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Mooli RGR, Zhu B, Khan SR, Nagati V, Michealraj KA, Jurczak MJ, Ramakrishnan SK. Epigenetically active chromatin in neonatal iWAT reveals GABPα as a potential regulator of beige adipogenesis. Front Endocrinol (Lausanne) 2024; 15:1385811. [PMID: 38765953 PMCID: PMC11099907 DOI: 10.3389/fendo.2024.1385811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/12/2024] [Indexed: 05/22/2024] Open
Abstract
Background Thermogenic beige adipocytes, which dissipate energy as heat, are found in neonates and adults. Recent studies show that neonatal beige adipocytes are highly plastic and contribute to >50% of beige adipocytes in adults. Neonatal beige adipocytes are distinct from recruited beige adipocytes in that they develop independently of temperature and sympathetic innervation through poorly defined mechanisms. Methods We characterized the neonatal beige adipocytes in the inguinal white adipose tissue (iWAT) of C57BL6 postnatal day 3 and 20 mice (P3 and P20) by imaging, genome-wide RNA-seq analysis, ChIP-seq analysis, qRT-PCR validation, and biochemical assays. Results We found an increase in acetylated histone 3 lysine 27 (H3K27ac) on the promoter and enhancer regions of beige-specific gene UCP1 in iWAT of P20 mice. Furthermore, H3K27ac ChIP-seq analysis in the iWAT of P3 and P20 mice revealed strong H3K27ac signals at beige adipocyte-associated genes in the iWAT of P20 mice. The integration of H3K27ac ChIP-seq and RNA-seq analysis in the iWAT of P20 mice reveal epigenetically active signatures of beige adipocytes, including oxidative phosphorylation and mitochondrial metabolism. We identify the enrichment of GA-binding protein alpha (GABPα) binding regions in the epigenetically active chromatin regions of the P20 iWAT, particularly on beige genes, and demonstrate that GABPα is required for beige adipocyte differentiation. Moreover, transcriptomic analysis and glucose oxidation assays revealed increased glycolytic activity in the neonatal iWAT from P20. Conclusions Our findings demonstrate that epigenetic mechanisms regulate the development of peri-weaning beige adipocytes via GABPα. Further studies to better understand the upstream mechanisms that regulate epigenetic activation of GABPα and characterization of the metabolic identity of neonatal beige adipocytes will help us harness their therapeutic potential in metabolic diseases.
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Affiliation(s)
- Raja Gopal Reddy Mooli
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, PA, United States
| | - Bokai Zhu
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, PA, United States
- Pittsburgh Liver Research Centre, University of Pittsburgh, Pittsburgh, PA, United States
- Aging Institute of University of Pittsburgh Medical Center (UPMC), University of Pittsburgh, Pittsburgh, PA, United States
| | - Saifur R. Khan
- Division of Cardiology, University of Pittsburgh, Pittsburgh, PA, United States
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, United States
- Pittsburgh VA Medical Centre, Pittsburgh, PA, United States
- Center for Immunometabolism, University of Pittsburgh, Pittsburgh, PA, United States
| | - Veerababu Nagati
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, PA, United States
| | | | - Michael J. Jurczak
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sadeesh K. Ramakrishnan
- Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, PA, United States
- Pittsburgh Liver Research Centre, University of Pittsburgh, Pittsburgh, PA, United States
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Sun T, Song C, Zhao G, Feng S, Wei J, Zhang L, Liu X, Li Z, Zhang H. HOMER3 promotes non-small cell lung cancer growth and metastasis primarily through GABPB1-mediated mitochondrial metabolism. Cell Death Dis 2023; 14:814. [PMID: 38081871 PMCID: PMC10713516 DOI: 10.1038/s41419-023-06335-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023]
Abstract
Cancer metabolism has emerged as a major target for cancer therapy, while the state of mitochondrial drugs has remained largely unexplored, partly due to an inadequate understanding of various mitochondrial functions in tumor contexts. Here, we report that HOMER3 is highly expressed in non-small cell lung cancer (NSCLC) and is closely correlated with poor prognosis. Lung cancer cells with low levels of HOMER3 are found to show significant mitochondrial dysfunction, thereby suppressing their proliferation and metastasis in vivo and in vitro. At the mechanistic level, we demonstrate that HOMER3 and platelet-activating factor acetylhydrolase 1b catalytic subunit 3 cooperate to upregulate the level of GA-binding protein subunit beta-1 (GABPB1), a key transcription factor involved in mitochondrial biogenesis, to control mitochondrial inner membrane genes and mitochondrial function. Concurrently, low levels of HOMER3 and its downstream target GABPB1 led to mitochondrial dysfunction and decreased proliferation and invasive activity of lung cancer cells, which raises the possibility that targeting mitochondrial synthesis is an important and promising therapeutic approach for NSCLC.
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Affiliation(s)
- Teng Sun
- Thoracic Surgery Laboratory, Xuzhou Medical University, Xuzhou, Jiangsu, 221006, China
- Department of Thoracic Surgery, Affiliated Hospital of Xuzhou Medical University, 99 West Huaihai Road, Xuzhou, 221006, Jiangsu, China
| | - Chao Song
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Guoqing Zhao
- Thoracic Surgery Laboratory, Xuzhou Medical University, Xuzhou, Jiangsu, 221006, China
| | - Shoujie Feng
- Department of Thoracic Surgery, Affiliated Hospital of Xuzhou Medical University, 99 West Huaihai Road, Xuzhou, 221006, Jiangsu, China
| | - Jianhao Wei
- Thoracic Surgery Laboratory, Xuzhou Medical University, Xuzhou, Jiangsu, 221006, China
| | - Lixia Zhang
- Thoracic Surgery Laboratory, Xuzhou Medical University, Xuzhou, Jiangsu, 221006, China
| | - Xiangming Liu
- Thoracic Surgery Laboratory, Xuzhou Medical University, Xuzhou, Jiangsu, 221006, China
| | - Zhuoqun Li
- Thoracic Surgery Laboratory, Xuzhou Medical University, Xuzhou, Jiangsu, 221006, China
| | - Hao Zhang
- Thoracic Surgery Laboratory, Xuzhou Medical University, Xuzhou, Jiangsu, 221006, China.
- Department of Thoracic Surgery, Affiliated Hospital of Xuzhou Medical University, 99 West Huaihai Road, Xuzhou, 221006, Jiangsu, China.
