 showed a positive correlation with six immune infiltrates, most notably with B cells and dendritic cells. F13A1 was also positively correlated with six immune infiltrates, particularly macrophage and dendritic cells, whereas LGALS9C was negatively correlated with all immune infiltrates except B cells. Additionally, the prognostic risk model was strongly correlated with the actual situation. We retained only three prognosis risk factors: age, pathologic stage, and prognostic risk model. The stratified analysis revealed that lower ages and pathologic stages have a better prognosis with READ. Age and mRNA prognostic factors were the most important factors in determining the possibility of 3- and 5-year survival. Conclusion: In summary, we identified a nine-gene prognosis risk model that is applicable to the treatment of READ. Altogether, characteristics such as the gene signature and age have a strong predictive value for prognosis risk.
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Affiliation(s)
- Linlin Jiang
- Department of Chemotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Peng Wang
- Department of General Surgery, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Mu Su
- Department of Chemotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Lili Yang
- Department of Chemotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qingbo Wang
- Department of Chemotherapy, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, China
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Molnar C, Heinen JP, Reina J, Llamazares S, Palumbo E, Breschi A, Gay M, Villarreal L, Vilaseca M, Pollarolo G, Gonzalez C. The histone code reader PHD finger protein 7 controls sex-linked disparities in gene expression and malignancy in Drosophila. SCIENCE ADVANCES 2019; 5:eaaw7965. [PMID: 31453329 PMCID: PMC6693905 DOI: 10.1126/sciadv.aaw7965] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/11/2019] [Indexed: 05/03/2023]
Abstract
The notable male predominance across many human cancer types remains unexplained. Here, we show that Drosophila l(3)mbt brain tumors are more invasive and develop as malignant neoplasms more often in males than in females. By quantitative proteomics, we have identified a signature of proteins that are differentially expressed between male and female tumor samples. Prominent among them is the conserved chromatin reader PHD finger protein 7 (Phf7). We show that Phf7 depletion reduces sex-dependent differences in gene expression and suppresses the enhanced malignant traits of male tumors. Our results identify potential regulators of sex-linked tumor dimorphism and show that these genes may serve as targets to suppress sex-linked malignant traits.
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Affiliation(s)
- Cristina Molnar
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jan Peter Heinen
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jose Reina
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Salud Llamazares
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Emilio Palumbo
- CRG, BIST, Carrer del Dr. Aiguader, 88, 08003 Barcelona, Spain
- UPF, Plaça de la Mercè, 10, 08002 Barcelona, Spain
- IMIM, Carrer del Dr. Aiguader, 88, 08003 Barcelona, Spain
| | | | - Marina Gay
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Laura Villarreal
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Marta Vilaseca
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Giulia Pollarolo
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Cayetano Gonzalez
- IRB Barcelona, BIST, Carrer de Baldiri Reixac, 10, 08028 Barcelona, Spain
- ICREA, Passeig Lluís Companys, 08010 Barcelona, Spain
- Corresponding author.
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8
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Wu W, Bai S, Zhu D, Li K, Dong W, He W, Peng S, Lai Y, Wang Q, Guo Z, Liu L, Huang H. Overexpression of malignant brain tumor domain containing protein 1 predicts a poor prognosis of prostate cancer. Oncol Lett 2019; 17:4640-4646. [PMID: 30944653 DOI: 10.3892/ol.2019.10109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 10/29/2018] [Indexed: 11/05/2022] Open
Abstract
Malignant brain tumor domain containing protein 1 (MBTD1) is a member of the polycomb group protein family that is associated with tumorigenesis. The present study investigated the role of MBTD1 within defined clinicopathological parameters and the prognosis of patients with prostate cancer (PCa). A human tissue microarray containing samples from 71 patients with PCa and seven healthy donors was employed for immunohistochemistry (IHC). The clinicopathological characteristics and prognostic value of MBTD1 were investigated using a dataset of 499 patients from The Cancer Genome Atlas (TCGA). IHC illustrated that the levels of MBTD1 protein were enhanced and markedly associated with aggressive clinical stage and advanced tumor invasion, distant metastasis and lymph node metastasis in patients with PCa. In the TCGA data set, the level of MBTD1 was found to positively correlate with the prostate-specific antigen level, Gleason score and distant metastasis. The multivariate analysis of Cox regression revealed that the levels of MBTD1 may act as an independent prognostic factor for low non-biochemical, recurrence-free survival. In conclusion, MBTD1 was overexpressed in PCa tissues and is associated with aggressive clinicopathological characteristics. It may therefore act as a novel prognostic factor and diagnostic marker in PCa.
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Affiliation(s)
- Wanhua Wu
- Department of Urology, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Shoumin Bai
- Department of Urology, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Dingjun Zhu
- Department of Urology, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Kaiwen Li
- Department of Urology, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Wen Dong
- Department of Urology, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Wang He
- Department of Urology, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Shengmeng Peng
- Department of Urology, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Yiming Lai
- Department of Urology, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Qiong Wang
- Department of Urology, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Zhenghui Guo
- Department of Urology, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China
| | - Leyuan Liu
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA.,Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77845, USA
| | - Hai Huang
- Department of Urology, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, The Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, P.R. China.,Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX 77030, USA
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9
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L3MBTL2 regulates chromatin remodeling during spermatogenesis. Cell Death Differ 2019; 26:2194-2207. [PMID: 30760872 DOI: 10.1038/s41418-019-0283-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 12/18/2018] [Accepted: 01/07/2019] [Indexed: 12/31/2022] Open
Abstract
Lethal (3) malignant brain tumor like 2 (L3MBTL2) is a member of the MBT-domain proteins, which are involved in transcriptional repression and implicated in chromatin compaction. Our previous study has shown that L3MBTL2 is highly expressed in the testis, but its role in spermatogenesis remains unclear. In the present study, we found that L3MBTL2 was most highly expressed in pachytene spermatocytes within the testis. Germ cell-specific ablation of L3mbtl2 in the testis led to increased abnormal spermatozoa, progressive decrease of sperm counts and premature testicular failure in mice. RNA-sequencing analysis on L3mbtl2 deficient testes confirmed that L3MBTL2 was a transcriptional repressor but failed to reveal any significant changes in spermatogenesis-associated genes. Interestingly, L3mbtl2 deficiency resulted in increased γH2AX deposition in the leptotene spermatocytes, subsequent inappropriate retention of γH2AX on autosomes, and defective crossing-over and synapsis during the pachytene stage of meiosis I, and more germ cell apoptosis and degeneration in aging mice. L3MBTL2 interacted with the histone ubiquitin ligase RNF8. Inhibition of L3MBTL2 reduced nuclear RNF8 and ubH2A levels in GC2 cells. L3mbtl2 deficiency led to decreases in the levels of the RNF8 and ubH2A pathway and in histone acetylation in elongating spermatids, and in protamine 1 deposition and chromatin condensation in sperm. These results suggest that L3MBTL2 plays important roles in chromatin remodeling during meiosis and spermiogenesis.
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10
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Wu X, Huang Y, Yu Z, Mu C, Song W, Li R, Liu L, Ye Y, Shi C, Wang C. An MBT domain containing anti-lipopolysaccharide factor (PtALF8) from Portunus trituberculatus is involved in immune response to bacterial challenge. FISH & SHELLFISH IMMUNOLOGY 2019; 84:252-258. [PMID: 30300736 DOI: 10.1016/j.fsi.2018.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/01/2018] [Accepted: 10/05/2018] [Indexed: 06/08/2023]
Abstract
Anti-lipopolysaccharide factors are effective antimicrobial peptides that can bind and neutralize lipopolysaccharide (LPS). In the present study, a new sequence encoding for ALF (designated as PtALF8) was cloned by suppression subtractive hybridization method using ovary of swimming crab Portunus trituberculatus as material. The full-length cDNA of PtALF8 consisted of 531 bp with an ORF of 348 bp encoding a peptide of 115 amino acids containing a putative signal peptide of 19 amino acids. The mature PtALF8 had a predicted molecular weight (MW) of 11.28 kDa and theoretical isoelectricpoint (pI) of 5.11. The PtALF8 contains an MBT domain which was not found in the other 7 isoforms of ALF reported in P. trituberculatus. Unlike most ALFs expressed in hemocytes, PtALF8 transcript was predominantly detected in hepatopancreas. After challenge with Vibrio alginolyticus, the temporal expression level of PtALF8 transcript in hemocytes reached the highest level at 3 h, then decreased to the lowest level at 24 h, and started to increase at 48 h. The recombinant protein showed antimicrobial and bactericidal activity against several bacteria, such as Gram-positive bacteria, Staphylococcus aureus, Micrococcus luteus and Gram-negative bacteria, V. alginolyticus, indicated that the PtALF8 isoform might play protective function against invading bacteria in P. trituberculatus.
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Affiliation(s)
- Xiaodong Wu
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, China; Collaborative Innovation Center for Zhejiang Marine High-efficiency and Healthy Aquaculture, Ningbo University, Ningbo, 315211, China
| | - Yanwei Huang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Zuoben Yu
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Changkao Mu
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, China.
| | - Weiwei Song
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Ronghua Li
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Lei Liu
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Yangfang Ye
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Ce Shi
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Chunlin Wang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, 315211, China.
