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Wang IF, Wang Y, Yang YH, Huang GJ, Tsai KJ, Shen CKJ. Activation of a hippocampal CREB-pCREB-miRNA-MEF2 axis modulates individual variation of spatial learning and memory capability. Cell Rep 2021; 36:109477. [PMID: 34348143 DOI: 10.1016/j.celrep.2021.109477] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/07/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022] Open
Abstract
Phenotypic variation is a fundamental prerequisite for cell and organism evolution by natural selection. Whereas the role of stochastic gene expression in phenotypic diversity of genetically identical cells is well studied, not much is known regarding the relationship between stochastic gene expression and individual behavioral variation in animals. We demonstrate that a specific miRNA (miR-466f-3p) is upregulated in the hippocampus of a portion of individual inbred mice upon a Morris water maze task. Significantly, miR-466f-3p positively regulates the neuron morphology, function and spatial learning, and memory capability of mice. Mechanistically, miR-466f-3p represses translation of MEF2A, a negative regulator of learning/memory. Finally, we show that varied upregulation of hippocampal miR-466f-3p results from randomized phosphorylation of hippocampal cyclic AMP (cAMP)-response element binding (CREB) in individuals. This finding of modulation of spatial learning and memory via a randomized hippocampal signaling axis upon neuronal stimulation represents a demonstration of how variation in tissue gene expression lead to varied animal behavior.
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Affiliation(s)
- I-Fang Wang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yihan Wang
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Hua Yang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan; Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Guo-Jen Huang
- Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan; Neuroscience Research Center, Chang Gung Memorial Hospital, Linkou 33302, Taiwan
| | - Kuen-Jer Tsai
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan; Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan.
| | - Che-Kun James Shen
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan.
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2
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Fu YH, Ou DL, Yang YR, Su KW, Chen CY, Tien HF, Lai ZS, Shen CKJ, Chien HF, Lin LI. Cabozantinib promotes erythroid differentiation in K562 erythroleukemia cells through global changes in gene expression and JNK activation. Cancer Gene Ther 2021; 29:784-792. [PMID: 34117374 DOI: 10.1038/s41417-021-00358-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 05/12/2021] [Accepted: 05/25/2021] [Indexed: 11/09/2022]
Abstract
Cabozantinib is a potent tyrosine kinase inhibitor with multiple targets including MET, VEGFR2, RET, KIT, and FLT3. Cabozantinib is widely used for the treatment of medullary thyroid cancer and renal cell carcinoma. We recently suggested cabozantinib as a potential therapeutic alternative for acute myeloid leukemia (AML) patients with FLT3-internal tandem duplication (FLT3-ITD). Here, we report that cabozantinib can promote differentiation in erythroid leukemia cells. We found that K562 erythroid leukemia cells treated with 1 μM cabozantinib for 72 h underwent erythroid lineage differentiation. Transcriptomic analysis revealed that various pathways associated with heme biosynthesis, hemoglobin production, and GATA1 targets were upregulated, whereas cell survival pathways were downregulated. Further examination revealed that cabozantinib-induced erythroid differentiation is at least in part regulated by JNK activation and phosphorylation. Levels of phosphorylated BCR-ABL, AKT, STAT5, ERK, and p38 also decreased following cabozantinib treatment. Therefore, we indicate that cabozantinib has dual functions. First, it induces K562 cell differentiation toward the erythroid lineage by upregulating heme biosynthesis, globin synthesis, and erythroid-associated reactions. Second, cabozantinib inhibits K562 cell proliferation by inhibiting the phosphorylation of BCR-ABL and the downstream MAPK, PI3K-AKT, and JAK-STAT signaling pathways.
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Affiliation(s)
- Yu-Hsuan Fu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Da-Liang Ou
- Department of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Ru Yang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Kuan-Wei Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Chien-Yuan Chen
- Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Hwei-Fan Tien
- Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Zheng-Sheng Lai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,The Ph.D. Program for Neural Regenerative Medicine, Taipei Medical University, Taipei, Taiwan
| | - Hsiung-Fei Chien
- Division of Plastic Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei, Taiwan. .,TMU Center for Cell Therapy and Regeneration Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Liang-In Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei, Taiwan. .,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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3
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Lai ZS, Yeh TK, Chou YC, Hsu T, Lu CT, Kung FC, Hsieh MY, Lin CH, Chen CT, James Shen CK, Jiaang WT. Potent and orally active purine-based fetal hemoglobin inducers for treating β-thalassemia and sickle cell disease. Eur J Med Chem 2021; 209:112938. [PMID: 33109398 DOI: 10.1016/j.ejmech.2020.112938] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/23/2020] [Accepted: 10/10/2020] [Indexed: 11/25/2022]
Abstract
Reactivation of fetal hemoglobin (HbF) expression by therapeutic agents has been suggested as an alternative treatment to modulate anemia and the related symptoms of severe β-thalassemia and sickle cell disease (SCD). Hydroxyurea (HU) is the first US FDA-approved HbF inducer for treating SCD. However, approximately 25% of the patients with SCD do not respond to HU. A previous study identified TN1 (1) as a small-molecule HbF inducer. However, this study found that the poor potency and oral bioavailability of compound 1 limits the development of this inducer for clinical use. To develop drug-like compounds, further structure-activity relationship studies on the purine-based structure of 1 were conducted. Herein, we report our discovery of a more potent inducer, compound 13a, that can efficiently induce γ-globin gene expression at non-cytotoxic concentrations. The molecular mechanism of 13a, for the regulation HbF expression, was also investigated. In addition, we demonstrated that oral administration of 13a can ameliorate anemia and the related symptoms in SCD mice. The results of this study suggest that 13a can be further developed as a novel agent for treating hemoglobinopathies, such as β-thalassemia and SCD.
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Affiliation(s)
- Zheng-Sheng Lai
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan, ROC; Institute of Molecular Medicine, College of Medicine, National Taiwan University, No.7.Chung San South Road, Taipei, 10002, Taiwan, ROC
| | - Teng-Kuang Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No. 35, Keyan Rd., Zhunan Town, Miaoli Country, 35053, Taiwan, ROC
| | - Yu-Chi Chou
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Tsu Hsu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No. 35, Keyan Rd., Zhunan Town, Miaoli Country, 35053, Taiwan, ROC
| | - Cheng-Tai Lu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No. 35, Keyan Rd., Zhunan Town, Miaoli Country, 35053, Taiwan, ROC
| | - Fang-Chun Kung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No. 35, Keyan Rd., Zhunan Town, Miaoli Country, 35053, Taiwan, ROC
| | - Ming-Yen Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Chun-Hung Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Chiung-Tong Chen
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No. 35, Keyan Rd., Zhunan Town, Miaoli Country, 35053, Taiwan, ROC
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Weir-Torn Jiaang
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, No. 35, Keyan Rd., Zhunan Town, Miaoli Country, 35053, Taiwan, ROC.
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4
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Hung CH, Wang KY, Liou YH, Wang JP, Huang AYS, Lee TL, Jiang ST, Liao NS, Shyu YC, Shen CKJ. Negative Regulation of the Differentiation of Flk2 - CD34 - LSK Hematopoietic Stem Cells by EKLF/KLF1. Int J Mol Sci 2020; 21:E8448. [PMID: 33182781 PMCID: PMC7697791 DOI: 10.3390/ijms21228448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
Erythroid Krüppel-like factor (EKLF/KLF1) was identified initially as a critical erythroid-specific transcription factor and was later found to be also expressed in other types of hematopoietic cells, including megakaryocytes and several progenitors. In this study, we have examined the regulatory effects of EKLF on hematopoiesis by comparative analysis of E14.5 fetal livers from wild-type and Eklf gene knockout (KO) mouse embryos. Depletion of EKLF expression greatly changes the populations of different types of hematopoietic cells, including, unexpectedly, the long-term hematopoietic stem cells Flk2- CD34- Lin- Sca1+ c-Kit+ (LSK)-HSC. In an interesting correlation, Eklf is expressed at a relatively high level in multipotent progenitor (MPP). Furthermore, EKLF appears to repress the expression of the colony-stimulating factor 2 receptor β subunit (CSF2RB). As a result, Flk2- CD34- LSK-HSC gains increased differentiation capability upon depletion of EKLF, as demonstrated by the methylcellulose colony formation assay and by serial transplantation experiments in vivo. Together, these data demonstrate the regulation of hematopoiesis in vertebrates by EKLF through its negative regulatory effects on the differentiation of the hematopoietic stem and progenitor cells, including Flk2- CD34- LSK-HSCs.