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McKelvey BA, Gilpatrick T, Wang Y, Timp W, Umbricht CB, Zeiger MA. Characterization of Allele-Specific Regulation of Telomerase Reverse Transcriptase in Promoter Mutant Thyroid Cancer Cell Lines. Thyroid 2020; 30:1470-1481. [PMID: 32228178 PMCID: PMC7583328 DOI: 10.1089/thy.2020.0055] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background: Telomerase reverse transcriptase (TERT) promoter mutations play a role in carcinogenesis and are found in both tumors and cancer cell lines. TERT promoter methylation, transcription factor binding, chromatin remodeling, and alternative splicing are also known to play an integral role in TERT regulation. Methods: Using nanopore Cas9 targeted sequencing, we characterized allele-specific methylation in thyroid cancer cell lines heterozygous for the TERT promoter mutation. Furthermore, using chromatin immunoprecipitation followed by Sanger sequencing, we probed allele-specific binding of the transcription factors GABPA (GA binding protein transcription factor subunit alpha) and MYC, as well as the chromatin marks H3K4me3 and H3K27me3. Finally, using coding single nucleotide polymorphisms and the long-read sequencing, we examined complementary DNA for monoallelic expression (MAE). Results: We found the mutant TERT promoter allele to be significantly less methylated than wild type, while more methylated in the gene body in heterozygous TERT mutant cell lines. We demonstrated that the transcriptional activators GABPA and MYC bind only to the mutant TERT allele. In addition, the activating and repressive chromatin marks H3K4me3 and H3K27me3, respectively, bind mutant and wild-type alleles exclusively. Finally, in heterozygous mutant cell lines, TERT exhibits MAE from the mutant allele only. Conclusions: In summary, by employing new long-read sequencing methods, we were able to definitively demonstrate allele-specific DNA methylation, histone modifications, transcription factor binding, and the resulting monoallelic transcription in cell lines with heterozygous TERT mutations.
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Affiliation(s)
- Brittany A. McKelvey
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Timothy Gilpatrick
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yongchun Wang
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Christopher B. Umbricht
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Oncology, and The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Martha A. Zeiger
- Surgical Oncology Program, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Long M, Zhu Y, Chen Z, Lin S, Peng X, Luo D, Li H, Tan L. Lysine-Specific Demethylase 1 Affects the Progression of Papillary Thyroid Carcinoma via HIF1α and microRNA-146a. J Clin Endocrinol Metab 2020; 105:5821525. [PMID: 32303750 DOI: 10.1210/clinem/dgaa182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/17/2020] [Indexed: 02/08/2023]
Abstract
CONTEXT Lysine-specific demethylase 1 (LSD1) stabilizes hypoxia-inducible factor 1α (HIF1α) to advance tumor progression, while HIF1α functions as a transcription factor to increase the expression of microRNA-146a (miR-146a). OBJECTIVE We aim to investigate whether LSD1 affects the development of papillary thyroid carcinoma (PTC) via HIF1α and miR-146a. DESIGN In vitro assays were performed with Nthy-ori 3-1, BHP5-16, BCPAP, K1, and BHP2-7 cell lines. In vivo assays were conducted with established xenograft tumors in nude mice. SETTING This study was conducted at our lab. PATIENTS AND MATERIALS PTC tissues and corresponding adjacent normal tissues were obtained from 45 patients hospitalized in Sun Yat-Sen Memorial Hospital. Assays were conducted using Nthy-ori 3-1, BHP5-16, BCPAP, K1, and BHP2-7 cell lines, as well as 50 male BALB/c nude mice. INTERVENTION Cells were transfected with sh-LSD1, sh-GABPA, oe-LSD1, oe-HIF1α, miR-146a mimic, and miR-146a inhibitor. In addition, K1 cells expressing lv-oe-LSD1, lv-miR-146a inhibitor, lv-oe-LSD1 or miR-146a inhibitor were injected into the right side of the mice. LSD1 gene and protein expression patterns were analyzed in 45 clinical PTC tissue samples. MAIN OUTCOME MEASURE Expression of LSD1, HIF1α, miR-146a, and GA-binding protein transcription factor alpha (GABPA), as well as their effects on PTC. RESULTS LSD1 was highly expressed in clinical PTC tissues. LSD1 stabilized HIF1α and inhibited the degradation of its ubiquitin proteasome. HIF1α was enriched in the promoter region of miR-146a, an upregulated miRNA in PTC. HIF1α increased miR-146a expression to promote PTC progression in vitro, which was achieved by inhibiting GABPA, a target gene of miR-146a. LSD1 upregulated miR-146a to enhance the development and metastasis of PTC in nude mice. CONCLUSION Our results show that LSD1 functions as an oncogene in PTC by upregulating HIF1α and miR-146a, elucidating an understanding of undefined mechanisms associated with tumor progression in PTC.
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Affiliation(s)
- Miaoyun Long
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yue Zhu
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zuhe Chen
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shaojian Lin
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xinzhi Peng
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Dingyuan Luo
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Honghao Li
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Langping Tan
- Department of Thyroid Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
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Qi W, Li Z, Xia L, Dai J, Zhang Q, Wu C, Xu S. LncRNA GABPB1-AS1 and GABPB1 regulate oxidative stress during erastin-induced ferroptosis in HepG2 hepatocellular carcinoma cells. Sci Rep 2019; 9:16185. [PMID: 31700067 PMCID: PMC6838315 DOI: 10.1038/s41598-019-52837-8] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [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: 10/31/2018] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
Ferroptosis is a non-apoptotic, iron-dependent oxidative form of cell death that is specifically induced by erastin in RAS mutant cancer cells. Ferroptotic cell death is the result of membrane lipid peroxide damage caused by the accumulation of hydroxyl radicals derived from H2O2 by the Fenton reaction. Peroxidases are key cellular antioxidant enzymes that block such damaging processes. Few studies have examined the roles of long non-coding RNAs (lncRNAs) in the regulation of cellular oxidative stress, especially in ferroptosis. Here, we demonstrated that erastin upregulated the lncRNA GABPB1-AS1, which downregulated GABPB1 protein levels by blocking GABPB1 translation, leading to the downregulation of the gene encoding Peroxiredoxin-5 (PRDX5) peroxidase and the eventual suppression of the cellular antioxidant capacity. Such effects critically inhibited the cellular antioxidant capacity and cell viability. Additionally, high expression levels of GABPB1 were correlated with poor prognosis of hepatocellular carcinoma (HCC) Patients, while high GABPB1-AS1 levels in HCC patients correlated with improved overall survival. Collectively, these data demonstrate a mechanistic link between GABPB1 and its antisense lncRNA GABPB1-AS1 in erastin-induced ferroptosis and establish GABPB1 and GABPB1-AS1 as attractive therapeutic targets for HCC.