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11
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Samir N, Matboli M, El-Tayeb H, El-Tawdi A, Hassan MK, Waly A, El-Akkad HAE, Ramadan MG, Al-Belkini TN, El-Khamisy S, El-Asmar F. Competing endogenous RNA network crosstalk reveals novel molecular markers in colorectal cancer. J Cell Biochem 2018; 119:6869-6881. [PMID: 29737552 DOI: 10.1002/jcb.26884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/21/2018] [Indexed: 01/09/2023]
Abstract
The competing endogenous RNA networks play a pivotal role in cancer diagnosis and progression. Novel properstrategies for early detection of colorectal cancer (CRC) are strongly needed. We investigated a novel CRC-specific RNA-based integrated competing endogenous network composed of lethal3 malignant brain tumor like1 (L3MBTL1) gene, long non-coding intergenic RNA- (lncRNA RP11-909B2.1) and homo sapiens microRNA-595 (hsa-miRNA-595) using in silico data analysis. RT-qPCR-based validation of the network was achieved in serum of 70 patients with CRC, 40 patients with benign colorectal neoplasm, and 20 healthy controls. Moreover, in cancer tissues of 20 of the 70 CRC cases were involved in the study. The expression of RNA-based biomarker network in both CRC and adjacent non-tumor tissues and their correlation with the serum levels of this network members was investigated. Lastly, the expression levels of the chosen ceRNA was verified in CRC cell line. Our results revealed that the three RNAs-based biomarker network (long non-coding intergenic RNA-[lncRNA RP11-909B2.1], Homo sapiens microRNA-595 [hsa-miRNA-595], and L3MBTL1 mRNA), had high sensitivity and specificity for discriminating CRC from healthy controls and also from benign colorectal neoplasm. The data suggest that among these three RNAs, serum lncRNA RP11-909B2.1 could be a promising independent prognostic factors in CRC. The circulatory RNA based biomarker panel can act as potential biomarker for CRC diagnosis and prognosis.
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Affiliation(s)
- Nehal Samir
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Abbassia, Cairo, Egypt
| | - Marwa Matboli
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Abbassia, Cairo, Egypt
| | - Hanaa El-Tayeb
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Abbassia, Cairo, Egypt
| | - Ahmed El-Tawdi
- Department of General Surgery, Military Medical Academy, Cairo, Egypt
| | - Mohmed K Hassan
- Center for Genomics, Helmy Institute, Zewail City for Science and Technology, Giza, Egypt.,Biotechnology Program, Department of Zoology, Port Said Faculty of Science, Port Said, Egypt
| | - Amr Waly
- Center for Genomics, Helmy Institute, Zewail City for Science and Technology, Giza, Egypt
| | - Hesham A E El-Akkad
- Department of General Surgery, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mohamed G Ramadan
- Department of Oncology Surgery, National Cancer Institute, Giza, Egypt
| | | | - Sherif El-Khamisy
- Center for Genomics, Helmy Institute, Zewail City for Science and Technology, Giza, Egypt
| | - Farid El-Asmar
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Abbassia, Cairo, Egypt
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12
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Xu T, Park SS, Giaimo BD, Hall D, Ferrante F, Ho DM, Hori K, Anhezini L, Ertl I, Bartkuhn M, Zhang H, Milon E, Ha K, Conlon KP, Kuick R, Govindarajoo B, Zhang Y, Sun Y, Dou Y, Basrur V, Elenitoba-Johnson KS, Nesvizhskii AI, Ceron J, Lee CY, Borggrefe T, Kovall RA, Rual JF. RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1. EMBO J 2017; 36:3232-3249. [PMID: 29030483 PMCID: PMC5666606 DOI: 10.15252/embj.201796525] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 08/31/2017] [Accepted: 09/12/2017] [Indexed: 12/21/2022] Open
Abstract
Notch signaling is an evolutionarily conserved signal transduction pathway that is essential for metazoan development. Upon ligand binding, the Notch intracellular domain (NOTCH ICD) translocates into the nucleus and forms a complex with the transcription factor RBPJ (also known as CBF1 or CSL) to activate expression of Notch target genes. In the absence of a Notch signal, RBPJ acts as a transcriptional repressor. Using a proteomic approach, we identified L3MBTL3 (also known as MBT1) as a novel RBPJ interactor. L3MBTL3 competes with NOTCH ICD for binding to RBPJ. In the absence of NOTCH ICD, RBPJ recruits L3MBTL3 and the histone demethylase KDM1A (also known as LSD1) to the enhancers of Notch target genes, leading to H3K4me2 demethylation and to transcriptional repression. Importantly, in vivo analyses of the homologs of RBPJ and L3MBTL3 in Drosophila melanogaster and Caenorhabditis elegans demonstrate that the functional link between RBPJ and L3MBTL3 is evolutionarily conserved, thus identifying L3MBTL3 as a universal modulator of Notch signaling in metazoans.
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Affiliation(s)
- Tao Xu
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sung-Soo Park
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Daniel Hall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Diana M Ho
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Kazuya Hori
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Lucas Anhezini
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Iris Ertl
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Marek Bartkuhn
- Institute for Genetics, University of Giessen, Giessen, Germany
| | - Honglai Zhang
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eléna Milon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kimberly Ha
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kevin P Conlon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Rork Kuick
- Center for Cancer Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Brandon Govindarajoo
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zhang
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yuqing Sun
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yali Dou
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Julian Ceron
- Cancer and Human Molecular Genetics, Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cheng-Yu Lee
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Tilman Borggrefe
- Institute of Biochemistry, University of Giessen, Giessen, Germany
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jean-François Rual
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
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13
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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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14
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Sumiyoshi T, Sato K, Yamamoto H, Iwasaki YW, Siomi H, Siomi MC. Loss of l(3)mbt leads to acquisition of the ping-pong cycle in Drosophila ovarian somatic cells. Genes Dev 2017; 30:1617-22. [PMID: 27474440 PMCID: PMC4973291 DOI: 10.1101/gad.283929.116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/15/2016] [Indexed: 11/24/2022]
Abstract
Sumiyoshi et al. show that CRISPR-mediated loss of function of lethal (3) malignant brain tumor [l(3)mbt] leads to ectopic activation of the germ-specific ping-pong cycle in ovarian somatic cells. Perinuclear foci resembling nuage, the ping-pong center, appeared following l(3)mbt mutation. In Drosophila germ cells, PIWI-interacting RNAs (piRNAs) are amplified through a PIWI slicer-dependent feed-forward loop termed the ping-pong cycle, yielding secondary piRNAs. However, the detailed mechanism remains poorly understood, largely because an ex vivo model system amenable to biochemical analyses has not been available. Here, we show that CRISPR-mediated loss of function of lethal (3) malignant brain tumor [l(3)mbt] leads to ectopic activation of the germ-specific ping-pong cycle in ovarian somatic cells. Perinuclear foci resembling nuage, the ping-pong center, appeared following l(3)mbt mutation. This activation of the ping-pong machinery in cultured cells will greatly facilitate elucidation of the mechanism underlying secondary piRNA biogenesis in Drosophila.
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Affiliation(s)
- Tetsutaro Sumiyoshi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Kaoru Sato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Hitomi Yamamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 162-8582, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 162-8582, Japan
| | - Mikiko C Siomi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
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15
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Nacci L, Valli R, Maria Pinto R, Zecca M, Cipolli M, Morini J, Cesaro S, Boveri E, Rosti V, Corti P, Ambroni M, Pasquali F, Danesino C, Maserati E, Minelli A. Parental origin of the deletion del(20q) in Shwachman-Diamond patients and loss of the paternally derived allele of the imprintedL3MBTL1gene. Genes Chromosomes Cancer 2016; 56:51-58. [DOI: 10.1002/gcc.22401] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 11/11/2022] Open
Affiliation(s)
- Lucia Nacci
- Department of Molecular Medicine; University of Pavia; Pavia Italy
| | - Roberto Valli
- Department of Clinical and Experimental Medicine; University of Insubria; Varese Italy
| | - Rita Maria Pinto
- Ospedale Bambino Gesù IRCCS; Oncoematologia e Medicina Trasfusionale; Roma Italy
| | - Marco Zecca
- Oncoematologia Pediatrica, Fondazione IRCCS Policlinico San Matteo; Pavia Italy
| | - Marco Cipolli
- Cystic Fibrosis Centre, Azienda Ospedaliera Universitaria; Verona Italy
| | | | - Simone Cesaro
- Oncoematologia Pediatrica, Azienda Ospedaliera Universitaria Integrata; Verona Italy
| | - Emanuela Boveri
- Fondazione IRCCS Policlinico; Anatomic Pathology Section; San Matteo, Pavia Italy
| | - Vittorio Rosti
- IRCCS Policlinico San Matteo; Center for the Study of Myelofibrosis, Biotechnology Research Area; Pavia Italy
| | - Paola Corti
- Pediatrics Unit, Fondazione Medico e Brianza per il Bambino e la sua Mamma; Monza Italy
| | - Maura Ambroni
- Cystic Fibrosis Regional Center, Ospedale M. Bufalini; Cesena Italy
| | - Francesco Pasquali
- Department of Clinical and Experimental Medicine; University of Insubria; Varese Italy
| | - Cesare Danesino
- Department of Molecular Medicine; University of Pavia; Pavia Italy
| | - Emanuela Maserati
- Department of Clinical and Experimental Medicine; University of Insubria; Varese Italy
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16
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Eid A, Torres-Padilla ME. Characterization of non-canonical Polycomb Repressive Complex 1 subunits during early mouse embryogenesis. Epigenetics 2016; 11:389-97. [PMID: 27081692 DOI: 10.1080/15592294.2016.1172160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
An intense period of chromatin remodeling takes place after fertilization in mammals, which is thought necessary for epigenetic reprogramming to start a new developmental program. While much attention has been given to the role of Polycomb Repressive Complex 2 (PRC2) and to canonical PRC1 complexes during this process, little is known as to whether there is any contribution of non-canonical PRC1 in shaping the chromatin landscape after fertilization. Here, we first describe in detail the temporal dynamics and abundance of H2A ubiquitylation (H2AK119ub), a histone modification catalyzed by PRC1, during pre-implantation mouse development. In addition, we have analyzed the presence of the 2 characteristic subunits of non-canonical PRC1 complexes, RYBP and its homolog YAF-2. Our results indicate that H2AK119ub is inherited from the sperm, rapidly removed from the paternal chromatin after fertilization, but detected again prior to the first mitosis, suggesting that PRC1 activity occurs as early as the zygotic stage. RYBP and YAF-2, together with the non-canonical subunit L3MBTL2, are all present during pre-implantation development but show different temporal dynamics. While RYBP is absent in the zygote, it is strongly induced from the 4-cell stage onwards. YAF-2 is inherited maternally and localizes to the pericentromeric regions in the zygote, is strongly induced between the 2- and 4-cell stages but then remains weak to undetectable subsequently. All together, our data suggest that non-canonical PRC1 is active during pre-implantation development and should be regarded as an additional component during epigenetic reprogramming and in the establishment of cellular plasticity of the early embryo.