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Affiliation(s)
- Chun-Hao Hung
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; (C.-H.H.); (K.-Y.W.); (Y.-H.L.); (J.-P.W.); (A.Y.-S.H.); (T.-L.L.); (N.-S.L.)
| | - Keh-Yang Wang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; (C.-H.H.); (K.-Y.W.); (Y.-H.L.); (J.-P.W.); (A.Y.-S.H.); (T.-L.L.); (N.-S.L.)
| | - Yae-Huei Liou
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; (C.-H.H.); (K.-Y.W.); (Y.-H.L.); (J.-P.W.); (A.Y.-S.H.); (T.-L.L.); (N.-S.L.)
| | - Jing-Ping Wang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; (C.-H.H.); (K.-Y.W.); (Y.-H.L.); (J.-P.W.); (A.Y.-S.H.); (T.-L.L.); (N.-S.L.)
| | - Anna Yu-Szu Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; (C.-H.H.); (K.-Y.W.); (Y.-H.L.); (J.-P.W.); (A.Y.-S.H.); (T.-L.L.); (N.-S.L.)
| | - Tung-Liang Lee
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; (C.-H.H.); (K.-Y.W.); (Y.-H.L.); (J.-P.W.); (A.Y.-S.H.); (T.-L.L.); (N.-S.L.)
| | - Si-Tse Jiang
- Department of Research and Development, National Laboratory Animal Center, National Applied Research Laboratories, Tainan 74147, Taiwan;
| | - Nah-Shih Liao
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; (C.-H.H.); (K.-Y.W.); (Y.-H.L.); (J.-P.W.); (A.Y.-S.H.); (T.-L.L.); (N.-S.L.)
| | - Yu-Chiau Shyu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; (C.-H.H.); (K.-Y.W.); (Y.-H.L.); (J.-P.W.); (A.Y.-S.H.); (T.-L.L.); (N.-S.L.)
- Department of Nursing, Chang Gung University of Science and Technology, Taoyuan City 333, Taiwan
- Community Medicine Research Center, Chang Gung Memorial Hospital, Keelung Branch, Keelung 204, Taiwan
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; (C.-H.H.); (K.-Y.W.); (Y.-H.L.); (J.-P.W.); (A.Y.-S.H.); (T.-L.L.); (N.-S.L.)
- The PhD Program for Neural Regenerative Medicine, Taipei Medical University, Taipei 115, Taiwan
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5
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Chu JF, Majumder P, Chatterjee B, Huang SL, Shen CKJ. TDP-43 Regulates Coupled Dendritic mRNA Transport-Translation Processes in Co-operation with FMRP and Staufen1. Cell Rep 2020; 29:3118-3133.e6. [PMID: 31801077 DOI: 10.1016/j.celrep.2019.10.061] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 07/12/2019] [Accepted: 10/14/2019] [Indexed: 01/24/2023] Open
Abstract
Tightly regulated transport of messenger ribonucleoprotein (mRNP) granules to diverse locations of dendrites and axons is essential for appropriately timed protein synthesis within distinct sub-neuronal compartments. Perturbations of this regulation lead to various neurological disorders. Using imaging and molecular approaches, we demonstrate how TDP-43 co-operates with two other RNA-binding proteins, FMRP and Staufen1, to regulate the anterograde and retrograde transport, respectively, of Rac1 mRNPs in mouse neuronal dendrites. We also analyze the mechanisms by which TDP-43 mediates coupled mRNA transport-translation processes in dendritic sub-compartments by following in real-time the co-movement of RNA and endogenous fluorescence-tagged protein in neurons and by simultaneous examination of transport/translation dynamics by using an RNA biosensor. This study establishes the pivotal roles of TDP-43 in transporting mRNP granules in dendrites, inhibiting translation inside those granules, and reactivating it once the granules reach the dendritic spines.
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Affiliation(s)
- Jen-Fei Chu
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Pritha Majumder
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan.
| | | | - Shih-Ling Huang
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
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6
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Huang SL, Wu LS, Lee M, Chang CW, Cheng WC, Fang YS, Chen YR, Cheng PL, Shen CKJ. A robust TDP-43 knock-in mouse model of ALS. Acta Neuropathol Commun 2020; 8:3. [PMID: 31964415 PMCID: PMC6975031 DOI: 10.1186/s40478-020-0881-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/10/2019] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, adult-onset degenerative disorder of motor neurons. The diseased spinal cord motor neurons of more than 95% of amyotrophic lateral sclerosis (ALS) patients are characterized by the mis-metabolism of the RNA/DNA-binding protein TDP-43 (ALS-TDP), in particular, the presence of cytosolic aggregates of the protein. Most available mouse models for the basic or translational studies of ALS-TDP are based on transgenic overexpression of the TDP-43 protein. Here, we report the generation and characterization of mouse lines bearing homologous knock-in of fALS-associated mutation A315T and sALS-associated mutation N390D, respectively. Remarkably, the heterozygous TDP-43 (N390D/+) mice but not those heterozygous for the TDP-43 (A315T/+) mice develop a full spectrum of ALS-TDP-like pathologies at the molecular, cellular and behavioral levels. Comparative analysis of the mutant mice and spinal cord motor neurons (MN) derived from their embryonic stem (ES) cells demonstrates that different ALS-associated TDP-43 mutations possess critical ALS-causing capabilities and pathogenic pathways, likely modified by their genetic background and the environmental factors. Mechanistically, we identify aberrant RNA splicing of spinal cord Bcl-2 pre-mRNA and consequent increase of a negative regulator of autophagy, Bcl-2, which correlate with and are caused by a progressive increase of TDP-43, one of the early events associated with ALS-TDP pathogenesis, in the spinal cord of TDP-43 (N390D/+) mice and spinal cord MN derived from their ES cells. The TDP-43 (N390D/+) knock-in mice appear to be an ideal rodent model for basic as well as translational studies of ALS- TDP.
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7
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Zhao L, Ke H, Xu H, Wang GD, Zhang H, Zou L, Xiang S, Li M, Peng L, Zhou M, Li L, Ao L, Yang Q, Shen CKJ, Yi P, Wang L, Jiao B. TDP-43 facilitates milk lipid secretion by post-transcriptional regulation of Btn1a1 and Xdh. Nat Commun 2020; 11:341. [PMID: 31953403 PMCID: PMC6969145 DOI: 10.1038/s41467-019-14183-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 12/13/2019] [Indexed: 12/31/2022] Open
Abstract
Milk lipid secretion is a critical process for the delivery of nutrition and energy from parent to offspring. However, the underlying molecular mechanism is less clear. Here we report that TDP-43, a RNA-binding protein, underwent positive selection in the mammalian lineage. Furthermore, TDP-43 gene (Tardbp) loss induces accumulation of large lipid droplets and severe lipid secretion deficiency in mammary epithelial cells to outside alveolar lumens, eventually resulting in lactation failure and pup starvation within three weeks postpartum. In human milk samples from lactating women, the expression levels of TDP-43 is positively correlated with higher milk output. Mechanistically, TDP-43 exerts post-transcriptional regulation of Btn1a1 and Xdh mRNA stability, which are required for the secretion of lipid droplets from epithelial cells to the lumen. Taken together, our results highlights the critical role of TDP-43 in milk lipid secretion, providing a potential strategy for the screening and intervention of clinical lactation insufficiency. Milk lipid secretion is a critical process for the delivery of nutrition and energy from parent to offspring. Here the authors found that TDP-43, a RNA-binding protein, is required for milk lipid secretion by post-transcriptional regulation of Btn1a1 and Xdh mRNA stability.