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Affiliation(s)
- Wenchuan Qi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, P.R. China
| | - Zhenhua Li
- Affiliated Hospital of Changchun University of Traditional Chinese Medicine, 130117, Changchun, Jilin, P.R. China
| | - Longjiang Xia
- Chengdu University of Traditional Chinese Medicine, 611130, Chengdu, Sichuan, P.R. China
| | - Jiangshan Dai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, P.R. China
| | - Qiao Zhang
- China-Japan Union Hospital of Jilin University, 130033, Changchun, Jilin, P.R. China
| | - Chuanfang Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, P.R. China
| | - Si Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, 610065, Chengdu, Sichuan, P.R. China.
- Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, 610072, Chengdu, Sichuan, P.R. China.
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Liu C, Dai SK, Sun Z, Wang Z, Liu PP, Du HZ, Yu S, Liu CM, Teng ZQ. GA-binding protein GABPβ1 is required for the proliferation of neural stem/progenitor cells. Stem Cell Res 2019; 39:101501. [PMID: 31344652 DOI: 10.1016/j.scr.2019.101501] [Citation(s) in RCA: 5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 01/02/2023] Open
Abstract
GA binding protein (GABP) is a ubiquitously expressed transcription factor that regulates the development of multiple cell types, including osteoblast, hematopoietic stem cells, B cells and T cells. However, so little is known about its biological function in the development of central nervous system. In this report, we show that GABP is highly expressed in neural stem/progenitor cells (NSPCs) and down-regulated in neurons, and that GABPβ1 is required for the proper proliferation of NSPCs. Knockdown of GABPα resulted in an elevated expression level of GABPβ1, and GABPβ1 down-regulation significantly decreased the proliferation of NSPCs, whereas GABPβ2 knockdown did not result in any changes in the proliferation of NSPCs. We observed that there was nearly a 21-fold increase of the GABPβ1S mRNA level in GABPβ1L KO NSPCs compared to WT cells, and knocking down of GABPβ1S in GABPβ1L KO NSPCs could further reduce their proliferation potential. We also found that knockdown of GABPβ1 promoted neuronal and astrocytic differentiation of NSPCs. Finally, we identified dozens of downstream target genes of GABPβ1, which are closely associated with the cell proliferation and differentiation. Collectively, our results suggest that both GABPβ1L and GABPβ1S play an essential role in regulating the proper proliferation and differentiation of NSPCs.
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Affiliation(s)
- Cong Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shang-Kun Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhen Sun
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhuo Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Pei-Pei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong-Zhen Du
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuyang Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Chang-Mei Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Zhao-Qian Teng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Goto S, Takahashi M, Yasutsune N, Inayama S, Kato D, Fukuoka M, Kashiwaba SI, Murakami Y. Identification of GA-Binding Protein Transcription Factor Alpha Subunit (GABPA) as a Novel Bookmarking Factor. Int J Mol Sci 2019; 20:E1093. [PMID: 30836589 PMCID: PMC6429373 DOI: 10.3390/ijms20051093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 02/07/2019] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 12/14/2022] Open
Abstract
Mitotic bookmarking constitutes a mechanism for transmitting transcriptional patterns through cell division. Bookmarking factors, comprising a subset of transcription factors (TFs), and multiple histone modifications retained in mitotic chromatin facilitate reactivation of transcription in the early G1 phase. However, the specific TFs that act as bookmarking factors remain largely unknown. Previously, we identified the "early G1 genes" and screened TFs that were predicted to bind to the upstream region of these genes, then identified GA-binding protein transcription factor alpha subunit (GABPA) and Sp1 transcription factor (SP1) as candidate bookmarking factors. Here we show that GABPA and multiple histone acetylation marks such as H3K9/14AC, H3K27AC, and H4K5AC are maintained at specific genomic sites in mitosis. During the M/G1 transition, the levels of these histone acetylations at the upstream regions of genes bound by GABPA in mitosis are decreased. Upon depletion of GABPA, levels of histone acetylation, especially H4K5AC, at several gene regions are increased, along with transcriptional induction at 1 h after release. Therefore, we proposed that GABPA cooperates with the states of histone acetylation to act as a novel bookmarking factor which, may negatively regulate transcription during the early G1 phase.
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Affiliation(s)
- Shunya Goto
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
| | - Masashi Takahashi
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
| | - Narumi Yasutsune
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
| | - Sumiki Inayama
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
| | - Dai Kato
- Order-MadeMedical Research Inc., 208Todai-Kashiwa VP, 5-4-19 Kashiwanoha, Kashiwa-shi, Chiba-ken 277-0882, Japan.
| | - Masashi Fukuoka
- Department of Molecular Pharmacology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo 187-8551, Japan.
| | - Shu-Ichiro Kashiwaba
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
| | - Yasufumi Murakami
- Department of Biological Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan.
- Order-MadeMedical Research Inc., 208Todai-Kashiwa VP, 5-4-19 Kashiwanoha, Kashiwa-shi, Chiba-ken 277-0882, Japan.
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Pinheiro DML, de Oliveira AHS, Coutinho LG, Fontes FL, de Medeiros Oliveira RK, Oliveira TT, Faustino ALF, Lira da Silva V, de Melo Campos JTA, Lajus TBP, de Souza SJ, Agnez-Lima LF. Resveratrol decreases the expression of genes involved in inflammation through transcriptional regulation. Free Radic Biol Med 2019; 130:8-22. [PMID: 30366059 DOI: 10.1016/j.freeradbiomed.2018.10.432] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/18/2018] [Accepted: 10/18/2018] [Indexed: 02/06/2023]
Abstract
Oxidative stress generated during inflammation is associated with a wide range of pathologies. Resveratrol (RESV) displays anti-inflammatory and antioxidant activities, being a candidate for the development of adjuvant therapies for several inflammatory diseases. Despite this potential, the cellular responses induced by RESV are not well known. In this work, transcriptomic analysis was performed following lipopolysaccharide (LPS) stimulation of monocyte cultures in the presence of RESV. Induction of an inflammatory response was observed after LPS treatment and the addition of RESV led to decreases in expression of the inflammatory mediators, tumor necrosis factor-alpha (TNF-α), interleukin-8 (IL-8), and monocyte chemoattractant protein-1 (MCP-1), without cytotoxicity. RNA sequencing revealed 823 upregulated and 2098 downregulated genes (cutoff ≥2.0 or ≤-2.0) after RESV treatment. Gene ontology analysis showed that the upregulated genes were associated with metabolic processes and the cell cycle, consistent with normal cell growth and differentiation under an inflammatory stimulus. The downregulated genes were associated with inflammatory responses, gene expression, and protein modification. The prediction of master regulators using the iRegulon tool showed nuclear respiratory factor 1 (NRF1) and GA-binding protein alpha subunit (GABPA) as the main regulators of the downregulated genes. Using immunoprecipitation and protein expression assays, we observed that RESV was able to decrease protein acetylation patterns, such as acetylated apurinic/apyrimidinic endonuclease-1/reduction-oxidation factor 1 (APE1/Ref-1), and increase histone methylation. In addition, reductions in p65 (nuclear factor-kappa B (NF-κB) subunit) and lysine-specific histone demethylase-1 (LSD1) expression were observed. In conclusion, our data indicate that treatment with RESV caused significant changes in protein acetylation and methylation patterns, suggesting the induction of deacetylase and reduction of demethylase activities that mainly affect regulatory cascades mediated by NF-кB and Janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling. NRF1 and GABPA seem to be the main regulators of the transcriptional profile observed after RESV treatment.