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Affiliation(s)
- André Eid
- a Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964 , U de S, F-67404 Illkirch , CU de Strasbourg , France
| | - Maria-Elena Torres-Padilla
- a Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964 , U de S, F-67404 Illkirch , CU de Strasbourg , France.,b Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München D-81377 , München , Germany
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17
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Abstract
Protein methylation is a common post-translational modification with diverse biological functions. Methyllysine reader proteins are increasingly a focus of epigenetics research and play important roles in regulating many cellular processes. These reader proteins are vital players in development, cell cycle regulation, stress responses, oncogenesis, and other disease pathways. The recent emergence of a small number of chemical inhibitors for methyllysine reader proteins supports the viability of these proteins as targets for drug development. This article introduces the biochemistry and biology of methyllysine reader proteins, provides an overview of functions for those families of readers that have been targeted to date (MBT, PHD, tudor, and chromodomains), and reviews the development of synthetic agents that directly block their methyllysine reading functions.
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Affiliation(s)
- Natalia Milosevich
- Department of Chemistry, University of Victoria , Victoria, British Columbia V8W 3V6, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria , Victoria, British Columbia V8W 3V6, Canada
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18
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Perna F, Vu LP, Themeli M, Kriks S, Hoya-Arias R, Khanin R, Hricik T, Mansilla-Soto J, Papapetrou EP, Levine RL, Studer L, Sadelain M, Nimer SD. The polycomb group protein L3MBTL1 represses a SMAD5-mediated hematopoietic transcriptional program in human pluripotent stem cells. Stem Cell Reports 2015; 4:658-69. [PMID: 25754204 PMCID: PMC4400644 DOI: 10.1016/j.stemcr.2015.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 01/11/2023] Open
Abstract
Epigenetic regulation of key transcriptional programs is a critical mechanism that controls hematopoietic development, and, thus, aberrant expression patterns or mutations in epigenetic regulators occur frequently in hematologic malignancies. We demonstrate that the Polycomb protein L3MBTL1, which is monoallelically deleted in 20q- myeloid malignancies, represses the ability of stem cells to drive hematopoietic-specific transcriptional programs by regulating the expression of SMAD5 and impairing its recruitment to target regulatory regions. Indeed, knockdown of L3MBTL1 promotes the development of hematopoiesis and impairs neural cell fate in human pluripotent stem cells. We also found a role for L3MBTL1 in regulating SMAD5 target gene expression in mature hematopoietic cell populations, thereby affecting erythroid differentiation. Taken together, we have identified epigenetic priming of hematopoietic-specific transcriptional networks, which may assist in the development of therapeutic approaches for patients with anemia. L3MBTL1 is a chromatin-binding protein that represses SMAD5 expression Lack of L3MBTL1 primes the hematopoietic development of pluripotent stem cells L3MBTL1 regulates erythroid differentiation
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Affiliation(s)
- Fabiana Perna
- Molecular Pharmacology and Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Ly P Vu
- Molecular Pharmacology and Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Maria Themeli
- Molecular Pharmacology and Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sonja Kriks
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ruben Hoya-Arias
- Molecular Pharmacology and Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Raya Khanin
- Bioinformatics Core, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Todd Hricik
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jorge Mansilla-Soto
- Molecular Pharmacology and Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Ross L Levine
- Human Oncology and Pathogenesis Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lorenz Studer
- Center for Stem Cell Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michel Sadelain
- Molecular Pharmacology and Chemistry Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
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19
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Meier K, Brehm A. Chromatin regulation: how complex does it get? Epigenetics 2014; 9:1485-95. [PMID: 25482055 PMCID: PMC4622878 DOI: 10.4161/15592294.2014.971580] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/18/2014] [Accepted: 09/29/2014] [Indexed: 12/16/2022] Open
Abstract
Gene transcription is tightly regulated at different levels to ensure that the transcriptome of the cell is appropriate for developmental stage and cell type. The chromatin state in which a gene is embedded determines its expression level to a large extent. Activation or repression of transcription is typically accomplished by the recruitment of chromatin-associated multisubunit protein complexes that combine several molecular tools, such as histone-binding and chromatin-modifying activities. Recent biochemical purifications of such complexes have revealed a substantial diversity. On the one hand, complexes that were thought to be unique have been revealed to be part of large complex families. On the other hand, protein subunits that were thought to only exist in separate complexes have been shown to coexist in novel assemblies. In this review we discuss our current knowledge of repressor complexes that contain MBT domain proteins and/or the CoREST co-repressor and use them as a paradigm to illustrate the unexpected heterogeneity and tool sharing of chromatin regulating protein complexes. These recent insights also challenge the ways we define and think about protein complexes in general.
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Key Words
- ATP, adenosine triphosphate
- BAP, brahma associated protein
- BHC80, BRAF-histone deacetylase complex 80
- BRG1, brahma Related Gene 1
- CHD, chromo domain helicase DNA binding
- CoREST
- CoREST REST, corepressor
- DNA, deoxyribonucleic acid
- DNMT, DNA methyltransferase
- DP-1, dimerization partner 1
- E2F, E2 transcription Factor
- ELM2, EGL-27 and MTA1 homology 2
- ES cell, embryonic stem cells
- H, histone
- HDAC, histone deacetylas
- HMTase, histone methylase
- HP1, heterochromatin protein 1
- K, lysine
- L3MBTL, lethal 3 malignant brain tumor-like
- LINT, l(3)mbt interacting
- LSD1, lysine-specific demethylase 1
- Lint-1, l(3)mbt interacting 1
- MBT protein
- MBT, malignant brain tumor
- MBTS, malignant brain tumor signature
- NPA1, nucleosome assembly protein
- NRSF, neural-restrictive silencing factor
- NuRD, nucleosome remodeling and deacetylase
- PBAP, polybromo-associated BAP
- PHD, plant homeo domain
- PRC1, polycomb repressive complex 1
- PRE, polycomb responsive element
- Pc, polycomb
- PcG, polycomb group
- Ph, polyhomeotic
- Pho, pleiohomeotic
- PhoRC, Pho repressive complex
- Psc, posterior sex combs
- RB, retinoblastoma
- REST, repressor element 1 silencing transcription factor
- RNA, ribonucleic acid
- Rpd3, reduced potassium dependency 3
- SANT, SWI/ADA2/N-CoR/TFIIIB
- SCML, sex combs on midleg-like
- SLC, SFMBT1, LSD1, CoREST
- SWH, Salvador-Warts-Hippo
- SWI/SNF, switching defective/sucrose non-fermenting
- Sce, sex combs extra
- Scm, sex combs on midleg
- Sfmbt, Scm-related gene containing 4 mbt domains
- TSS, transcription start site
- YY1, ying-yang 1
- ZNF, zinc finger
- complex family
- dL(3)mbt, Drosophila Lethal 3 malignant brain tumor
- hBRM, human Brahma
- l(3)mbt, lethal 3 malignant brain tumor
- protein complex
- transcriptional regulation
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Affiliation(s)
- Karin Meier
- Institut für Molekularbiologie und Tumorforschung; Philipps-Universität Marburg; Marburg, Germany
- Instituto de Fisiología Celular; Departamento de Genética Molecular; Universidad Nacional Autónoma de México; México City, México
| | - Alexander Brehm
- Institut für Molekularbiologie und Tumorforschung; Philipps-Universität Marburg; Marburg, Germany
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Chromatin reader L(3)mbt requires the Myb-MuvB/DREAM transcriptional regulatory complex for chromosomal recruitment. Proc Natl Acad Sci U S A 2014; 111:E4234-43. [PMID: 25249635 DOI: 10.1073/pnas.1416321111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Lethal malignant brain tumors (lmbt) result from the loss of the conserved transcriptional repressor l(3)mbt, in Drosophila melanogaster. Similar mutations in the human homolog L3MBTL1 correlate with some cancers. The protein's C-terminal MBT repeats bind mono and dimethylated histones in vitro, which could influence recruitment of L3MBTL1 to its target sites. The L(3)mbt chromatin targeting mechanism, however, is controversial and several studies suggest insufficiency or a minor role for histone methylation in determining the site specificity for recruitment. We report that L(3)mbt colocalizes with core members of the Myb-MuvB/DREAM (MMB/DREAM) transcriptional regulatory complex genome-wide, and that L(3)mbt-mediated repression requires this complex in salivary glands and larval brains. Loss of l(3)mbt or of MMB components through mutation cause similar spurious expression of genes, including the transposon regulatory gene piwi, in terminally differentiated cells. The DNA-binding MMB core component Mip120 (Lin54) is required for L(3)mbt recruitment to chromosomes, whereas Mip130 (Lin9) (an MMB core protein) and E2f2 (an MMB transcriptional repressor) are not, but are essential for repression. Cytolocalization experiments suggest the presence of site-specific differential composition of MMB in polytene chromosomes where some loci were bound by a Myb-containing or alternatively, an E2f2 and L(3)mbt form of the complex.