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Affiliation(s)
- Limin Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, 650223, Kunming, China
| | - Hao Ke
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, 650223, Kunming, China
| | - Haibo Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, 650223, Kunming, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China
| | - Honglei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
| | - Li Zou
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
| | - Shu Xiang
- The First Hospital of Kunming, Calmette International Hospital, 650011, Kunming, China
| | - Mengyuan Li
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, 401120, Chongqing, China
| | - Li Peng
- Yubei District Maternal and Child Health Care Hospital, 401120, Chongqing, China
| | - Mingfang Zhou
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, 401120, Chongqing, China
| | - Lingling Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.,School of Life Sciences, University of Science and Technology of China, 230026, Hefei, China
| | - Lei Ao
- Kunming Angel Women's and Children's Hospital, 650032, Kunming, China
| | - Qin Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, 11529, Taipei, Nankang, Taiwan
| | - Ping Yi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, 401120, Chongqing, China.
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, 650091, Kunming, China.
| | - Baowei Jiao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223, Kunming, China. .,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223, Kunming, China.
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8
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Zhao L, Li L, Xu H, Ke H, Zou L, Yang Q, Shen CKJ, Nie J, Jiao B. TDP-43 is Required for Mammary Gland Repopulation and Proliferation of Mammary Epithelial Cells. Stem Cells Dev 2019; 28:944-953. [PMID: 31062657 DOI: 10.1089/scd.2019.0011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Mammary gland stem cells (MaSCs), assumed to be the original cells of breast cancer, play essential roles in regulating mammary gland homeostasis and development. Previously, we identified a crucial regulatory role of TAR DNA-binding protein 43 (TDP-43), an RNA-binding protein, in the progression of triple-negative breast cancer. However, the function of TDP-43 in MaSCs is unclear. Based on single-cell data analysis of the mammary gland, TDP-43 showed potential involvement in the regulation of MaSCs. We therefore investigated the effects of TDP-43 on the mammary gland development. Our data both in vitro and in vivo demonstrated that TDP-43 was required for the mammary gland repopulation, which suggested the potential role in the regulation of MaSCs. Knockdown of TDP-43 inhibited proliferation of mammary epithelial cells (MECs) and mammary morphogenesis. RNA-seq data and other experiments identified that loss of TDP-43 induced the upregulation of genes related to the cell cycle, providing a possible mechanism for TDP-43 in regulating mammary gland repopulation. Thus, our findings indicate a previously unknown role of TDP-43 in MECs.
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Affiliation(s)
- Limin Zhao
- 1School of Life Sciences, University of Science and Technology of China, Hefei, China.,2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,3Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Lingling Li
- 1School of Life Sciences, University of Science and Technology of China, Hefei, China.,2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Haibo Xu
- 2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,3Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Hao Ke
- 2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Li Zou
- 2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Qin Yang
- 2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Che-Kun James Shen
- 4Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Jianyun Nie
- 5Department of Breast Cancer, Third Affiliated Hospital, Kunming Medical University, Kunming, China
| | - Baowei Jiao
- 2State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,6KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,7Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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9
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Lee YC, Huang WC, Lin JH, Kao TJ, Lin HC, Lee KH, Lin HC, Shen CKJ, Chang WC, Huang CC. Znf179 E3 ligase-mediated TDP-43 polyubiquitination is involved in TDP-43- ubiquitinated inclusions (UBI) (+)-related neurodegenerative pathology. J Biomed Sci 2018; 25:76. [PMID: 30404641 PMCID: PMC6223059 DOI: 10.1186/s12929-018-0479-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/24/2018] [Indexed: 12/13/2022] Open
Abstract
Background The brain predominantly expressed RING finger protein, Znf179, is known to be important for embryonic neuronal differentiation during brain development. Downregulation of Znf179 has been observed in motor neurons of adult mouse models for amyotrophic lateral sclerosis (ALS), yet the molecular function of Znf179 in neurodegeneration has never been previously described. Znf179 contains the classical C3HC4 RING finger domain, and numerous proteins containing C3HC4 RING finger domain act as E3 ubiquitin ligases. Hence, we are interested to identify whether Znf179 possesses E3 ligase activity and its role in ALS neuropathy. Methods We used in vivo and in vitro ubiquitination assay to examine the E3 ligase autoubiquitination activity of Znf179 and its effect on 26S proteasome activity. To search for the candidate substrates of Znf179, we immunoprecipitated Znf179 and subjected to mass spectrometry (MS) analysis to identify its interacting proteins. We found that ALS/ FTLD-U (frontotemporal lobar degeneration (FTLD) with ubiquitin inclusions)-related neurodegenerative TDP-43 protein is the E3 ligase substrate of Znf179. To further clarify the role of E3 ubiquitin ligase Znf179 in neurodegenerative TDP-43-UBI (ubiquitinated inclusions) (+) proteinopathy, the effect of Znf179-mediated TDP-43 polyubiquitination on TDP-43 protein stability, aggregate formation and nucleus/cytoplasm mislocalization were evaluated in vitro cell culture system and in vivo animal model. Results Here we report that Znf179 is a RING E3 ubiquitin ligase which possesses autoubiquitination feature and regulates 26S proteasome activity through modulating the protein expression levels of 19S/20S proteasome subunits. Our immunoprecipitation assay and MS analysis results revealed that the neuropathological TDP-43 protein is one of its E3 ligase substrate. Znf179 interactes with TDP-43 protein and mediates polyubiquitination of TDP-43 in vitro and in vivo. In neurodegenerative TDP-43 proteinopathy, we found that Znf179-mediated polyubiquitination of TDP-43 accelerates its protein turnover rate and attenuates insoluble pathologic TDP-43 aggregates, while knockout of Znf179 in mouse brain results in accumulation of insoluble TDP-43 and cytosolic TDP-43 inclusions in cortex, hippocampus and midbrain regions. Conclusions Here we unveil the important role for the novel E3 ligase Znf179 in TDP-43-mediated neuropathy, and provide a potential therapeutic strategy for combating ALS/ FTLD-U neurodegenerative pathologies. Electronic supplementary material The online version of this article (10.1186/s12929-018-0479-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yi-Chao Lee
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology/Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, 115, Taiwan
| | - Wan-Chen Huang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Jiann-Her Lin
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology/Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, 115, Taiwan.,Department of Neurosurgery, Taipei Medical University, Taipei, Taiwan.,Division of Neurosurgery, Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tzu-Jen Kao
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology/Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, 115, Taiwan
| | - Hui-Ching Lin
- Institute and Department of Physiology, School of Medicine, National Yang-Ming University, Taipei, 112, Taiwan
| | - Kuen-Haur Lee
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 115, Taiwan
| | - Hsin-Chuan Lin
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
| | | | - Wen-Chang Chang
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
| | - Chi-Chen Huang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology/Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, 115, Taiwan.
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10
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Chatterjee B, Lin MH, Chen CC, Peng KL, Wu MS, Tseng MC, Chen YJ, Shen CKJ. DNA Demethylation by DNMT3A and DNMT3B in vitro and of Methylated Episomal DNA in Transiently Transfected Cells. Biochim Biophys Acta Gene Regul Mech 2018; 1861:1048-1061. [PMID: 30300721 DOI: 10.1016/j.bbagrm.2018.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/03/2018] [Accepted: 09/25/2018] [Indexed: 12/24/2022]
Abstract
The DNA methylation program in vertebrates is an essential part of the epigenetic regulatory cascade of development, cell differentiation, and progression of diseases including cancer. While the DNA methyltransferases (DNMTs) are responsible for the in vivo conversion of cytosine (C) to methylated cytosine (5mC), demethylation of 5mC on cellular DNA could be accomplished by the combined action of the ten-eleven translocation (TET) enzymes and DNA repair. Surprisingly, the mammalian DNMTs also possess active DNA demethylation activity in vitro in a Ca2+- and redox conditions-dependent manner, although little is known about its molecular mechanisms and occurrence in a cellular context. In this study, we have used LC-MS/MS to track down the fate of the methyl group removed from 5mC on DNA by mouse DNMT3B in vitro and found that it becomes covalently linked to the DNA methylation catalytic cysteine of the enzyme. We also show that Ca2+ homeostasis-dependent but TET1/TET2/TET3/TDG-independent demethylation of methylated episomal DNA by mouse DNMT3A or DNMT3B can occur in transfected human HEK 293 and mouse embryonic stem (ES) cells. Based on these results, we present a tentative working model of Ca2+ and redox conditions-dependent active DNA demethylation by DNMTs. Our study substantiates the potential roles of the vertebrate DNMTs as double-edged swords in DNA methylation-demethylation during Ca2+-dependent physiological processes.