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Affiliation(s)
| | - Ana Helena Sales de Oliveira
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil; Chemistry Department, New York University, New York, NY, United States
| | - Leonam Gomes Coutinho
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil; Instituto Federal de Educação Tecnológica do Rio Grande do Norte, IFRN, São Paulo do Potengi, Brazil
| | - Fabrícia Lima Fontes
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | | | - Thais Teixeira Oliveira
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | - André Luís Fonseca Faustino
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Bioinformatics Multidisciplinary Environment (BioME), IMD, UFRN, Brazil
| | - Vandeclécio Lira da Silva
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Bioinformatics Multidisciplinary Environment (BioME), IMD, UFRN, Brazil
| | | | - Tirzah Braz Petta Lajus
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | - Sandro José de Souza
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Bioinformatics Multidisciplinary Environment (BioME), IMD, UFRN, Brazil
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Mancini A, Xavier-Magalhães A, Woods WS, Nguyen KT, Amen AM, Hayes JL, Fellmann C, Gapinske M, McKinney AM, Hong C, Jones LE, Walsh KM, Bell RJA, Doudna JA, Costa BM, Song JS, Perez-Pinera P, Costello JF. Disruption of the β1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner. Cancer Cell 2018; 34:513-528.e8. [PMID: 30205050 PMCID: PMC6135086 DOI: 10.1016/j.ccell.2018.08.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 07/02/2018] [Accepted: 08/03/2018] [Indexed: 12/27/2022]
Abstract
TERT promoter mutations reactivate telomerase, allowing for indefinite telomere maintenance and enabling cellular immortalization. These mutations specifically recruit the multimeric ETS factor GABP, which can form two functionally independent transcription factor species: a dimer or a tetramer. We show that genetic disruption of GABPβ1L (β1L), a tetramer-forming isoform of GABP that is dispensable for normal development, results in TERT silencing in a TERT promoter mutation-dependent manner. Reducing TERT expression by disrupting β1L culminates in telomere loss and cell death exclusively in TERT promoter mutant cells. Orthotopic xenografting of β1L-reduced, TERT promoter mutant glioblastoma cells rendered lower tumor burden and longer overall survival in mice. These results highlight the critical role of GABPβ1L in enabling immortality in TERT promoter mutant glioblastoma.
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Affiliation(s)
- Andrew Mancini
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Ana Xavier-Magalhães
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, 4710-057 Braga, Portugal
| | - Wendy S Woods
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Kien-Thiet Nguyen
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Alexandra M Amen
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Josie L Hayes
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Michael Gapinske
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew M McKinney
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Lindsey E Jones
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Kyle M Walsh
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Robert J A Bell
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Howard Hughes Medical Institute (HHMI), Berkeley, CA 94720, USA
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, 4710-057 Braga, Portugal
| | - Jun S Song
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA.
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10
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Xu Y, Guo W, Li P, Zhang Y, Zhao M, Fan Z, Zhao Z, Yan J. Long-Range Chromosome Interactions Mediated by Cohesin Shape Circadian Gene Expression. PLoS Genet 2016; 12:e1005992. [PMID: 27135601 PMCID: PMC4852938 DOI: 10.1371/journal.pgen.1005992] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 03/27/2016] [Indexed: 01/08/2023] Open
Abstract
Mammalian circadian rhythm is established by the negative feedback loops consisting of a set of clock genes, which lead to the circadian expression of thousands of downstream genes in vivo. As genome-wide transcription is organized under the high-order chromosome structure, it is largely uncharted how circadian gene expression is influenced by chromosome architecture. We focus on the function of chromatin structure proteins cohesin as well as CTCF (CCCTC-binding factor) in circadian rhythm. Using circular chromosome conformation capture sequencing, we systematically examined the interacting loci of a Bmal1-bound super-enhancer upstream of a clock gene Nr1d1 in mouse liver. These interactions are largely stable in the circadian cycle and cohesin binding sites are enriched in the interactome. Global analysis showed that cohesin-CTCF co-binding sites tend to insulate the phases of circadian oscillating genes while cohesin-non-CTCF sites are associated with high circadian rhythmicity of transcription. A model integrating the effects of cohesin and CTCF markedly improved the mechanistic understanding of circadian gene expression. Further experiments in cohesin knockout cells demonstrated that cohesin is required at least in part for driving the circadian gene expression by facilitating the enhancer-promoter looping. This study provided a novel insight into the relationship between circadian transcriptome and the high-order chromosome structure.
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Affiliation(s)
- Yichi Xu
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Weimin Guo
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, China
| | - Yan Zhang
- Beijing Institute of Biotechnology, Beijing, China
| | - Meng Zhao
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zenghua Fan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Zhihu Zhao
- Beijing Institute of Biotechnology, Beijing, China
| | - Jun Yan
- CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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11
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Manukjan G, Ripperger T, Santer L, von Neuhoff N, Ganser A, Schambach A, Schlegelberger B, Steinemann D. Expression of the ETS transcription factor GABPα is positively correlated to the BCR-ABL1/ABL1 ratio in CML patients and affects imatinib sensitivity in vitro. Exp Hematol 2015; 43:880-90. [PMID: 26072332 DOI: 10.1016/j.exphem.2015.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 03/10/2015] [Revised: 05/18/2015] [Accepted: 05/23/2015] [Indexed: 11/18/2022]
Abstract
In Philadelphia-positive chronic myeloid leukemia (CML), imatinib resistance frequently emerges because of point mutations in the ABL1 kinase domain, but may also be the consequence of uncontrolled upstream signaling. Recently, the heteromeric transcription factor GA-binding protein (GABP) was found to promote CML-like myeloproliferative disease in mice. In a cohort of 70 CML patients, we found that expression of the GABP α subunit (GABPα) is positively correlated to the BCR-ABL1/ABL1 ratio. Moreover, significantly higher GABPα expression was detected in blast crisis than in chronic phase CML after performing data mining on 91 CML patients. In functional studies, imatinib sensitivity is enhanced after GABPα knockdown in tyrosine kinase inhibitors (TKI)-sensitive K-562, as well as by overexpression of a deletion mutant in TKI-resistant NALM-1 cells. Moreover, in K-562 cells, GABP-dependent expression variations of PRKD2 and RAC2, relevant signaling mediators in CML, were observed. Notably, protein kinase D2 (Prkd2) was reported to be a GABP target gene in mice. In line with this, we detected a positive correlation between GABPA and PRKD2 expression in primary human CML, indicating that the effects of GABP are mediated by PRKD2. These findings illustrate an important role for GABP in disease development and imatinib sensitivity in human CML.