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21
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Liu Y, Liu K, Qin S, Xu C, Min J. Epigenetic targets and drug discovery: part 1: histone methylation. Pharmacol Ther 2014; 143:275-94. [PMID: 24704322 DOI: 10.1016/j.pharmthera.2014.03.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/24/2014] [Indexed: 01/10/2023]
Abstract
Dynamic chromatin structure is modulated by post-translational modifications on histones, such as acetylation, phosphorylation and methylation. Research on histone methylation has become the most flourishing area of epigenetics in the past fourteen years, and a large amount of data has been accumulated regarding its biology and disease implications. Correspondingly, a lot of efforts have been made to develop small molecule compounds that can specifically modulate histone methyltransferases and methylation reader proteins, aiming for potential therapeutic drugs. Here, we summarize recent progress in chemical probe and drug discovery of histone methyltransferases and methylation reader proteins. For each target, we will review their biological/biochemical functions first, and then focus on their disease implications and drug discovery. We can also see that structure-based compound design and optimization plays a critical role in facilitating the development of highly potent and selective chemical probes and inhibitors for these targets.
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Affiliation(s)
- Yanli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada; Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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22
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Dewaele B, Przybyl J, Quattrone A, Finalet Ferreiro J, Vanspauwen V, Geerdens E, Gianfelici V, Kalender Z, Wozniak A, Moerman P, Sciot R, Croce S, Amant F, Vandenberghe P, Cools J, Debiec‐Rychter M. Identification of a novel, recurrent
MBTD1‐CXorf67
fusion in low‐grade endometrial stromal sarcoma. Int J Cancer 2013; 134:1112-22. [DOI: 10.1002/ijc.28440] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 07/15/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Barbara Dewaele
- Department of Human GeneticsKU Leuven and University Hospitals LeuvenLeuven Belgium
| | - Joanna Przybyl
- Department of Human GeneticsKU Leuven and University Hospitals LeuvenLeuven Belgium
- Department of Molecular and Translational OncologyThe Maria Sklodowska‐Curie Memorial Cancer Centre and Institute of OncologyWarsaw Poland
- Postgraduate School of Molecular MedicineWarsaw Medical UniversityWarsaw Poland
| | - Anna Quattrone
- Department of Human GeneticsKU Leuven and University Hospitals LeuvenLeuven Belgium
| | | | - Vanessa Vanspauwen
- Department of Human GeneticsKU Leuven and University Hospitals LeuvenLeuven Belgium
| | - Ellen Geerdens
- Department of Human GeneticsKU Leuven and Flanders Interuniversity Institute for Biotechnology (VIB)Leuven Belgium
| | - Valentina Gianfelici
- Department of Human GeneticsKU Leuven and Flanders Interuniversity Institute for Biotechnology (VIB)Leuven Belgium
| | - Zeynep Kalender
- Department of Human GeneticsKU Leuven and Flanders Interuniversity Institute for Biotechnology (VIB)Leuven Belgium
| | - Agnieszka Wozniak
- Laboratory of Experimental OncologyDepartment of OncologyKU Leuven and Department of General Medical OncologyUniversity Hospitals LeuvenLeuven Belgium
| | - Philippe Moerman
- Department of PathologyKU Leuven and University Hospitals LeuvenLeuven Belgium
| | - Raf Sciot
- Department of PathologyKU Leuven and University Hospitals LeuvenLeuven Belgium
| | - Sabrina Croce
- Department of PathologyInstitute BergoniéBordeaux France
| | - Frederic Amant
- Department of OncologyKU Leuven and Leuven Cancer InstituteUniversity Hospitals LeuvenLeuven Belgium
| | - Peter Vandenberghe
- Department of Human GeneticsKU Leuven and University Hospitals LeuvenLeuven Belgium
| | - Jan Cools
- Department of Human GeneticsKU Leuven and Flanders Interuniversity Institute for Biotechnology (VIB)Leuven Belgium
| | - Maria Debiec‐Rychter
- Department of Human GeneticsKU Leuven and University Hospitals LeuvenLeuven Belgium
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23
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Aziz A, Baxter EJ, Edwards C, Cheong CY, Ito M, Bench A, Kelley R, Silber Y, Beer PA, Chng K, Renfree MB, McEwen K, Gray D, Nangalia J, Mufti GJ, Hellstrom-Lindberg E, Kiladjian JJ, McMullin MF, Campbell PJ, Ferguson-Smith AC, Green AR. Cooperativity of imprinted genes inactivated by acquired chromosome 20q deletions. J Clin Invest 2013; 123:2169-82. [PMID: 23543057 DOI: 10.1172/jci66113] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 02/07/2013] [Indexed: 12/14/2022] Open
Abstract
Large regions of recurrent genomic loss are common in cancers; however, with a few well-characterized exceptions, how they contribute to tumor pathogenesis remains largely obscure. Here we identified primate-restricted imprinting of a gene cluster on chromosome 20 in the region commonly deleted in chronic myeloid malignancies. We showed that a single heterozygous 20q deletion consistently resulted in the complete loss of expression of the imprinted genes L3MBTL1 and SGK2, indicative of a pathogenetic role for loss of the active paternally inherited locus. Concomitant loss of both L3MBTL1 and SGK2 dysregulated erythropoiesis and megakaryopoiesis, 2 lineages commonly affected in chronic myeloid malignancies, with distinct consequences in each lineage. We demonstrated that L3MBTL1 and SGK2 collaborated in the transcriptional regulation of MYC by influencing different aspects of chromatin structure. L3MBTL1 is known to regulate nucleosomal compaction, and we here showed that SGK2 inactivated BRG1, a key ATP-dependent helicase within the SWI/SNF complex that regulates nucleosomal positioning. These results demonstrate a link between an imprinted gene cluster and malignancy, reveal a new pathogenetic mechanism associated with acquired regions of genomic loss, and underline the complex molecular and cellular consequences of "simple" cancer-associated chromosome deletions.
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Affiliation(s)
- Athar Aziz
- Cambridge Institute for Medical Research and Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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Johnson NM, Lemmens BBLG, Tijsterman M. A role for the malignant brain tumour (MBT) domain protein LIN-61 in DNA double-strand break repair by homologous recombination. PLoS Genet 2013; 9:e1003339. [PMID: 23505385 PMCID: PMC3591299 DOI: 10.1371/journal.pgen.1003339] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 01/08/2013] [Indexed: 11/18/2022] Open
Abstract
Malignant brain tumour (MBT) domain proteins are transcriptional repressors that function within Polycomb complexes. Some MBT genes are tumour suppressors, but how they prevent tumourigenesis is unknown. The Caenorhabditis elegans MBT protein LIN-61 is a member of the synMuvB chromatin-remodelling proteins that control vulval development. Here we report a new role for LIN-61: it protects the genome by promoting homologous recombination (HR) for the repair of DNA double-strand breaks (DSBs). lin-61 mutants manifest numerous problems associated with defective HR in germ and somatic cells but remain proficient in meiotic recombination. They are hypersensitive to ionizing radiation and interstrand crosslinks but not UV light. Using a novel reporter system that monitors repair of a defined DSB in C. elegans somatic cells, we show that LIN-61 contributes to HR. The involvement of this MBT protein in HR raises the possibility that MBT–deficient tumours may also have defective DSB repair. The genome is continually under threat from exogenous sources of DNA damage, as well as from sources that originate within the cell. DNA double-strand breaks (DSBs) are arguably the most problematic type of damage as they can cause dangerous chromosome rearrangements, which can lead to cancer, as well as mutation at the break site and/or cell death. A complex network of molecular pathways, collectively referred to as the DNA damage response (DDR), have evolved to protect the cell from these threats. We have discovered a new DDR factor, LIN-61, that promotes the repair of DSBs. This is a novel and unexpected role for LIN-61, which was previously known to act as a regulator of gene transcription during development.