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Affiliation(s)
| | - Miao-Hsia Lin
- Institute of Chemistry, Academia Sinica, Taipei City 115, Taiwan
| | - Chun-Chang Chen
- Institute of Molecular Biology, Academia Sinica, Taipei City 115, Taiwan
| | - Kai-Lin Peng
- Genomics Research Center, Academia Sinica, Taipei City 115, Taiwan
| | - Mu-Sheng Wu
- Genomics Research Center, Academia Sinica, Taipei City 115, Taiwan; Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei City 112, Taiwan
| | - Mei-Chun Tseng
- Institute of Chemistry, Academia Sinica, Taipei City 115, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei City 115, Taiwan.
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Taipei City 115, Taiwan.
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11
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Yang P, Wang Y, Hoang D, Tinkham M, Patel A, Sun MA, Wolf G, Baker M, Chien HC, Lai KYN, Cheng X, Shen CKJ, Macfarlan TS. A placental growth factor is silenced in mouse embryos by the zinc finger protein ZFP568. Science 2018; 356:757-759. [PMID: 28522536 DOI: 10.1126/science.aah6895] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 04/20/2017] [Indexed: 12/27/2022]
Abstract
Insulin-like growth factor 2 (IGF2) is the major fetal growth hormone in mammals. We identify zinc finger protein 568 (ZFP568), a member of the rapidly evolving Kruppel-associated box-zinc finger protein (KRAB-ZFP) family linked primarily to silencing of endogenous retroelements, as a direct repressor of a placental-specific Igf2 transcript (designated Igf2-P0) in mice. Loss of Zfp568, which causes gastrulation failure, or mutation of the ZFP568-binding site at the Igf2-P0 promoter causes inappropriate Igf2-P0 activation. Deletion of Igf2 can completely rescue Zfp568 gastrulation phenotypes through late gestation. Our data highlight the exquisite selectivity with which members of the KRAB-ZFP family repress their targets and identify an additional layer of transcriptional control of a key growth factor regulating fetal and placental development.
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Affiliation(s)
- Peng Yang
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yixuan Wang
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.,Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Don Hoang
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Tinkham
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anamika Patel
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ming-An Sun
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gernot Wolf
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mairead Baker
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huan-Chieh Chien
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, Republic of China.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Kuan-Yu Nick Lai
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, Republic of China.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Che-Kun James Shen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan, Republic of China. .,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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12
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Wang KY, Chen CC, Tsai SF, Shen CKJ. Epigenetic Enhancement of the Post-replicative DNA Mismatch Repair of Mammalian Genomes by a Hemi- mCpG-Np95-Dnmt1 Axis. Sci Rep 2016; 6:37490. [PMID: 27886214 PMCID: PMC5122852 DOI: 10.1038/srep37490] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 10/26/2016] [Indexed: 01/02/2023] Open
Abstract
DNA methylation at C of CpG dyads (mCpG) in vertebrate genomes is essential for gene regulation, genome stability and development. We show in this study that proper functioning of post-replicative DNA mismatch repair (MMR) in mammalian cells relies on the presence of genomic mCpG, as well as on the maintenance DNA methyltransferase Dnmt1 independently of its catalytic activity. More importantly, high efficiency of mammalian MMR surveillance is achieved through a hemi-mCpG-Np95(Uhrf1)-Dnmt1 axis, in which the MMR surveillance complex(es) is recruited to post-replicative DNA by Dnmt1, requiring its interactions with MutSα, as well as with Np95 bound at the hemi-methylated CpG sites. Thus, efficiency of MMR surveillance over the mammalian genome in vivo is enhanced at the epigenetic level. This synergy endows vertebrate CpG methylation with a new biological significance and, consequently, an additional mechanism for the maintenance of vertebrate genome stability.
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Affiliation(s)
- Keh-Yang Wang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Chun-Chang Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | - Shih-Feng Tsai
- Genome Research Center, National Yang-Ming University, Taipei 11221, Taiwan.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan.,Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan
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13
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Majumder P, Chu JF, Chatterjee B, Swamy KBS, Shen CKJ. Co-regulation of mRNA translation by TDP-43 and Fragile X Syndrome protein FMRP. Acta Neuropathol 2016; 132:721-738. [PMID: 27518042 PMCID: PMC5073124 DOI: 10.1007/s00401-016-1603-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/28/2016] [Accepted: 07/28/2016] [Indexed: 01/15/2023]
Abstract
For proper mammalian brain development and functioning, the translation of many neuronal mRNAs needs to be repressed without neuronal activity stimulations. We have discovered that the expression of a subclass of neuronal proteins essential for neurodevelopment and neuron plasticity is co-regulated at the translational level by TDP-43 and the Fragile X Syndrome protein FMRP. Using molecular, cellular and imaging approaches, we show that these two RNA-binding proteins (RBP) co-repress the translation initiation of Rac1, Map1b and GluR1 mRNAs, and consequently the hippocampal spinogenesis. The co-repression occurs through binding of TDP-43 to mRNA(s) at specific UG/GU sequences and recruitment of the inhibitory CYFIP1-FMRP complex by its glycine-rich domain. This novel regulatory scenario could be utilized to silence a significant portion of around 160 common target mRNAs of the two RBPs. The study establishes a functional/physical partnership between FMRP and TDP-43 that mechanistically links several neurodevelopmental disorders and neurodegenerative diseases.
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14
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Chang CF, Lee YC, Lee KH, Lin HC, Chen CL, Shen CKJ, Huang CC. Therapeutic effect of berberine on TDP-43-related pathogenesis in FTLD and ALS. J Biomed Sci 2016; 23:72. [PMID: 27769241 PMCID: PMC5073438 DOI: 10.1186/s12929-016-0290-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/14/2016] [Indexed: 01/17/2023] Open
Abstract
Background In the central nervous system regions of the sporadic and familial FTLD and ALS patients, TDP-43 has been identified as the major component of UBIs inclusions which is abnormally hyperphosphorylated, ubiquitinated, and cleaved into C-terminal fragments to form detergent-insoluble aggregates. So far, the effective drugs for FTLD and ALS neurodegenerative diseases are yet to be developed. Autophagy has been demonstrated as the major metabolism route of the pathological TDP-43 inclusions, hence activation of autophagy is a potential therapeutic strategy for TDP-43 pathogenesis in FTLD and ALS. Berberine, a traditional herbal medicine, is an inhibitor of mTOR signal and an activator for autophagy. Berberine has been implicated in several kinds of diseases, including the neuronal-related pathogenesis, such as Parkinson’s, Huntington’s and Alzheimer’s diseases. However, the therapeutic effect of berberine on FTLD or ALS pathology has never been investigated. Results Here we studied the molecular mechanism of berberine in cell culture model with TDP-43 proteinopathies, and found that berberine is able to reverse the processing of insoluble TDP-43 aggregates formation through deregulation of mTOR/p70S6K signal and activation of autophagic degradation pathway. And inhibition of autophagy by specific autophagosome inhibitor, 3-MA, reverses the effect of berberine on reducing the accumulation of insoluble TDP-43 and aggregates formation. These results gave us the notion that inhibition of autophagy by 3-MA reverses the effect of berberine on TDP-43 pathogenesis, and activation of mTOR-regulated autophagy plays an important role in berberine-mediated therapeutic effect on TDP-43 proteinopathies. Conclusion We supported an important notion that the traditional herb berberine is a potential alternative therapy for TDP-43-related neuropathology. Here we demonstrated that berberine is able to reverse the processing of insoluble TDP-43 aggregates formation through deregulation of mTOR/p70S6K signal and activation of autophagic degradation pathway. mTOR-autophagy signals plays an important role in berberine-mediated autophagic clearance of TDP-43 aggregates. Exploring the detailed mechanism of berberine on TDP-43 proteinopathy provides a better understanding for the therapeutic development in FTLD and ALS.