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MESH Headings
- Drug Resistance, Neoplasm
- Female
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- GA-Binding Protein Transcription Factor/genetics
- GA-Binding Protein Transcription Factor/metabolism
- Gene Expression Regulation, Leukemic
- Gene Knockdown Techniques
- Humans
- Imatinib Mesylate/pharmacology
- K562 Cells
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Male
- Middle Aged
- Proto-Oncogene Proteins c-ets/biosynthesis
- Proto-Oncogene Proteins c-ets/genetics
- rac GTP-Binding Proteins/genetics
- rac GTP-Binding Proteins/metabolism
- RAC2 GTP-Binding Protein
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Affiliation(s)
- Georgi Manukjan
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany.
| | - Tim Ripperger
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Laura Santer
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Nils von Neuhoff
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany
| | | | - Doris Steinemann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
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12
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He ZH, Hu Y, Li YC, Gong LJ, Cieszczyk P, Maciejewska-Karlowska A, Leonska-Duniec A, Muniesa CA, Marín-Peiro M, Santiago C, Garatachea N, Eynon N, Lucia A. PGC-related gene variants and elite endurance athletic status in a Chinese cohort: a functional study. Scand J Med Sci Sports 2015; 25:184-95. [PMID: 25170593 DOI: 10.1111/sms.12188] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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] [Accepted: 01/07/2014] [Indexed: 01/07/2023]
Abstract
This study aims to examine the association between proliferator-activated receptor γ (PGC)-gene family-related single nucleotide polymorphisms (SNPs) and elite endurance runners' status in a Chinese cohort, and to gain insights into the functionality of a subset of SNPs. Genotype distributions of 133 SNPs in PPARGC1A, PPARGC1B, PPRC1, TFAM, TFB1M, TFB2M, NRF1, GABPA, GABPB1, ERRα, and SIRT1 genes were compared between 235 elite Chinese (Han) endurance runners (127 women) and 504 healthy non-athletic controls (237 women). Luciferase gene reporter activity was determined in 20 SNPs. After adjusting for multiple comparisons (in which threshold P-value was set at 0.00041), no significant differences were found in allele/genotype frequencies between athletes and controls (when both sexes were analyzed either together or separately). The lowest P-value was found in PPARGC1A rs4697425 (P = 0.001 for the comparison of allele frequencies between elite female endurance runners and their gender-matched controls). However, no association (all P > 0.05) was observed for this SNP in a replication cohort from Poland (194 endurance athletes and 190 controls). Using functional genomics tool, the following SNPs were found to have functional significance: PPARGC1A rs6821591, rs12650562, rs12374310, rs4697425, rs13113110, and rs4452416; PPARGC1B rs251466 and rs17110586; and PPRC1 rs17114388 (all P < 0.001). This study found no significant association between PGC-related SNPs and elite endurance athlete status in the Chinese population, despite some SNPs showing potential functional significance and the strong biological rationale to hypothesize that this gene pathway is a candidate to influence endurance exercise capacity.
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Affiliation(s)
- Z-H He
- Biology Centre, China Institute of Sport Science, Beijing, China
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13
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Kang YK, Putluri N, Maity S, Tsimelzon A, Ilkayeva O, Mo Q, Lonard D, Michailidis G, Sreekumar A, Newgard CB, Wang M, Tsai SY, Tsai MJ, O'Malley BW. CAPER is vital for energy and redox homeostasis by integrating glucose-induced mitochondrial functions via ERR-α-Gabpa and stress-induced adaptive responses via NF-κB-cMYC. PLoS Genet 2015; 11:e1005116. [PMID: 25830341 PMCID: PMC4382186 DOI: 10.1371/journal.pgen.1005116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 03/03/2015] [Indexed: 01/01/2023] Open
Abstract
Ever since we developed mitochondria to generate ATP, eukaryotes required intimate mito-nuclear communication. In addition, since reactive oxygen species are a cost of mitochondrial oxidative phosphorylation, this demands safeguards as protection from these harmful byproducts. Here we identified a critical transcriptional integrator which eukaryotes share to orchestrate both nutrient-induced mitochondrial energy metabolism and stress-induced nuclear responses, thereby maintaining carbon-nitrogen balance, and preserving life span and reproductive capacity. Inhibition of nutrient-induced expression of CAPER arrests nutrient-dependent cell proliferation and ATP generation and induces autophagy-mediated vacuolization. Nutrient signaling to CAPER induces mitochondrial transcription and glucose-dependent mitochondrial respiration via coactivation of nuclear receptor ERR-α-mediated Gabpa transcription. CAPER is also a coactivator for NF-κB that directly regulates c-Myc to coordinate nuclear transcriptome responses to mitochondrial stress. Finally, CAPER is responsible for anaplerotic carbon flux into TCA cycles from glycolysis, amino acids and fatty acids in order to maintain cellular energy metabolism to counter mitochondrial stress. Collectively, our studies reveal CAPER as an evolutionarily conserved 'master' regulatory mechanism by which eukaryotic cells control vital homeostasis for both ATP and antioxidants via CAPER-dependent coordinated control of nuclear and mitochondrial transcriptomic programs and their metabolisms. These CAPER dependent bioenergetic programs are highly conserved, as we demonstrated that they are essential to preserving life span and reproductive capacity in human cells-and even in C. elegans.