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Affiliation(s)
- Nicholas M. Johnson
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Marcel Tijsterman
- Department of Toxicogenetics, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
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25
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Lin S, Shen H, Li JL, Tang S, Gu Y, Chen Z, Hu C, Rice JC, Lu J, Wu L. Proteomic and functional analyses reveal the role of chromatin reader SFMBT1 in regulating epigenetic silencing and the myogenic gene program. J Biol Chem 2013; 288:6238-47. [PMID: 23349461 PMCID: PMC3585059 DOI: 10.1074/jbc.m112.429605] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/23/2013] [Indexed: 01/24/2023] Open
Abstract
SFMBT1 belongs to the malignant brain tumor domain-containing chromatin reader family that recognizes repressive histone marks and represses transcription. The biological functions and molecular basis underlying SFMBT1-mediated transcriptional repression are poorly elucidated. Here, our proteomic analysis revealed that SFMBT1 is associated with multiple transcriptional corepressor complexes, including CtBP/LSD1/HDAC complexes, polycomb repressive complexes, and malignant brain tumor family proteins, that collectively contribute to SFMBT1 repressor activity. During myogenesis, Sfmbt1 represses myogenic differentiation of cultured and primary myoblasts. Mechanistically, Sfmbt1 interacts with MyoD and mediates epigenetic silencing of MyoD target genes via recruitment of its associated corepressors and subsequent induction of epigenetic modifications and chromatin compaction. Therefore, our study identified novel mechanisms accounting for SFMBT1-mediated transcription repression and revealed an essential role of Sfmbt1 in regulating MyoD-mediated transcriptional silencing that is required for the maintenance of undifferentiated states of myogenic progenitor cells.
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Affiliation(s)
- Shuibin Lin
- From the Department of Molecular Genetics and Microbiology
| | - Huangxuan Shen
- From the Department of Molecular Genetics and Microbiology
- the State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, 510060 China
| | - Jian-Liang Li
- the Sanford-Burnham Medical Research Institute at Lake Nona, Orlando, Florida 32827
| | | | - Yumei Gu
- From the Department of Molecular Genetics and Microbiology
| | - Zirong Chen
- From the Department of Molecular Genetics and Microbiology
| | - Chengbin Hu
- From the Department of Molecular Genetics and Microbiology
| | - Judd C. Rice
- the Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California 90089
| | - Jianrong Lu
- Department of Biochemistry and Molecular Biology, Shands Cancer Center, University of Florida, Gainesville, Florida 32610
| | - Lizi Wu
- From the Department of Molecular Genetics and Microbiology
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Richter C, Oktaba K, Steinmann J, Müller J, Knoblich JA. The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements. Nat Cell Biol 2011; 13:1029-39. [PMID: 21857667 PMCID: PMC3173870 DOI: 10.1038/ncb2306] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 06/24/2011] [Indexed: 12/19/2022]
Abstract
In Drosophila, defects in asymmetric cell division often result in the formation of stem-cell-derived tumours. Here, we show that very similar terminal brain tumour phenotypes arise through a fundamentally different mechanism. We demonstrate that brain tumours in l(3)mbt mutants originate from overproliferation of neuroepithelial cells in the optic lobes caused by derepression of target genes in the Salvador-Warts-Hippo (SWH) pathway. We use ChIP-sequencing to identify L(3)mbt binding sites and show that L(3)mbt binds to chromatin insulator elements. Mutating l(3)mbt or inhibiting expression of the insulator protein gene mod(mdg4) results in upregulation of SWH pathway reporters. As l(3)mbt tumours are rescued by mutations in bantam or yorkie or by overexpression of Expanded, the deregulation of SWH pathway target genes is an essential step in brain tumour formation. Therefore, very different primary defects result in the formation of brain tumours, which behave quite similarly in their advanced stages.
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Affiliation(s)
- Constance Richter
- Institute of Molecular Biotechnology of the Austrian Academy of Science, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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27
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Hoya-Arias R, Tomishima M, Perna F, Voza F, Nimer SD. L3MBTL1 deficiency directs the differentiation of human embryonic stem cells toward trophectoderm. Stem Cells Dev 2011; 20:1889-900. [PMID: 21341991 DOI: 10.1089/scd.2010.0437] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human embryonic stem cells (hESCs) can be used to study the early events in human development and, hopefully, to understand how to differentiate human pluripotent cells for clinical use. To define how L3MBTL1, a chromatin-associated polycomb group protein with transcriptional repressive activities, regulates early events in embryonic cell differentiation, we created hESC lines that constitutively express shRNAs directed against L3MBTL1. The L3MBTL1 knockdown (KD) hESCs maintained normal morphology, proliferation, cell cycle kinetics, cell surface markers, and karyotype after 40 passages. However, under conditions that promote spontaneous differentiation, the L3MBTL1 KD cells differentiated into a relatively homogeneous population of large, flat trophoblast-like cells, unlike the multilineage differentiation seen with the control cells. The differentiated L3MBTL1 KD cells expressed numerous trophoblast markers and secreted placental hormones. Although the L3MBTL1 KD cells could be induced to differentiate into various embryonic lineages, they adopted an exclusive trophoblast fate during spontaneous differentiation. Our data demonstrate that depletion of L3MBTL1 does not affect hESC self-renewal, rather it enhances differentiation toward extra-embryonic trophoblast tissues.
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Affiliation(s)
- Ruben Hoya-Arias
- Molecular Pharmacology and Chemistry Program, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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28
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Koester-Eiserfunke N, Fischle W. H3K9me2/3 binding of the MBT domain protein LIN-61 is essential for Caenorhabditis elegans vulva development. PLoS Genet 2011; 7:e1002017. [PMID: 21437264 PMCID: PMC3060068 DOI: 10.1371/journal.pgen.1002017] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 01/18/2011] [Indexed: 11/18/2022] Open
Abstract
MBT domain proteins are involved in developmental processes and tumorigenesis. In vitro binding and mutagenesis studies have shown that individual MBT domains within clustered MBT repeat regions bind mono- and dimethylated histone lysine residues with little to no sequence specificity but discriminate against the tri- and unmethylated states. However, the exact function of promiscuous histone methyl-lysine binding in the biology of MBT domain proteins has not been elucidated. Here, we show that the Caenorhabditis elegans four MBT domain protein LIN-61, in contrast to other MBT repeat factors, specifically interacts with histone H3 when methylated on lysine 9, displaying a strong preference for di- and trimethylated states (H3K9me2/3). Although the fourth MBT repeat is implicated in this interaction, H3K9me2/3 binding minimally requires MBT repeats two to four. Further, mutagenesis of residues conserved with other methyl-lysine binding MBT regions in the fourth MBT repeat does not abolish interaction, implicating a distinct binding mode. In vivo, H3K9me2/3 interaction of LIN-61 is required for C. elegans vulva development within the synMuvB pathway. Mutant LIN-61 proteins deficient in H3K9me2/3 binding fail to rescue lin-61 synMuvB function. Also, previously identified point mutant synMuvB alleles are deficient in H3K9me2/3 interaction although these target residues that are outside of the fourth MBT repeat. Interestingly, lin-61 genetically interacts with two other synMuvB genes, hpl-2, an HP1 homologous H3K9me2/3 binding factor, and met-2, a SETDB1 homologous H3K9 methyl transferase (H3K9MT), in determining C. elegans vulva development and fertility. Besides identifying the first sequence specific and di-/trimethylation binding MBT domain protein, our studies imply complex multi-domain regulation of ligand interaction of MBT domains. Our results also introduce a mechanistic link between LIN-61 function and biology, and they establish interplay of the H3K9me2/3 binding proteins, LIN-61 and HPL-2, as well as the H3K9MT MET-2 in distinct developmental pathways.
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Affiliation(s)
- Nora Koester-Eiserfunke
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail:
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29
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Hemp, an mbt domain-containing protein, plays essential roles in hematopoietic stem cell function and skeletal formation. Proc Natl Acad Sci U S A 2011; 108:2468-73. [PMID: 21252303 DOI: 10.1073/pnas.1003403108] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
To clarify the molecular pathways governing hematopoietic stem cell (HSC) development, we screened a fetal liver (FL) HSC cDNA library and identified a unique gene, hematopoietic expressed mammalian polycomb (hemp), encoding a protein with a zinc-finger domain and four malignant brain tumor (mbt) repeats. To investigate its biological role, we generated mice lacking Hemp (hemp(-/-)). Hemp(-/-) mice exhibited a variety of skeletal malformations and died soon after birth. In the FL, hemp was preferentially expressed in the HSC and early progenitor cell fractions, and analyses of fetal hematopoiesis revealed that the number of FL mononuclear cells, including HSCs, was reduced markedly in hemp(-/-) embryos, especially during early development. In addition, colony-forming and competitive repopulation assays demonstrated that the proliferative and reconstitution abilities of hemp(-/-) FL HSCs were significantly impaired. Microarray analysis revealed alterations in the expression levels of several genes implicated in hematopoietic development and differentiation in hemp(-/-) FL HSCs. These results demonstrate that Hemp, an mbt-containing protein, plays essential roles in HSC function and skeletal formation. It is also hypothesized that Hemp might be involved in certain congenital diseases, such as Klippel-Feil anomaly.
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30
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Balakrishnan L, Milavetz B. Decoding the histone H4 lysine 20 methylation mark. Crit Rev Biochem Mol Biol 2011; 45:440-52. [PMID: 20735237 DOI: 10.3109/10409238.2010.504700] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The molecular biology of histone H4 lysine 20 (H4K20) methylation, like many other post-translational modifications of histones, has been the subject of intensive interest in recent years. While there is an emerging consensus linking H4K20me1, H4K20me2, and H4K20me3 to transcription, repair, and constitutive heterochromatin, respectively, the specific details of these associations and the biological mechanisms by which the methylated histones are introduced and function are now the subject of active investigation. Although a large number of methylases capable of methylating H4K20 have been identified and characterized; there is no known demethylase of H4K20, though the search is ongoing. Additionally, many recent studies have been directed at understanding the role of methylated H4K20 and other histone modifications associated with different biological processes in the context of a combinatorial histone code. It seems likely that continued study of the methylation of H4K20 will yield extremely valuable insights concerning the regulation of histone modifications before and during cell division and the impact of these modifications on subsequent gene expression.