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Affiliation(s)
- Cheng-Fu Chang
- Department of Neurosurgery, Taipei Medical University Hospital, Taipei, Taiwan.,Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yi-Chao Lee
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Kuen-Haur Lee
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Hui-Ching Lin
- Institute and Department of Physiology, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chia-Ling Chen
- Translational Research Center, Taipei Medical University, Taipei, Taiwan
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Chi-Chen Huang
- Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
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15
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Chiang CH, Grauffel C, Wu LS, Kuo PH, Doudeva LG, Lim C, Shen CKJ, Yuan HS. Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation. Sci Rep 2016; 6:21581. [PMID: 26883171 PMCID: PMC4756693 DOI: 10.1038/srep21581] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/25/2016] [Indexed: 12/12/2022] Open
Abstract
The RNA-binding protein TDP-43 forms intracellular inclusions in amyotrophic lateral sclerosis (ALS). While TDP-43 mutations have been identified in ALS patients, how these mutations are linked to ALS remains unclear. Here we examined the biophysical properties of six ALS-linked TDP-43 mutants and found that one of the mutants, D169G, had higher thermal stability than wild-type TDP-43 and that it was cleaved by caspase 3 more efficiently, producing increased levels of the C-terminal 35 kD fragments (TDP-35) in vitro and in neuroblastoma cells. The crystal structure of the TDP-43 RRM1 domain containing the D169G mutation in complex with DNA along with molecular dynamics simulations reveal that the D169G mutation induces a local conformational change in a β turn and increases the hydrophobic interactions in the RRM1 core, thus enhancing the thermal stability of the RRM1 domain. Our results provide the first crystal structure of TDP-43 containing a disease-linked D169G mutation and a disease-related mechanism showing that D169G mutant is more susceptible to proteolytic cleavage by caspase 3 into the pathogenic C-terminal 35-kD fragments due to its increased stability in the RRM1 domain. Modulation of TDP-43 stability and caspase cleavage efficiency could present an avenue for prevention and treatment of TDP-43-linked neurodegeneration.
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Affiliation(s)
- Chien-Hao Chiang
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin Chu, 30013, Taiwan
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Lien-Szu Wu
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Pan-Hsien Kuo
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | | | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | | | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
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16
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17
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Wang KY, Chen CC, Shen CKJ. Active DNA demethylation of the vertebrate genomes by DNA methyltransferases: deaminase, dehydroxymethylase or demethylase? Epigenomics 2015; 6:353-63. [PMID: 25111488 DOI: 10.2217/epi.14.21] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Vertebrate DNA methyltransferases (DNMTs) have been thought to primarily function to covalently add a methyl group to the 5-position of cytosine. However, recent discovery of the DNA demethylation and dehydroxymethylation activities of DNMTs in vitro suggest new routes to complete the dynamic cycle of DNA methylation-demethylation of the vertebrate genomes. The in vitro reaction conditions suggest that vertebrate DNMTs can switch from DNA methylases to DNA dehydroxymethylases under oxidative stress and to DNA demethylases in the presence of calcium ion under nonreducing conditions. These environmental parameters provide clues regarding the choices in vivo of DNMT activities utilized in different physiological systems. In particular, the nature of these parameters suggest that the DNA demethylation and dehydroxymethylation activities of the vertebrate DNMTs play essential roles in multiple biological processes including early embryo development, regulation of neuronal plasticity, tumorigenesis and hormone-regulated transcription.
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Affiliation(s)
- Keh-Yang Wang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
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18
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Affiliation(s)
- I-Fang Wang
- Institute of Life Science; National Defense Medical Center; Taipei, Taiwan
- Institute of Molecular Biology; Academia Sinica; Taipei, Taiwan
- Institute of Clinical Medicine; National Cheng Kung University; Tainan, Taiwan
| | - Kuen-Jer Tsai
- Institute of Clinical Medicine; National Cheng Kung University; Tainan, Taiwan
| | - Che-Kun James Shen
- Institute of Life Science; National Defense Medical Center; Taipei, Taiwan
- Institute of Molecular Biology; Academia Sinica; Taipei, Taiwan
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19
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Liu KY, Shyu YC, Barbaro BA, Lin YT, Chern Y, Thompson LM, James Shen CK, Marsh JL. Disruption of the nuclear membrane by perinuclear inclusions of mutant huntingtin causes cell-cycle re-entry and striatal cell death in mouse and cell models of Huntington's disease. Hum Mol Genet 2014; 24:1602-16. [PMID: 25398943 DOI: 10.1093/hmg/ddu574] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Accumulation of N-terminal fragments of mutant huntingtin (mHTT) in the cytoplasm, nuclei and axons of neurons is a hallmark of Huntington's disease (HD), although how these fragments negatively impact neurons remains unclear. We followed the distribution of mHTT in the striata of transgenic R6/2-J2 HD mice as their motor function declined. The fraction of cells with diffuse, perinuclear or intranuclear mHTT changed in parallel with decreasing motor function. In transgenic mice, medium spiny neurons (MSNs) that exhibited perinuclear inclusions expressed cell-cycle markers typically not seen in the striata of normal mice, and these cells are preferentially lost as disease progresses. Electron microscopy reveals that perinuclear inclusions disrupt the nuclear envelope. The progression of perinuclear inclusions being accompanied by cell-cycle activation and culminating in cell death was also observed in 1° cortical neurons. These observations provide a strong correlation between the subcellular location of mHTT, disruption of the nucleus, re-entry into the cell-cycle and eventual neuronal death. They also highlight the fact that the subcellular distribution of mHTT is highly dynamic such that the distribution of mHTT observed depends greatly on the stage of the disease being examined.
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Affiliation(s)
- Kuan-Yu Liu
- Department of Life Sciences and Institute of Genome Sciences and Institute of Molecular Biology and
| | - Yu-Chiau Shyu
- VYM Genome Research Center, National Yang-Ming University, Taipei 112, Taiwan, Institute of Molecular Biology and
| | - Brett A Barbaro
- Developmental Biology Center, Department of Developmental and Cell Biology
| | | | - Yijuang Chern
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
| | - Leslie Michels Thompson
- Department of Psychiatry and Human Behavior, Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Che-Kun James Shen
- Department of Life Sciences and Institute of Genome Sciences and Institute of Molecular Biology and
| | - J Lawrence Marsh
- Developmental Biology Center, Department of Developmental and Cell Biology
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20
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Huang CC, Bose JK, Majumder P, Lee KH, Huang JTJ, Huang JK, Shen CKJ. Metabolism and mis-metabolism of the neuropathological signature protein TDP-43. J Cell Sci 2014; 127:3024-38. [PMID: 24860144 DOI: 10.1242/jcs.136150] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TDP-43 (also known as TARDBP) is a pathological signature protein of neurodegenerative diseases, with TDP-43 proteinopathies including frontotemporal lobar degeneration (FTLD)-TDP and amyotrophic lateral sclerosis (ALS)-TDP. These TDP-43 proteinopathies are characterized by cytoplasmic insoluble TDP-43-positive aggregates in the diseased cells, the formation of which requires the seeding of TDP-25 fragment generated by caspase cleavage of TDP-43. We have investigated the metabolism and mis-metabolism of TDP-43 in cultured cells and found that endogenous and exogenously overexpressed TDP-43 is degraded not only by the ubiquitin proteasome system (UPS) and macroautophagy, but also by the chaperone-mediated autophagy (CMA) mediated through an interaction between Hsc70 (also known as HSPA8) and ubiquitylated TDP-43. Furthermore, proteolytic cleavage of TDP-43 by caspase(s) is a necessary intermediate step for degradation of the majority of the TDP-43 protein, with the TDP-25 and TDP-35 fragments being the main substrates. Finally, we have determined the threshold level of the TDP-25 fragment that is necessary for formation of the cytosolic TDP-43-positive aggregates in cells containing the full-length TDP-43 at an elevated level close to that found in patients with TDP-43 proteinopathies. A comprehensive model of the metabolism and mis-metabolism of TDP-43 in relation to these findings is presented.