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Affiliation(s)
- Yun Kyoung Kang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nagireddy Putluri
- Verna and Marrs McLean Department of Biochemistry and Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Suman Maity
- Verna and Marrs McLean Department of Biochemistry and Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anna Tsimelzon
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Olga Ilkayeva
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical School, Durham, North Carolina, United States of America
| | - Qianxing Mo
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - George Michailidis
- Department of Statistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Arun Sreekumar
- Verna and Marrs McLean Department of Biochemistry and Alkek Center for Molecular Discovery, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Christopher B. Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke University Medical School, Durham, North Carolina, United States of America
| | - Meng Wang
- Huffington Center on Aging, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sophia Y. Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ming-Jer Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Bert W. O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
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14
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Brault V, Duchon A, Romestaing C, Sahun I, Pothion S, Karout M, Borel C, Dembele D, Bizot JC, Messaddeq N, Sharp AJ, Roussel D, Antonarakis SE, Dierssen M, Hérault Y. Opposite phenotypes of muscle strength and locomotor function in mouse models of partial trisomy and monosomy 21 for the proximal Hspa13-App region. PLoS Genet 2015; 11:e1005062. [PMID: 25803843 PMCID: PMC4372517 DOI: 10.1371/journal.pgen.1005062] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 02/09/2015] [Indexed: 12/22/2022] Open
Abstract
The trisomy of human chromosome 21 (Hsa21), which causes Down syndrome (DS), is the most common viable human aneuploidy. In contrast to trisomy, the complete monosomy (M21) of Hsa21 is lethal, and only partial monosomy or mosaic monosomy of Hsa21 is seen. Both conditions lead to variable physiological abnormalities with constant intellectual disability, locomotor deficits, and altered muscle tone. To search for dosage-sensitive genes involved in DS and M21 phenotypes, we created two new mouse models: the Ts3Yah carrying a tandem duplication and the Ms3Yah carrying a deletion of the Hspa13-App interval syntenic with 21q11.2-q21.3. Here we report that the trisomy and the monosomy of this region alter locomotion, muscle strength, mass, and energetic balance. The expression profiling of skeletal muscles revealed global changes in the regulation of genes implicated in energetic metabolism, mitochondrial activity, and biogenesis. These genes are downregulated in Ts3Yah mice and upregulated in Ms3Yah mice. The shift in skeletal muscle metabolism correlates with a change in mitochondrial proliferation without an alteration in the respiratory function. However, the reactive oxygen species (ROS) production from mitochondrial complex I decreased in Ms3Yah mice, while the membrane permeability of Ts3Yah mitochondria slightly increased. Thus, we demonstrated how the Hspa13-App interval controls metabolic and mitochondrial phenotypes in muscles certainly as a consequence of change in dose of Gabpa, Nrip1, and Atp5j. Our results indicate that the copy number variation in the Hspa13-App region has a peripheral impact on locomotor activity by altering muscle function.
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Affiliation(s)
- Véronique Brault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Arnaud Duchon
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | | | - Ignasi Sahun
- Genes and Disease Program, Center for Genomic Regulation, Barcelona, Spain, and CIBER de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Stéphanie Pothion
- Transgenese et Archivage Animaux Modèles, TAAM, CNRS, UPS44, Orléans, France
| | - Mona Karout
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Christelle Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Doulaye Dembele
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | | | - Nadia Messaddeq
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Andrew J. Sharp
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Damien Roussel
- LEHNA, CNRS UMR502, Université de Lyon, Villeurbanne, France
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- iGE3 Institute of Genetics and Genomics of Geneva, Geneva, Switzerland
| | - Mara Dierssen
- Genes and Disease Program, Center for Genomic Regulation, Barcelona, Spain, and CIBER de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Yann Hérault
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Institut Clinique de la Souris, PHENOMIN, GIE CERBM, Illkirch, France
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15
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Reiff RE, Ali BR, Baron B, Yu TW, Ben-Salem S, Coulter ME, Schubert CR, Hill RS, Akawi NA, Al-Younes B, Kaya N, Evrony GD, Al-Saffar M, Felie JM, Partlow JN, Sunu CM, Schembri-Wismayer P, Alkuraya FS, Meyer BF, Walsh CA, Al-Gazali L, Mochida GH. METTL23, a transcriptional partner of GABPA, is essential for human cognition. Hum Mol Genet 2014; 23:3456-66. [PMID: 24501276 DOI: 10.1093/hmg/ddu054] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [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: 02/06/2023] Open
Abstract
Whereas many genes associated with intellectual disability (ID) encode synaptic proteins, transcriptional defects leading to ID are less well understood. We studied a large, consanguineous pedigree of Arab origin with seven members affected with ID and mild dysmorphic features. Homozygosity mapping and linkage analysis identified a candidate region on chromosome 17 with a maximum multipoint logarithm of odds score of 6.01. Targeted high-throughput sequencing of the exons in the candidate region identified a homozygous 4-bp deletion (c.169_172delCACT) in the METTL23 (methyltransferase like 23) gene, which is predicted to result in a frameshift and premature truncation (p.His57Valfs*11). Overexpressed METTL23 protein localized to both nucleus and cytoplasm, and physically interacted with GABPA (GA-binding protein transcription factor, alpha subunit). GABP, of which GABPA is a component, is known to regulate the expression of genes such as THPO (thrombopoietin) and ATP5B (ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide) and is implicated in a wide variety of important cellular functions. Overexpression of METTL23 resulted in increased transcriptional activity at the THPO promoter, whereas knockdown of METTL23 with siRNA resulted in decreased expression of ATP5B, thus revealing the importance of METTL23 as a regulator of GABPA function. The METTL23 mutation highlights a new transcriptional pathway underlying human intellectual function.
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Affiliation(s)
- Rachel E Reiff
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences
| | - Byron Baron
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, Msida MSD2080, Malta
| | - Timothy W Yu
- Division of Genetics and Genomics, Department of Medicine Department of Pediatrics Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA Program in Medical and Population Genetics, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Salma Ben-Salem
- Department of Pathology, College of Medicine and Health Sciences
| | - Michael E Coulter
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - Christian R Schubert
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics Research Laboratory of Electronics and Department of Electrical Engineering and Computer Science, Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02139, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Nadia A Akawi
- Department of Pathology, College of Medicine and Health Sciences
| | - Banan Al-Younes
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Gilad D Evrony
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Program in Biological and Biomedical Sciences and
| | - Muna Al-Saffar
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al-Ain, United Arab Emirates
| | - Jillian M Felie
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jennifer N Partlow
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christine M Sunu
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pierre Schembri-Wismayer
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, Msida MSD2080, Malta
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Brian F Meyer
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA Department of Pediatrics Department of Neurology, Harvard Medical School, Boston, MA 02115, USA Program in Medical and Population Genetics, Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al-Ain, United Arab Emirates
| | - Ganeshwaran H Mochida
- Division of Genetics and Genomics, Department of Medicine Manton Center for Orphan Disease Research and Department of Pediatrics Pediatric Neurology Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
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16
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Priya A, Johar K, Wong-Riley MTT. Nuclear respiratory factor 2 regulates the expression of the same NMDA receptor subunit genes as NRF-1: both factors act by a concurrent and parallel mechanism to couple energy metabolism and synaptic transmission. Biochim Biophys Acta 2012; 1833:48-58. [PMID: 23085505 DOI: 10.1016/j.bbamcr.2012.10.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/13/2012] [Accepted: 10/14/2012] [Indexed: 11/19/2022]
Abstract
Neuronal activity and energy metabolism are tightly coupled processes. Previously, we found that nuclear respiratory factor 1 (NRF-1) transcriptionally co-regulates energy metabolism and neuronal activity by regulating all 13 subunits of the critical energy generating enzyme, cytochrome c oxidase (COX), as well as N-methyl-d-aspartate (NMDA) receptor subunits 1 and 2B, GluN1 (Grin1) and GluN2B (Grin2b). We also found that another transcription factor, nuclear respiratory factor 2 (NRF-2 or GA-binding protein) regulates all subunits of COX as well. The goal of the present study was to test our hypothesis that NRF-2 also regulates specific subunits of NMDA receptors, and that it functions with NRF-1 via one of three mechanisms: complementary, concurrent and parallel, or a combination of complementary and concurrent/parallel. By means of multiple approaches, including in silico analysis, electrophoretic mobility shift and supershift assays, in vivo chromatin immunoprecipitation of mouse neuroblastoma cells and rat visual cortical tissue, promoter mutations, real-time quantitative PCR, and western blot analysis, NRF-2 was found to functionally regulate Grin1 and Grin2b genes, but not any other NMDA subunit genes. Grin1 and Grin2b transcripts were up-regulated by depolarizing KCl, but silencing of NRF-2 prevented this up-regulation. On the other hand, over-expression of NRF-2 rescued the down-regulation of these subunits by the impulse blocker TTX. NRF-2 binding sites on Grin1 and Grin2b are conserved among species. Our data indicate that NRF-2 and NRF-1 operate in a concurrent and parallel manner in mediating the tight coupling between energy metabolism and neuronal activity at the molecular level.