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Affiliation(s)
- Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, USA
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31
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Addou-Klouche L, Adélaïde J, Finetti P, Cervera N, Ferrari A, Bekhouche I, Sircoulomb F, Sotiriou C, Viens P, Moulessehoul S, Bertucci F, Birnbaum D, Chaffanet M. Loss, mutation and deregulation of L3MBTL4 in breast cancers. Mol Cancer 2010; 9:213. [PMID: 20698951 PMCID: PMC2933619 DOI: 10.1186/1476-4598-9-213] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Accepted: 08/10/2010] [Indexed: 12/13/2022] Open
Abstract
Background Many alterations are involved in mammary oncogenesis, including amplifications of oncogenes and losses of tumor suppressor genes (TSG). Losses may affect almost all chromosome arms and many TSGs remain to be identified. Results We studied 307 primary breast tumors and 47 breast cancer cell lines by high resolution array comparative genomic hybridization (aCGH). We identified a region on 18p11.31 lost in about 20% of the tumors and 40% of the cell lines. The minimal common region of loss (Chr18:6,366,938-6,375,929 bp) targeted the L3MBTL4 gene. This gene was also targeted by breakage in one tumor and in two cell lines. We studied the exon sequence of L3MBTL4 in 180 primary tumor samples and 47 cell lines and found six missense and one nonsense heterozygous mutations. Compared with normal breast tissue, L3MBTL4 mRNA expression was downregulated in 73% of the tumors notably in luminal, ERBB2 and normal-like subtypes. Losses of the 18p11 region were associated with low L3MBTL4 expression level. Integrated analysis combining genome and gene expression profiles of the same tumors pointed to 14 other potential 18p TSG candidates. Downregulated expression of ZFP161, PPP4R1 and YES1 was correlated with luminal B molecular subtype. Low ZFP161 gene expression was associated with adverse clinical outcome. Conclusion We have identified L3MBTL4 as a potential TSG of chromosome arm 18p. The gene is targeted by deletion, breakage and mutations and its mRNA is downregulated in breast tumors. Additional 18p TSG candidates might explain the aggressive phenotype associated with the loss of 18p in breast tumors.
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Affiliation(s)
- Lynda Addou-Klouche
- Marseille Cancer Research Center, Department of Molecular Oncology, UMR891 Inserm, Institut Paoli-Calmettes, Marseille, France
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Qin J, Van Buren D, Huang HS, Zhong L, Mostoslavsky R, Akbarian S, Hock H. Chromatin protein L3MBTL1 is dispensable for development and tumor suppression in mice. J Biol Chem 2010; 285:27767-75. [PMID: 20592034 DOI: 10.1074/jbc.m110.115410] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
L3MBTL1, a paralogue of Drosophila tumor suppressor lethal(3)malignant brain tumor (l(3)mbt), binds histones in a methylation state-dependent manner and contributes to higher order chromatin structure and transcriptional repression. It is the founding member of a family of MBT domain-containing proteins that has three members in Drosophila and nine in mice and humans. Knockdown experiments in cell lines suggested that L3MBTL1 has non-redundant roles in the suppression of oncogene expression. We generated a mutant mouse strain that lacks exons 13-20 of L3mbtl1. Markedly reduced levels of a mutant mRNA with an out-of-frame fusion of exons 12 and 21 were expressed, but a mutant protein was undetectable by Western blot analysis. L3MBTL1(-/-) mice developed and reproduced normally. The highest expression of L3MBTL1 was detected in the brain, but its disruption did not affect brain development, spontaneous movement, and motor coordination. Despite previous implications of L3mbtl1 in the biology of hematopoietic transcriptional regulators, lack of L3MBTL1 did not result in deficiencies in lymphopoiesis or hematopoiesis. In contrast with its demonstrated biochemical activities, embryonic stem (ES) cells lacking L3MBTL1 displayed no abnormalities in H4 lysine 20 (H4K20) mono-, di-, or trimethylation; had normal global chromatin density as assessed by micrococcal nuclease digests; and expressed normal levels of c-myc. Embryonic fibroblasts lacking L3MBTL1 displayed unaltered cell cycle arrest and down-regulation of cyclin E expression after irradiation. In cohorts of mice followed for more than 2 years, lack of L3MBTL1 did not alter normal lifespan or survival with or without sublethal irradiation.
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Affiliation(s)
- Jinzhong Qin
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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Depletion of L3MBTL1 promotes the erythroid differentiation of human hematopoietic progenitor cells: possible role in 20q- polycythemia vera. Blood 2010; 116:2812-21. [PMID: 20585043 DOI: 10.1182/blood-2010-02-270611] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
L3MBTL1, the human homolog of the Drosophila L(3)MBT polycomb group tumor suppressor gene, is located on chromosome 20q12, within the common deleted region identified in patients with 20q deletion-associated polycythemia vera, myelodysplastic syndrome, and acute myeloid leukemia. L3MBTL1 is expressed within hematopoietic CD34(+) cells; thus, it may contribute to the pathogenesis of these disorders. To define its role in hematopoiesis, we knocked down L3MBTL1 expression in primary hematopoietic stem/progenitor (ie, CD34(+)) cells isolated from human cord blood (using short hairpin RNAs) and observed an enhanced commitment to and acceleration of erythroid differentiation. Consistent with this effect, overexpression of L3MBTL1 in primary hematopoietic CD34(+) cells as well as in 20q- cell lines restricted erythroid differentiation. Furthermore, L3MBTL1 levels decrease during hemin-induced erythroid differentiation or erythropoietin exposure, suggesting a specific role for L3MBTL1 down-regulation in enforcing cell fate decisions toward the erythroid lineage. Indeed, L3MBTL1 knockdown enhanced the sensitivity of hematopoietic stem/progenitor cells to erythropoietin (Epo), with increased Epo-induced phosphorylation of STAT5, AKT, and MAPK as well as detectable phosphorylation in the absence of Epo. Our data suggest that haploinsufficiency of L3MBTL1 contributes to some (20q-) myeloproliferative neoplasms, especially polycythemia vera, by promoting erythroid differentiation.
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Cao X, Yang KZ, Xia C, Zhang XQ, Chen LQ, Ye D. Characterization of DUF724 gene family in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2010; 72:61-73. [PMID: 19795213 DOI: 10.1007/s11103-009-9551-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2008] [Accepted: 09/18/2009] [Indexed: 05/05/2023]
Abstract
Eighteen genes that encode the proteins with highly conserved Domain of Unknown Function 724 (DUF724) and Agenet domains were identified in plant taxa but not in animals and fungi. They are actively expressed in many different plant tissues, implying that they may play important roles in plants. Here we report the characterization of their structural organizations, expression patterns and protein-protein interactions. In Arabidopsis, the DUF724 genes were expressed in roots, leaves, shoot apical meristems, anthers and pollen grains. At least seven of the ten Arabidopsis DUF724 proteins (AtDuf1 to AtDuf10) were localized in nucleus. Three of them (AtDuf3, AtDuf5 and AtDuf7) may form homodimers or homopolymers, but did not interact with other members of the same family. Together with the significant similarity between DUF724 proteins and FMRP in the fundamental and characteristic molecular architecture, the results implies the DUF724 gene family may be involved in the polar growth of plant cells via transportation of RNAs.
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Affiliation(s)
- Xi Cao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
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35
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Eryilmaz J, Pan P, Amaya MF, Allali-Hassani A, Dong A, Adams-Cioaba MA, MacKenzie F, Vedadi M, Min J. Structural studies of a four-MBT repeat protein MBTD1. PLoS One 2009; 4:e7274. [PMID: 19841675 PMCID: PMC2747274 DOI: 10.1371/journal.pone.0007274] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 09/08/2009] [Indexed: 11/18/2022] Open
Abstract
Background The Polycomb group (PcG) of proteins is a family of important developmental regulators. The respective members function as large protein complexes involved in establishment and maintenance of transcriptional repression of developmental control genes. MBTD1, Malignant Brain Tumor domain-containing protein 1, is one such PcG protein. MBTD1 contains four MBT repeats. Methodology/Principal Findings We have determined the crystal structure of MBTD1 (residues 130–566aa covering the 4 MBT repeats) at 2.5 Å resolution by X-ray crystallography. The crystal structure of MBTD1 reveals its similarity to another four-MBT-repeat protein L3MBTL2, which binds lower methylated lysine histones. Fluorescence polarization experiments confirmed that MBTD1 preferentially binds mono- and di-methyllysine histone peptides, like L3MBTL1 and L3MBTL2. All known MBT-peptide complex structures characterized to date do not exhibit strong histone peptide sequence selectivity, and use a “cavity insertion recognition mode” to recognize the methylated lysine with the deeply buried methyl-lysine forming extensive interactions with the protein while the peptide residues flanking methyl-lysine forming very few contacts [1]. Nevertheless, our mutagenesis data based on L3MBTL1 suggested that the histone peptides could not bind to MBT repeats in any orientation. Conclusions The four MBT repeats in MBTD1 exhibits an asymmetric rhomboid architecture. Like other MBT repeat proteins characterized so far, MBTD1 binds mono- or dimethylated lysine histones through one of its four MBT repeats utilizing a semi-aromatic cage. Enhanced version This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.