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Affiliation(s)
- Chi-Chen Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology/Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, Taiwan
| | | | - Pritha Majumder
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Kuen-Haur Lee
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | | | - Jeffrey K Huang
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan Graduate Institute of Neural Regenerative Medicine, College of Medical Science and Technology/Center for Neurotrauma and Neuroregeneration, Taipei Medical University, Taipei, Taiwan
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21
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Shyu YC, Lee TL, Chen X, Hsu PH, Wen SC, Liaw YW, Lu CH, Hsu PY, Lu MJ, Hwang J, Tsai MD, Hwang MJ, Chen JR, Shen CKJ. Tight regulation of a timed nuclear import wave of EKLF by PKCθ and FOE during Pro-E to Baso-E transition. Dev Cell 2014; 28:409-22. [PMID: 24576425 DOI: 10.1016/j.devcel.2014.01.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 11/24/2013] [Accepted: 01/13/2014] [Indexed: 11/28/2022]
Abstract
Erythropoiesis is a highly regulated process during which BFU-E are differentiated into RBCs through CFU-E, Pro-E, PolyCh-E, OrthoCh-E, and reticulocyte stages. Uniquely, most erythroid-specific genes are activated during the Pro-E to Baso-E transition. We show that a wave of nuclear import of the erythroid-specific transcription factor EKLF occurs during the Pro-E to Baso-E transition. We further demonstrate that this wave results from a series of finely tuned events, including timed activation of PKCθ, phosphorylation of EKLF at S68 by P-PKCθ(S676), and sumoylation of EKLF at K74. The latter EKLF modifications modulate its interactions with a cytoplasmic ankyrin-repeat-protein FOE and importinβ1, respectively. The role of FOE in the control of EKLF nuclear import is further supported by analysis of the subcellular distribution patterns of EKLF in FOE-knockout mice. This study reveals the regulatory mechanisms of the nuclear import of EKLF, which may also be utilized in the nuclear import of other factors.
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Affiliation(s)
- Yu-Chiau Shyu
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Beitou, Taipei 112, Taiwan, ROC; Department of Education and Research, Taipei City Hospital, Da'an, Taipei 103, Taiwan, ROC; Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC.
| | - Tung-Liang Lee
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
| | - Xin Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
| | - Pang-Hung Hsu
- The Genomics Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
| | - Shau-Ching Wen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
| | - Yi-Wei Liaw
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
| | - Chi-Huan Lu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
| | - Po-Yen Hsu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
| | - Mu-Jie Lu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
| | - JauLang Hwang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
| | - Ming-Jing Hwang
- Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
| | - Jim-Ray Chen
- Department of Pathology, Keelung Chang Gung Memorial Hospital, Anle, Keelung 204, Taiwan, ROC; College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan 259, Taiwan, ROC
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan 115, ROC.
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Chien Y, Cheng WC, Wu MR, Jiang ST, Shen CKJ, Chung BC. Misregulated Progesterone Secretion and Impaired Pregnancy in Cyp11a1 Transgenic Mice1. Biol Reprod 2013; 89:91. [DOI: 10.1095/biolreprod.113.110833] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Wu LS, Cheng WC, Shen CKJ. Similar dose-dependence of motor neuron cell death caused by wild type human TDP-43 and mutants with ALS-associated amino acid substitutions. J Biomed Sci 2013; 20:33. [PMID: 23721326 PMCID: PMC3684520 DOI: 10.1186/1423-0127-20-33] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 05/03/2013] [Indexed: 12/11/2022] Open
Abstract
Background TDP-43, a multi-functional DNA/ RNA-binding protein encoded by the TARDBP gene, has emerged as a major patho-signature factor of the ubiquitinated intracellular inclusions (UBIs) in the diseased cells of a range of neurodegenerative diseases. Mutations in at least 9 different genes including TARDBP have been identified in ALS with TDP-43 (+)-UBIs. Thus far, the pathogenic role(s) of the more than 30 ALS-associated mutations in the TARDBP gene has not been well defined. Results By transient DNA transfection studies, we show that exogenously expressed human TDP-43 (hTDP-43), either wild type (WT) or 2 different ALS mutant (MT) forms, could cause significantly higher apoptotic death rate of a mouse spinal motor neuron-like cell line (NSC34) than other types of cells, e.g. mouse neuronal Neuro2a and human fibroblast HEK293T cells. Furthermore, at the same plasmid DNA dose(s) used for transfection, the percentages of NSC34 cell death caused by the 2 exogenously expressed hTDP-43 mutants are all higher than that caused by the WT hTDP-43. Significantly, the above observations are correlated with higher steady-state levels of the mutant hTDP-43 proteins as well as their stabilities than the WT. Conclusions Based on these data and previous transgenic TDP-43 studies in animals or cell cultures, we suggest that one major common consequence of the different ALS-associated TDP-43 mutations is the stabilization of the hTDP-43 polypeptide. The resulting elevation of the steady state level of hTDP-43 in combination with the relatively low tolerance of the spinal motor neurons to the increased amount of hTDP-43 lead to the neurodegeneration and pathogenesis of ALS, and of diseases with TDP-43 proteinopathies in general.
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Affiliation(s)
- Lien-Szu Wu
- Institute of Molecular Medicine, National Taiwan University, Taipei, Taiwan
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Chen CC, Wang KY, Shen CKJ. DNA 5-methylcytosine demethylation activities of the mammalian DNA methyltransferases. J Biol Chem 2013; 288:9084-91. [PMID: 23393137 PMCID: PMC3610981 DOI: 10.1074/jbc.m112.445585] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 02/06/2013] [Indexed: 01/19/2023] Open
Abstract
Methylation at the 5-position of DNA cytosine on the vertebrate genomes is accomplished by the combined catalytic actions of three DNA methyltransferases (DNMTs), the de novo enzymes DNMT3A and DNMT3B and the maintenance enzyme DNMT1. Although several metabolic routes have been suggested for demethylation of the vertebrate DNA, whether active DNA demethylase(s) exist has remained elusive. Surprisingly, we have found that the mammalian DNMTs, and likely the vertebrates DNMTs in general, can also act as Ca(2+) ion- and redox state-dependent active DNA demethylases. This finding suggests new directions for reinvestigation of the structures and functions of these DNMTs, in particular their roles in Ca(2+) ion-dependent biological processes, including the genome-wide/local DNA demethylation during early embryogenesis, cell differentiation, neuronal activity-regulated gene expression, and carcinogenesis.
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Affiliation(s)
- Chun-Chang Chen
- From the Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112 and
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Keh-Yang Wang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Che-Kun James Shen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan
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Wang IF, Tsai KJ, Shen CKJ. Autophagy activation ameliorates neuronal pathogenesis of FTLD-U mice: a new light for treatment of TARDBP/TDP-43 proteinopathies. Autophagy 2012; 9:239-40. [PMID: 23108236 DOI: 10.4161/auto.22526] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The administration of rapamycin, an MTOR-dependent autophagy activator, for the treatment of neurodegenerative diseases has been tested in several animal models. Thus, whether autophagy activation would lead to the clearance of abnormal accumulation of aggregated proteins in neurodegenerative diseases is worthy of exploration. We have recently shown that rapamycin administration at the early pathological stage of a mouse model with frontotemporal lobar dementia (FTLD-U) characterized with cytoplasmic TARDBP/TDP-43(+)/ubiquitin(+) inclusions (UBIs) in the diseased neurons could rescue the learning/memory deficiency and the abnormal motor function disorder of the mice. This was accompanied by a decreased level of CASP3/caspase-3 and a reduction of the neuronal loss in the mouse forehead. Moreover, autophagy activation at a late pathological stage also could improve motor function, which was accompanied by a reduction of the TARDBP(+) UBIs. This study has set the principal for therapy of neurodegenerative diseases with the TARDBP protein, i.e., amyotrophic lateral sclerosis (ALS)-TDP and FTLD-TDP43, with the use of autophagy activators.