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Affiliation(s)
- Anusha Priya
- Department of Cell Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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17
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Abstract
Next generation sequencing (NGS) technologies are now widely used in many biological studies. In NGS, sequence reads are randomly sampled from the genome sequence of interest. Most computational approaches for NGS data first map the reads to the genome and then analyze the data based on the mapped reads. Since many organisms have unknown genome sequences and many reads cannot be uniquely mapped to the genomes even if the genome sequences are known, alternative analytical methods are needed for the study of NGS data. Here we suggest using word patterns to analyze NGS data. Word pattern counting (the study of the probabilistic distribution of the number of occurrences of word patterns in one or multiple long sequences) has played an important role in molecular sequence analysis. However, no studies are available on the distribution of the number of occurrences of word patterns in NGS reads. In this article, we build probabilistic models for the background sequence and the sampling process of the sequence reads from the genome. Based on the models, we provide normal and compound Poisson approximations for the number of occurrences of word patterns from the sequence reads, with bounds on the approximation error. The main challenge is to consider the randomness in generating the long background sequence, as well as in the sampling of the reads using NGS. We show the accuracy of these approximations under a variety of conditions for different patterns with various characteristics. Under realistic assumptions, the compound Poisson approximation seems to outperform the normal approximation in most situations. These approximate distributions can be used to evaluate the statistical significance of the occurrence of patterns from NGS data. The theory and the computational algorithm for calculating the approximate distributions are then used to analyze ChIP-Seq data using transcription factor GABP. Software is available online (www-rcf.usc.edu/∼fsun/Programs/NGS_motif_power/NGS_motif_power.html). In addition, Supplementary Material can be found online (www.liebertonline.com/cmb).
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Affiliation(s)
- Zhiyuan Zhai
- School of Mathematics, Shandong University, Jinan, Shandong, China
| | - Gesine Reinert
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Kai Song
- School of Mathematics, Peking University, Beijing, China
| | - Michael S. Waterman
- Molecular and Computational Biology, University of Southern California, Los Angeles, California
- TNLIST/Department of Automation, Tsinghua University, Beijing, China
| | - Yihui Luan
- School of Mathematics, Shandong University, Jinan, Shandong, China
| | - Fengzhu Sun
- Molecular and Computational Biology, University of Southern California, Los Angeles, California
- TNLIST/Department of Automation, Tsinghua University, Beijing, China
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18
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Lettice L, Williamson I, Wiltshire J, Peluso S, Devenney P, Hill A, Essafi A, Hagman J, Mort R, Grimes G, DeAngelis C, Hill R. Opposing functions of the ETS factor family define Shh spatial expression in limb buds and underlie polydactyly. Dev Cell 2012; 22:459-67. [PMID: 22340503 PMCID: PMC3314984 DOI: 10.1016/j.devcel.2011.12.010] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 09/20/2011] [Accepted: 12/15/2011] [Indexed: 12/11/2022]
Abstract
Sonic hedgehog (Shh) expression during limb development is crucial for specifying the identity and number of digits. The spatial pattern of Shh expression is restricted to a region called the zone of polarizing activity (ZPA), and this expression is controlled from a long distance by the cis-regulator ZRS. Here, members of two groups of ETS transcription factors are shown to act directly at the ZRS mediating a differential effect on Shh, defining its spatial expression pattern. Occupancy at multiple GABPα/ETS1 sites regulates the position of the ZPA boundary, whereas ETV4/ETV5 binding restricts expression outside the ZPA. The ETS gene family is therefore attributed with specifying the boundaries of the classical ZPA. Two point mutations within the ZRS change the profile of ETS binding and activate Shh expression at an ectopic site in the limb bud. These molecular changes define a pathogenetic mechanism that leads to preaxial polydactyly (PPD).
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Affiliation(s)
- Laura A. Lettice
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Iain Williamson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - John H. Wiltshire
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Silvia Peluso
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Paul S. Devenney
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Alison E. Hill
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Abdelkader Essafi
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - James Hagman
- Integrated Department of Immunology, National Jewish Health, Denver, CO 80206, USA
| | - Richard Mort
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Graeme Grimes
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Carlo L. DeAngelis
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Robert E. Hill
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
- Corresponding author
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Schoepe M, Schrepper A, Schwarzer M, Osterholt M, Doenst T. Exercise can induce temporary mitochondrial and contractile dysfunction linked to impaired respiratory chain complex activity. Metabolism 2012; 61:117-26. [PMID: 21816448 DOI: 10.1016/j.metabol.2011.05.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 05/09/2011] [Accepted: 05/28/2011] [Indexed: 11/24/2022]
Abstract
Exercise is considered to elicit a physiological response of the heart. Previous studies investigated the influence of repetitive exercise only at the end of the training period. We assessed the impact of 2 exercise protocols, differing in their treadmill inclination, on cardiac and mitochondrial function at different times during the training period. Within 10 weeks, animals trained with 16% incline developed hypertrophy (left ventricular posterior wall thickness: 1.6 ± 0.1 vs 2.4 ± 0.1 mm; P < .05) with normal function (ejection fraction: 75.2% ± 2.5% vs 75.6% ± 2.1%). However, at 6 weeks, there was temporary impairment of contractile function (ejection fraction: 74.5% ± 1.67% vs 65.8% ± 2.3%; P < .05) associated with decreased mitochondrial respiratory capacity (state 3 respiration: 326 ± 71 vs 161 ± 22 natoms/[min mg protein]; P < .05) and a gene expression shift from the adult (α) to the fetal (β) myosin heavy chain isoform. Although peroxisome proliferator-activated receptor gamma coactivator-1α expression was normal, nuclear respiratory factors (NRFs)-1 and -2 were significantly reduced (NRF-1: 1.00 ± 0.16 vs 0.55 ± 0.09; NRF-2: 1.00 ± 0.11 vs 0.63 ± 0.07; P < .05) after 6 weeks. These findings were associated with a reduction of electron transport chain complexes I and IV activity (complex I: 1016 ± 67 vs 758 ± 71 nmol/[min mg protein]; complex IV: 18768 ± 1394 vs 14692 ± 960 nmol/[min mg protein]; P < .05). Messenger RNA expression of selected nuclear encoded subunits of the electron transport chain was unchanged at all investigated time points. In contrast, animals trained with 10% incline showed less hypertrophy and normal function in echocardiography, normal maximal respiratory capacity, and unchanged complex activities at all 3 time points. Repetitive exercise may cause contractile and mitochondrial dysfunction characterized by impaired respiratory chain complex activities. This activity reduction is temporary and intensity related.