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Affiliation(s)
- Jitka Eryilmaz
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Patricia Pan
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Maria F. Amaya
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | | | - Farrell MacKenzie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Bonasio R, Lecona E, Reinberg D. MBT domain proteins in development and disease. Semin Cell Dev Biol 2009; 21:221-30. [PMID: 19778625 DOI: 10.1016/j.semcdb.2009.09.010] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2009] [Accepted: 09/11/2009] [Indexed: 12/22/2022]
Abstract
The Malignant Brain Tumor (MBT) domain is a "chromatin reader", a protein module that binds to post-translational modifications on histone tails that are thought to affect a variety of chromatin processes, including transcription. More specifically, MBT domains recognize mono- and di-methylated lysines at a number of different positions on histone H3 and H4 tails. Three Drosophila proteins, SCM, L(3)MBT and SFMBT contain multiple adjacent MBT repeats and have critical roles in development, maintenance of cell identity, and tumor suppression. Although they function in different pathways, these proteins all localize to chromatin in vivo and repress transcription by a currently unknown molecular mechanism that requires the MBT domains. The human genome contains several homologues of these MBT proteins, some of which have been linked to important gene regulatory pathways, such as E2F/Rb- and Polycomb-mediated repression, and to the insurgence of certain neurological tumors. Here, we review the genetics, biochemistry, and cell biology of MBT proteins and their role in development and disease.
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Affiliation(s)
- Roberto Bonasio
- Howard Hughes Medical Institute and Department of Biochemistry, School of Medicine, New York University, New York, NY 10016, USA
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37
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Adams-Cioaba MA, Min J. Structure and function of histone methylation binding proteins. Biochem Cell Biol 2009; 87:93-105. [PMID: 19234526 DOI: 10.1139/o08-129] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chromatin structure is regulated by chromatin remodeling factors, histone exchange, linker histone association, and histone modification. Covalent modification of histones is an important factor in the regulation of the associated processes. The implementation and removal of various histone modifications have been implicated in DNA replication, repair, recombination, and transcription, and in RNA processing. In recent years, histone methylation has emerged as one of the key modifications regulating chromatin function. However, the mechanisms involved are complex and not well understood. A large volume of structural and biochemical information has been recently amassed for the Tudor, plant homeodomain (PHD), and malignant brain tumor (MBT) protein families. This review summarizes current knowledge of the structures and modes of recognition employed by the PHD, Tudor, and MBT domains in their interactions with target histone peptides.
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Guo Y, Nady N, Qi C, Allali-Hassani A, Zhu H, Pan P, Adams-Cioaba MA, Amaya MF, Dong A, Vedadi M, Schapira M, Read RJ, Arrowsmith CH, Min J. Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2. Nucleic Acids Res 2009; 37:2204-10. [PMID: 19233876 PMCID: PMC2673432 DOI: 10.1093/nar/gkp086] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The MBT repeat has been recently identified as a key domain capable of methyl–lysine histone recognition. Functional work has pointed to a role for MBT domain-containing proteins in transcriptional repression of developmental control genes such as Hox genes. In this study, L3MBTL2, a human homolog of Drosophila Sfmbt critical for Hox gene silencing, is demonstrated to preferentially recognize lower methylation states of several histone-derived peptides through its fourth MBT repeat. High-resolution crystallographic analysis of the four MBT repeats of this protein reveals its unique asymmetric rhomboid architecture, as well as binding mechanism, which preclude the interaction of the first three MBT repeats with methylated peptides. Structural elucidation of an L3MBTL2–H4K20me1 complex and comparison with other MBT-histone peptide complexes also suggests that an absence of distinct surface contours surrounding the methyl–lysine-binding pocket may underlie the lack of sequence specificity observed for members of this protein family.
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Affiliation(s)
- Yahong Guo
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L6, Ontario, Canada
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Gelato KA, Fischle W. Role of histone modifications in defining chromatin structure and function. Biol Chem 2008; 389:353-63. [PMID: 18225984 DOI: 10.1515/bc.2008.048] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chromosomes in eukaryotic cell nuclei are not uniformly organized, but rather contain distinct chromatin elements, with each state having a defined biochemical structure and biological function. These are recognizable by their distinct architectures and molecular components, which can change in response to cellular stimuli or metabolic requirements. Chromatin elements are characterized by the fundamental histone and DNA components, as well as other associated non-histone proteins and factors. Post-translational modifications of histone proteins in particular often correlate with a specific chromatin structure and function. Patterns of histone modifications are implicated as having a role in directing the level of chromatin compaction, as well as playing roles in multiple functional pathways directing the readout of distinct regions of the genome. We review the properties of various chromatin elements and the apparent links of histone modifications with chromatin organization and functional output.
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Affiliation(s)
- Kathy A Gelato
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
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40
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Abstract
Abstract
There has been a remarkable explosion of knowledge into the molecular defects that underlie the acute and chronic leukemias, leading to the introduction of targeted therapies that can block key cellular events essential for the viability of the leukemic cell. Our understanding of the pathogenesis of the myelodysplastic syndromes (MDSs) has lagged behind, at least in part, because they represent a more heterogeneous group of disorders. The significant immunologic abnormalities described in this disease, coupled with the admixture of MDS stem or progenitor cells within the myriad types of dysplastic and normal cells in the bone marrow and peripheral blood, have made it difficult to molecularly characterize and model MDS. The recent availability of several, effective (ie, FDA-approved) therapies for MDS and newly described mouse models that mimic aspects of the human disease provide an opportune moment to try to leverage this new knowledge into a better understanding of and better therapies for MDS.
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Abstract
Lethal 3 malignant brain tumor 1 (L3MBTL1), a homolog of the Drosophila polycomb tumor suppressor l(3)mbt, contains three tandem MBT repeats (3xMBT) that are critical for transcriptional repression. We recently reported that the 3xMBT repeats interact with mono- and dimethylated lysines in the amino termini of histones H4 and H1b to promote methylation-dependent chromatin compaction. Using a series of histone peptides, we now show that the recognition of mono- and dimethylated lysines in histones H3, H4 and H1.4 (but not their trimethylated or unmodified counterparts) by 3xMBT occurs in the context of a basic environment, requiring a conserved aspartic acid (D355) in the second MBT repeat. Despite the broad range of in vitro binding, the chromatin association of L3MBTL1 mirrors the progressive accumulation of H4K20 monomethylation during the cell cycle. Furthermore, transcriptional repression by L3MBTL1 is enhanced by the H4K20 monomethyltransferase PR-SET7 (to which it binds) but not SUV420H1 (an H4K20 trimethylase) or G9a (an H3K9 dimethylase) and knockdown of PR-SET7 decreases H4K20me1 levels and the chromatin association of L3MBTL1. Our studies identify the importance of H4K20 monomethylation and of PR-SET7 for L3MBTL1 function.
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Kustatscher G, Ladurner AG. Modular paths to ‘decoding’ and ‘wiping’ histone lysine methylation. Curr Opin Chem Biol 2007; 11:628-35. [DOI: 10.1016/j.cbpa.2007.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 09/26/2007] [Indexed: 12/27/2022]
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Min J, Allali-Hassani A, Nady N, Qi C, Ouyang H, Liu Y, MacKenzie F, Vedadi M, Arrowsmith CH. L3MBTL1 recognition of mono- and dimethylated histones. Nat Struct Mol Biol 2007; 14:1229-30. [PMID: 18026117 DOI: 10.1038/nsmb1340] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Accepted: 10/23/2007] [Indexed: 12/29/2022]
Abstract
Crystal structures of the L3MBTL1 MBT repeats in complex with histone H4 peptides dimethylated on Lys20 (H4K20me2) show that only the second of the three MBT repeats can bind mono- and dimethylated histone peptides. Its binding pocket has similarities to that of 53BP1 and is able to recognize the degree of histone lysine methylation. An unexpected mode of peptide-mediated dimerization suggests a possible mechanism for chromatin compaction by L3MBTL1.
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Affiliation(s)
- Jinrong Min
- Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, Ontario, M5G 1L5, Canada
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Hayakawa T, Ohtani Y, Hayakawa N, Shinmyozu K, Saito M, Ishikawa F, Nakayama JI. RBP2 is an MRG15 complex component and down-regulates intragenic histone H3 lysine 4 methylation. Genes Cells 2007; 12:811-26. [PMID: 17573780 DOI: 10.1111/j.1365-2443.2007.01089.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MRG15 is a conserved chromodomain protein that associates with histone deacetylases (HDACs) and Tip60-containing histone acetyltransferase (HAT) complexes. Here we further characterize MRG15-containing complexes and show a functional link between MRG15 and histone H3K4 demethylase activity in mammalian cells. MRG15 was predominantly localized to discrete nuclear subdomains enriched for Ser(2)-phosphorylated RNA polymerase II, suggesting it is involved specifically with active transcription. Protein analysis of the MRG15-containing complexes led to the identification of RBP2, a JmjC domain-containing protein. Remarkably, over-expression of RBP2 greatly reduced the H3K4 methylation in culture human cells in vivo, and recombinant RBP2 efficiently removed H3K4 methylation of histone tails in vitro. Knockdown of RBP2 resulted in increased H3K4 methylation levels within transcribed regions of active genes. Our findings demonstrate that RBP2 associated with MRG15 complex to maintain reduced H3K4 methylation at transcribed regions, which may ensure the transcriptional elongation state.