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Affiliation(s)
- I-Fang Wang
- Institute of Life Science, National Defense Medical Center, Taipei, Taiwan
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26
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Chen CC, Wang KY, Shen CKJ. The mammalian de novo DNA methyltransferases DNMT3A and DNMT3B are also DNA 5-hydroxymethylcytosine dehydroxymethylases. J Biol Chem 2012; 287:33116-21. [PMID: 22898819 PMCID: PMC3460417 DOI: 10.1074/jbc.c112.406975] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 08/15/2012] [Indexed: 12/14/2022] Open
Abstract
For cytosine (C) demethylation of vertebrate DNA, it is known that the TET proteins could convert 5-methyl C (5-mC) to 5-hydroxymethyl C (5-hmC). However, DNA dehydroxymethylase(s), or enzymes able to directly convert 5-hmC to C, have been elusive. We present in vitro evidence that the mammalian de novo DNA methyltransferases DNMT3A and DNMT3B, but not the maintenance enzyme DNMT1, are also redox-dependent DNA dehydroxymethylases. Significantly, intactness of the C methylation catalytic sites of these de novo enzymes is also required for their 5-hmC dehydroxymethylation activity. That DNMT3A and DNMT3B function bidirectionally both as DNA methyltransferases and as dehydroxymethylases raises intriguing and new questions regarding the structural and functional aspects of these enzymes and their regulatory roles in the dynamic modifications of the vertebrate genomes during development, carcinogenesis, and gene regulation.
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Affiliation(s)
- Chun-Chang Chen
- From the Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan and
- the Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Keh-Yang Wang
- From the Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan and
| | - Che-Kun James Shen
- From the Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan and
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27
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Abstract
Nuclear factor erythroid-derived 2 (NF-E2), a heterodimer composed of p45 and p18, is a transcriptional activator in hematopoietic progenitors. The transcriptional activity of NF-E2 is not only upregulated by SUMOylation but also stimulated by the cAMP-dependent protein kinase A (PKA). However, the relationship between SUMOylation and phosphorylation in the activation of NF-E2 is unclear. In the present studies, we have demonstrated that PKA enhances NF-E2 SUMOylation in an in vitro system using purified proteins, suggesting a possible mechanism for PKA-dependent activation of the NF-E2 transcription factor through SUMOylation.
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Affiliation(s)
- Yee-Fun Su
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Yu-Chiau Shyu
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan
- Department of Education and Research, Taipei City Hospital, Taipei, Taiwan
| | | | - Jaulang Hwang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
- Department of Biochemistry, Medical School, Taipei Medical University, Taipei, Taiwan
- * E-mail:
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28
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Majumder P, Chen YT, Bose JK, Wu CC, Cheng WC, Cheng SJ, Fang YH, Chen YL, Tsai KJ, Lien CC, Shen CKJ. TDP-43 regulates the mammalian spinogenesis through translational repression of Rac1. Acta Neuropathol 2012; 124:231-45. [PMID: 22760527 DOI: 10.1007/s00401-012-1006-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 06/18/2012] [Accepted: 06/19/2012] [Indexed: 12/13/2022]
Abstract
Impairment of learning and memory is a significant pathological feature of many neurodegenerative diseases including FTLD-TDP. Appropriate regulation and fine tuning of spinogenesis of the dendrites, which is an integral part of the learning/memory program of the mammalian brain, are essential for the normal function of the hippocampal neurons. TDP-43 is a nucleic acid-binding protein implicated in multi-cellular functions and in the pathogenesis of a range of neurodegenerative diseases including FTLD-TDP and ALS. We have combined the use of single-cell dye injection, shRNA knockdown, plasmid rescue, immunofluorescence staining, Western blot analysis and patch clamp electrophysiological measurement of primary mouse hippocampal neurons in culture to study the functional role of TDP-43 in mammalian spinogenesis. We found that depletion of TDP-43 leads to an increase in the number of protrusions/spines as well as the percentage of matured spines among the protrusions. Significantly, the knockdown of TDP-43 also increases the level of Rac1 and its activated form GTP-Rac1, a known positive regulator of spinogenesis. Clustering of the AMPA receptors on the dendritic surface and neuronal firing are also induced by depletion of TDP-43. Furthermore, use of an inhibitor of Rac1 activation negatively regulated spinogenesis of control hippocampal neurons as well as TDP-43-depleted hippocampal neurons. Mechanistically, RT-PCR assay and cycloheximide chase experiments have indicated that increases in Rac1 protein upon TDP-43 depletion is regulated at the translational level. These data together establish that TDP-43 is an upstream regulator of spinogenesis in part through its action on the Rac1 → GTP-Rac1 → AMPAR pathway. This study provides the first evidence connecting TDP-43 with the GTP-Rac1 → AMPAR regulatory pathway of spinogenesis. It establishes that mis-metabolism of TDP-43, as occurs in neurodegenerative diseases with TDP-43 proteinopathies, e.g., FTLD-TDP, would alter its homeostatic cellular concentration, thus leading to impairment of hippocampal plasticity.
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Affiliation(s)
- Pritha Majumder
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, 115, Taiwan
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29
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Tsai KJ, Yang CH, Fang YH, Cho KH, Chien WL, Wang WT, Wu TW, Lin CP, Fu WM, Shen CKJ. Elevated expression of TDP-43 in the forebrain of mice is sufficient to cause neurological and pathological phenotypes mimicking FTLD-U. ACTA ACUST UNITED AC 2010; 207:1661-73. [PMID: 20660618 PMCID: PMC2916125 DOI: 10.1084/jem.20092164] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
TDP-43 is a multifunctional DNA/RNA-binding factor that has been implicated in the regulation of neuronal plasticity. TDP-43 has also been identified as the major constituent of the neuronal cytoplasmic inclusions (NCIs) that are characteristic of a range of neurodegenerative diseases, including the frontotemporal lobar degeneration with ubiquitin(+) inclusions (FTLD-U) and amyotrophic lateral sclerosis (ALS). We have generated a FTLD-U mouse model (CaMKII-TDP-43 Tg) in which TDP-43 is transgenically overexpressed in the forebrain resulting in phenotypic characteristics mimicking those of FTLD-U. In particular, the transgenic (Tg) mice exhibit impaired learning/memory, progressive motor dysfunction, and hippocampal atrophy. The cognitive and motor impairments are accompanied by reduced levels of the neuronal regulators phospho-extracellular signal-regulated kinase and phosphorylated cAMP response element-binding protein and increased levels of gliosis in the brains of the Tg mice. Moreover, cells with TDP-43(+), ubiquitin(+) NCIs and TDP-43-deleted nuclei appear in the Tg mouse brains in an age-dependent manner. Our data provide direct evidence that increased levels of TDP-43 protein in the forebrain is sufficient to lead to the formation of TDP-43(+), ubiquitin(+) NCIs and neurodegeneration. This FTLD-U mouse model should be valuable for the mechanistic analysis of the role of TDP-43 in the pathogenesis of FTLD-U and for the design of effective therapeutic approaches of the disease.
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Affiliation(s)
- Kuen-Jer Tsai
- Institute of Clinical Medicine, National Cheng Kung University, Tainan 704, Taiwan
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30
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Abstract
TDP-43 is a pathogenic protein: its normal function in binding to UG-rich RNA is related to cystic fibrosis, and inclusion of its C-terminal fragments in brain cells is directly linked to frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Here we report the 1.65 Å crystal structure of the C-terminal RRM2 domain of TDP-43 in complex with a single-stranded DNA. We show that TDP-43 is a dimeric protein with two RRM domains, both involved in DNA and RNA binding. The crystal structure reveals the basis of TDP-43's TG/UG preference in nucleic acids binding. It also reveals that RRM2 domain has an atypical RRM-fold with an additional β-strand involved in making protein–protein interactions. This self association of RRM2 domains produced thermal-stable RRM2 assemblies with a melting point greater than 85°C as monitored by circular dichroism at physiological conditions. These studies thus characterize the recognition between TDP-43 and nucleic acids and the mode of RRM2 self association, and provide molecular models for understanding the role of TDP-43 in cystic fibrosis and the neurodegenerative diseases related to TDP-43 proteinopathy.
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Affiliation(s)
- Pan-Hsien Kuo
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Taipei, Taiwan, ROC
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Abstract
Most of the current clinical treatments for Alzheimer's disease (AD) are largely symptomatic and can have serious side effects. We have tested the feasibility of using the granulocyte colony-stimulating factor (G-CSF), which is known to mobilize hematopoietic stem cells (HSCs) from the bone marrow into the peripheral blood, as a therapeutic agent for AD. Subcutaneous administration of G-CSF into two different β-amyloid (Aβ)–induced AD mouse models substantially rescued their cognitive/memory functions. The rescue was accompanied by the accumulation of 5-bromo-2′deoxyuridine–positive HSCs, as well as local neurogenesis surrounding the Aβ aggregates. Furthermore, the level of acetylcholine in the brains of Tg2576 mice was considerably enhanced upon G-CSF treatment. We suggest that G-CSF, a drug already extensively used for treating chemotherapy-induced neutropenia, should be pursued as a novel, noninvasive therapeutic agent for the treatment of AD.