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Affiliation(s)
- Tomohiro Hayakawa
- Laboratory for Chromatin Dynamics, Center for Developmental Biology, RIKEN, Kobe, Hyogo 650-0047, Japan
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Trojer P, Li G, Sims RJ, Vaquero A, Kalakonda N, Boccuni P, Lee D, Erdjument-Bromage H, Tempst P, Nimer SD, Wang YH, Reinberg D. L3MBTL1, a histone-methylation-dependent chromatin lock. Cell 2007; 129:915-28. [PMID: 17540172 DOI: 10.1016/j.cell.2007.03.048] [Citation(s) in RCA: 262] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 12/27/2006] [Accepted: 03/12/2007] [Indexed: 12/31/2022]
Abstract
Distinct histone lysine methylation marks are involved in transcriptional repression linked to the formation and maintenance of facultative heterochromatin, although the underlying mechanisms remain unclear. We demonstrate that the malignant-brain-tumor (MBT) protein L3MBTL1 is in a complex with core histones, histone H1b, HP1gamma, and Rb. The MBT domain is structurally related to protein domains that directly bind methylated histone residues. Consistent with this, we found that the L3MBTL1 MBT domains compact nucleosomal arrays dependent on mono- and dimethylation of histone H4 lysine 20 and of histone H1b lysine 26. The MBT domains bind at least two nucleosomes simultaneously, linking repression of transcription to recognition of different histone marks by L3MBTL1. Consistently, L3MBTL1 was found to negatively regulate the expression of a subset of genes regulated by E2F, a factor that interacts with Rb.
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Affiliation(s)
- Patrick Trojer
- Howard Hughes Medical Institute, University of Medicine and Dentistry of New Jersey, 683 Hoes Lane, Piscataway, NJ 08854, USA
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Wu S, Trievel RC, Rice JC. Human SFMBT is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3. FEBS Lett 2007; 581:3289-96. [PMID: 17599839 PMCID: PMC2045647 DOI: 10.1016/j.febslet.2007.06.025] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Revised: 06/07/2007] [Accepted: 06/14/2007] [Indexed: 12/27/2022]
Abstract
Human SFMBT (hSFMBT) is postulated to be a Polycomb (PcG) protein. Similar to other PcG proteins, we found that hSFMBT displays robust transcriptional repressor activity. In addition, hSFMBT localized to the nucleus where it strongly associates with chromatin by directly and selectively binding the N-terminal tail of histone H3. Importantly, we discovered that the four tandem MBT repeats of hSFMBT were sufficient for nuclear matrix-association, N-terminal tail H3 binding, and required for transcriptional repression. These findings indicate that the tandem MBT repeats form a functional structure required for biological activity of hSFMBT and predict similar properties for other MBT domain-containing proteins.
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Affiliation(s)
- Shumin Wu
- University of Southern California Keck School of Medicine, Department of Biochemistry and Molecular Biology, Los Angeles, CA 90033, USA
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Lu J, Ruhf ML, Perrimon N, Leder P. A genome-wide RNA interference screen identifies putative chromatin regulators essential for E2F repression. Proc Natl Acad Sci U S A 2007; 104:9381-6. [PMID: 17517653 PMCID: PMC1890503 DOI: 10.1073/pnas.0610279104] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Regulation of chromatin structure is critical in many fundamental cellular processes. Previous studies have suggested that the Rb tumor suppressor may recruit multiple chromatin regulatory proteins to repress E2F, a key regulator of cell proliferation and differentiation. Taking advantage of the evolutionary conservation of the E2F pathway, we have conducted a genome-wide RNAi screen in cultured Drosophila cells for genes required for repression of E2F activity. Among the genes identified are components of the putative Domino chromatin remodeling complex, as well as the Polycomb Group (PcG) protein-like fly tumor suppressor, L3mbt, and the related CG16975/dSfmbt. These factors are recruited to E2F-responsive promoters through physical association with E2F and are required for repression of endogenous E2F target genes. Surprisingly, their inhibitory activities on E2F appear to be independent of Rb. In Drosophila, domino mutation enhances cell proliferation induced by E2F overexpression and suppresses a loss-of-function cyclin E mutation. These findings suggest that potential chromatin regulation mediated by Domino and PcG-like factors plays an important role in controlling E2F activity and cell growth.
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Affiliation(s)
- Jianrong Lu
- Department of Genetics, Harvard Medical School, Boston, MA 02115; and
- To whom correspondence should be addressed at the present address:
Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, P.O. Box 103633, Gainesville, FL 32610. E-mail:
| | - Marie-Laure Ruhf
- Genome Research Institute, University of Cincinnati, Cincinnati, OH 45237
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, MA 02115; and
| | - Philip Leder
- Department of Genetics, Harvard Medical School, Boston, MA 02115; and
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Harrison MM, Lu X, Horvitz HR. LIN-61, one of two Caenorhabditis elegans malignant-brain-tumor-repeat-containing proteins, acts with the DRM and NuRD-like protein complexes in vulval development but not in certain other biological processes. Genetics 2007; 176:255-71. [PMID: 17409073 PMCID: PMC1893064 DOI: 10.1534/genetics.106.069633] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Vulval development in Caenorhabiditis elegans is inhibited by the redundant functions of the synthetic multivulva (synMuv) genes. At least 26 synMuv genes have been identified, many of which appear to act via transcriptional repression. Here we report the molecular identification of the class B synMuv gene lin-61, which encodes a protein composed of four malignant brain tumor (MBT) repeats. MBT repeats, domains of approximately 100 amino acids, have been found in multiple copies in a number of transcriptional repressors, including Polycomb-group proteins. MBT repeats are important for the transcriptional repression mediated by these proteins and in some cases have been shown to bind modified histones. C. elegans contains one other MBT-repeat-containing protein, MBTR-1. We demonstrate that a deletion allele of mbtr-1 does not cause a synMuv phenotype nor does mbtr-1 appear to act redundantly with or in opposition to lin-61. We further show that lin-61 is phenotypically and biochemically distinct from other class B synMuv genes. Our data indicate that while the class B synMuv genes act together to regulate vulval development, lin-61 functions separately from some class B synMuv proteins in other biological processes.
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Affiliation(s)
- Melissa M Harrison
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Cui XS, Song H, Kim NH. Identification of metaphase II-specific gene transcripts in porcine oocytes and their expression in early stage embryos. Reprod Fertil Dev 2006; 17:625-31. [PMID: 16263068 DOI: 10.1071/rd05019] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2005] [Accepted: 05/26/2005] [Indexed: 12/21/2022] Open
Abstract
Annealing control primer (ACP)-based GeneFishing polymerase chain reaction (PCR) was used to identify the genes that are specifically or prominently expressed in porcine oocytes at the metaphase II (MII) and germinal vesicle (GV) stages. By using 60 ACPs, 13 differentially expressed genes (DEGs) were identified. The cloned genes or expressed sequence tags (ESTs) showed sequence similarity with known genes or ESTs of other species in GenBank. The mRNA expression during oocyte maturation and early embryonic development in both pigs and mice of four of these genes (namely transcription factor TZP, annexin A2, hypoxia-inducible protein 2, and ATPase 6) was further characterised by real-time quantitative reverse transcription-PCR. All four genes were markedly upregulated in pig and mouse MII oocytes compared with GV-stage oocytes. The expression levels of the four genes decreased gradually during early cleavage. Thus, these genes may play important roles during oocyte maturation and/or early cleavage in mammals. Although the detailed functions of these genes remain to be determined, their identification in the present study provides insights into meiotic maturation and fertilisation.
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Affiliation(s)
- Xiang-Shun Cui
- Department of Animal Science, Chungbuk National University, Cheongju, Korea
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50
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Li J, Bench AJ, Piltz S, Vassiliou G, Baxter EJ, Ferguson-Smith AC, Green AR. L3mbtl, the mouse orthologue of the imprinted L3MBTL, displays a complex pattern of alternative splicing and escapes genomic imprinting. Genomics 2006; 86:489-94. [PMID: 16081246 DOI: 10.1016/j.ygeno.2005.06.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2004] [Revised: 04/22/2005] [Accepted: 06/15/2005] [Indexed: 10/25/2022]
Abstract
L3mbtl encodes a member of the Polycomb group of proteins, which function as transcriptional repressors in large protein complexes. The Drosophila D-l(3)mbt protein is considered a tumor suppressor since its inactivation results in brain tumors. The human L3MBTL gene lies in a region of chromosome 20 frequently deleted in patients with myeloid malignancies and has been proposed as a candidate 20q tumor suppressor gene. Recently we have shown that L3MBTL undergoes monoallelic methylation in hematopoietic tissues and is transcribed from the paternally derived allele. The mouse L3mbtl gene is located on chromosome 2, a region of syntenic homology with human chromosome 20, and in a region containing a number of genes subject to epigenetic regulation. Here we analyze the genomic structure and alternative splicing of L3mbtl and assess its imprinting status in mouse. L3mbtl displays a complex pattern of alternative splicing involving both 5' noncoding and coding exons and is transcribed from two promoters. Unlike its human counterpart, L3mbtl escapes imprinting and there is no differential methylation of its CpG island.
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Affiliation(s)
- Juan Li
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 2XY, UK
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