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Affiliation(s)
- Kuen-Jer Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan, Republic of China
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Shyu YC, Lee TL, Wen SC, Chen H, Hsiao WY, Chen X, Hwang J, Shen CKJ. Subcellular transport of EKLF and switch-on of murine adult beta maj globin gene transcription. Mol Cell Biol 2007; 27:2309-23. [PMID: 17242208 PMCID: PMC1820495 DOI: 10.1128/mcb.01875-06] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Erythroid Krüppel-like factor (EKLF) is an essential transcription factor for mammalian beta-like globin gene switching, and it specifically activates transcription of the adult beta globin gene through binding of its zinc fingers to the promoter. It has been a puzzle that in the mouse, despite its expression throughout the erythroid development, EKLF activates the adult beta(maj) globin promoter only in erythroid cells beyond the stage of embryonic day 10.5 (E10.5) but not before. We show here that expression of the mouse beta(maj) globin gene in the aorta-gonad-mesonephros region of E10.5 embryos and in the E14.5 fetal liver is accompanied by predominantly nuclear localization of EKLF. In contrast, EKLF is mainly cytoplasmic in the erythroid cells of E9.5 blood islands in which beta(maj) is silenced. Remarkably, in a cultured mouse adult erythroleukemic (MEL) cell line, the activation of the beta(maj) globin gene by dimethyl sulfoxide (DMSO) or hexamethylene-bis-acetamide (HMBA) induction is also paralleled by a shift of the subcellular location of EKLF from the cytoplasm to the nucleus. Blockage of the nuclear import of EKLF in DMSO-induced MEL cells with a nuclear export inhibitor repressed the transcription of the beta(maj) globin gene. Transient transfection experiments further indicated that the full-sequence context of EKLF was required for the regulation of its subcellular locations in MEL cells during DMSO induction. Finally, in both the E14.5 fetal liver cells and induced MEL cells, the beta-like globin locus is colocalized the PML oncogene domain nuclear body, and concentrated with EKLF, RNA polymerase II, and the splicing factor SC35. These data together provide the first evidence that developmental stage- and differentiation state-specific regulation of the nuclear transport of EKLF might be one of the steps necessary for the switch-on of the mammalian adult beta globin gene transcription.
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Affiliation(s)
- Yu-Chiau Shyu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, Republic of China
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Wang JW, Jiang YN, Huang CY, Huang PY, Huang MC, Cheng WTK, Shen CKJ, Ju YT. Proliferin enhances microvilli formation and cell growth of neuroblastoma cells. Neurosci Res 2006; 56:80-90. [PMID: 16876275 DOI: 10.1016/j.neures.2006.05.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 05/15/2006] [Accepted: 05/29/2006] [Indexed: 11/19/2022]
Abstract
Proliferins (also termed mitogen-regulated proteins; MRP/PLFs) belong to the prolactin gene family. Mrp/Plfs are involved in angiogenesis of the uterus and placenta and maximally expressed during midgestation and decline through the remainder of the gestation period in mouse placenta. The tissue expressions of Mrp/Plfs are mainly documented in placenta, hair follicles of skin and in wound healing. In this report, we demonstrate that Plf1, Plf1 minus exon3, Plf2 and Mrp3 but not Mrp4 are expressed in mouse whole brain by diagnostic RT-PCR and Western blotting. The expression levels of Mrp/Plf mRNAs in mouse brains were low during the neonatal period, but higher in embryonic and adult stages, indicating Mrp/Plfs expression profiles are different in mouse brain and placenta. Interestingly, endogenous Mrp/Plfs were detected using immunostaining both in mouse brain sections and the neuroblastoma cell line, Neuro-2a cells. The function of PLF1 was explored by expressing exogenous PLF1 in Neuro-2a cells. This resulted in increased microvilli. Neuro-2a cells with stable expression of PLF1 had increased proliferation compared with normal and stable expressing EGFP cells when cell reached saturation density. Together these data, strongly suggest that MRP/PLFs mediate microvilli formation and contribute to cell proliferation of neuroblastoma cells.
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Affiliation(s)
- Jyhi-Wai Wang
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan, ROC
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Shyu YC, Wen SC, Lee TL, Chen X, Hsu CT, Chen H, Chen RL, Hwang JL, Shen CKJ. Chromatin-binding in vivo of the erythroid kruppel-like factor, EKLF, in the murine globin loci. Cell Res 2006; 16:347-55. [PMID: 16617330 DOI: 10.1038/sj.cr.7310045] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
EKLF is an erythroid-specific, zinc finger-containing transcription factor essential for the activation of the mammalian beta globin gene in erythroid cells of definitive lineage. We have prepared a polyclonal anti-mouse EKLF antibody suitable for Western blotting and immunoprecipitation (IP) qualities, and used it to define the expression patterns of the EKLF protein during mouse erythroid development. We have also used this antibody for the chromatin-immunoprecipitation (ChIP) assay. EKLF was found to bind in vivo at both the mouse beta-major-globin promoter and the HS2 site of beta-LCR in the mouse erythroleukemia cells (MEL) in a DMSO-inducible manner. The DMSO-induced bindings of EKLF as well as three other proteins, namely, RNA polymerase II, acetylated histone H3, and methylated histone H3, were not abolished but significantly lowered in CB3, a MEL-derived cell line with null-expression of p45/NF-E2, an erythroid-enriched factor needed for activation of the mammalian globin loci. Interestingly, binding of EKLF in vivo was also detected in the mouse alpha-like globin locus, at the adult alpha globin promoter and its far upstream regulatory element alpha-MRE (HS26). This study provides direct evidence for EKLF-binding in vivo at the major regulatory elements of the mouse beta-like globin gene clusters the data also have interesting implications with respect to the role of EKLF-chromatin interaction in mammalian globin gene regulation.
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Affiliation(s)
- Yu-Chiau Shyu
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115
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Gavva NR, Wen SC, Daftari P, Moniwa M, Yang WM, Yang-Feng LPT, Seto E, Davie JR, Shen CKJ. NAPP2, a peroxisomal membrane protein, is also a transcriptional corepressor. Genomics 2002; 79:423-31. [PMID: 11863372 DOI: 10.1006/geno.2002.6714] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nuclear factor-erythroid number 2 (NF-E2) is a positive regulatory, DNA binding transcription factor for gene expression in erythroid and megakaryocytic cells. To further understand the mechanisms of NF-E2 function, we used expression cloning to identify coregulators interacting with the erythroid-specific subunit of NF-E2, p45. We have isolated a protein, NAPP2, which contains an aspartic-acid- and glutamic-acid-rich region and a nuclear localization signal. The gene encoding NAPP2, PEX14, is located on chromosome 1p36 and is ubiquitously expressed. The domains of interaction in vitro and in vivo between p45 and NAPP2 were mapped by a yeast two-hybrid system and cotransfection experiments. In mammalian cell culture, ectopically expressed NAPP2 inhibited p45-directed transcriptional activation. Furthermore, NAPP2 functions as a corepressor and interacts specifically with histone deacetylase l (HDAC1), but not HDAC2 or HDAC3. NAPP2 is thus potentially a negative coregulator of NF-E2. NAPP2 is identical to PEX14, an integral membrane protein essential for protein docking onto the peroxisomes. These studies have identified a novel, bifunctional protein capable of acting as a transcriptional corepressor and a polypeptide transport modulator. They also suggest that NF-E2 may function both positively and negatively in the transcription regulation of specific erythroid and megakaryocytic genes.
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Affiliation(s)
- Narender R Gavva
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
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Gomez-Pedrozo M, Mohandas T, Sparkes R, Shaw JP, Hess JF, Ayres T, Shen CKJ. Evolution of human cytoplasmic actin gene sequences: chromosome mapping and structural characterizations of three cytoplasmic actin-like pseudogenes including one on the Y chromosome. J Hum Evol 1987. [DOI: 10.1016/0047-2484(87)90077-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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