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Affiliation(s)
- Maria Schoepe
- Department of Cardiac Surgery, Heart Center Leipzig, University of Leipzig, Germany
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20
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Wagatsuma A, Kotake N, Mabuchi K, Yamada S. Expression of nuclear-encoded genes involved in mitochondrial biogenesis and dynamics in experimentally denervated muscle. J Physiol Biochem 2011; 67:359-70. [PMID: 21394548 DOI: 10.1007/s13105-011-0083-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [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: 11/29/2010] [Accepted: 02/22/2011] [Indexed: 12/28/2022]
Abstract
The abundance, morphology, and functional properties of mitochondria become altered in response to denervation. To gain insight into the regulation of this process, mitochondrial enzyme activities and gene expression involved in mitochondrial biogenesis and dynamics in mouse gastrocnemius muscle was investigated. Sciatic nerve transactions were performed on mice, and then gastrocnemius muscles were isolated at days 5 and 30 after surgery. Muscle weight was decreased significantly by 15% and 62% at days 5 and 30 after surgery, respectively. The activity of citrate synthase, a marker of oxidative enzyme, was reduced significantly by 31% and 53% at days 5 and 30, respectively. Enzyme histochemical analysis revealed that subsarcolemmal mitochondria were largely lost than intermyofibrillar mitochondria at day 5, and this trend was further progressed at day 30 after surgery. Expression levels of peroxisome proliferator-activated receptor, γ coactivator 1 (PGC-1)α, estrogen-related receptor α (ERRα), and mitofusin 2 were down-regulated throughout the experimental period, whereas those of PGC-1β, PRC, nuclear respiratory factor (NRF)-1, NRF-2, TFAM, and Lon protease were down-regulated at day 30 after surgery. These results suggest that PGC-1α, ERRα, and mitofusin 2 may be important factors in the process of denervation-induced mitochondrial adaptation. In addition, other PGC-1 family of transcriptional coactivators and DNA binding transcription factors may also contribute to mitochondrial adaptation after early response to denervation.
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Affiliation(s)
- Akira Wagatsuma
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
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21
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Yu S, Cui K, Jothi R, Zhao DM, Jing X, Zhao K, Xue HH. GABP controls a critical transcription regulatory module that is essential for maintenance and differentiation of hematopoietic stem/progenitor cells. Blood 2011; 117:2166-78. [PMID: 21139080 PMCID: PMC3062326 DOI: 10.1182/blood-2010-09-306563] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [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] [Received: 09/10/2010] [Accepted: 11/30/2010] [Indexed: 12/15/2022] Open
Abstract
Maintaining a steady pool of self-renewing hematopoietic stem cells (HSCs) is critical for sustained production of multiple blood lineages. Many transcription factors and molecules involved in chromatin and epigenetic modifications have been found to be critical for HSC self-renewal and differentiation; however, their interplay is less understood. The transcription factor GA binding protein (GABP), consisting of DNA-binding subunit GABPα and transactivating subunit GABPβ, is essential for lymphopoiesis as shown in our previous studies. Here we demonstrate cell-intrinsic, absolute dependence on GABPα for maintenance and differentiation of hematopoietic stem/progenitor cells. Through genome-wide mapping of GABPα binding and transcriptomic analysis of GABPα-deficient HSCs, we identified Zfx and Etv6 transcription factors and prosurvival Bcl-2 family members including Bcl-2, Bcl-X(L), and Mcl-1 as direct GABP target genes, underlying its pivotal role in HSC survival. GABP also directly regulates Foxo3 and Pten and hence sustains HSC quiescence. Furthermore, GABP activates transcription of DNA methyltransferases and histone acetylases including p300, contributing to regulation of HSC self-renewal and differentiation. These systematic analyses revealed a GABP-controlled gene regulatory module that programs multiple aspects of HSC biology. Our studies thus constitute a critical first step in decoding how transcription factors are orchestrated to regulate maintenance and multipotency of HSCs.
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Affiliation(s)
- Shuyang Yu
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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22
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Takahashi K, Hayashi N, Shimokawa T, Umehara N, Kaminogawa S, Ra C. Cooperative regulation of Fc receptor gamma-chain gene expression by multiple transcription factors, including Sp1, GABP, and Elf-1. J Biol Chem 2008; 283:15134-41. [PMID: 18378679 PMCID: PMC3258888 DOI: 10.1074/jbc.m800498200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [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: 01/18/2008] [Revised: 03/05/2008] [Indexed: 11/06/2022] Open
Abstract
The Fc receptor gamma-chain (FcRgamma), which was first identified as a constituent of the high affinity IgE receptor, associates with various cell surface receptors to mediate intracellular signals. We identified three transcriptional enhancer elements in the 5' region of the human FcRgamma gene; one of the cis-elements was recognized by the transcription factor Sp-1 and another was recognized by GABP or Elf-1. The sequence of the other element was similar to a binding motif of the C/EBP family. Overexpression experiments showed that these transcription factors cooperatively activated the FcRgamma promoter. Furthermore, inactivation of the GABP-binding site by nucleotide substitutions as well as repression of GABPalpha expression by RNA interference reduced Sp1-mediated transactivation of the FcRgamma promoter, demonstrating that Sp1 and GABP synergistically activated the FcRgamma promoter. This synergistic activation was suggested to require physical interaction between the two transcription factors, because the Ets domain of GABPalpha was demonstrated to directly bind Sp1. On the other hand, GABP and Elf-1, whose recognition sequences overlapped, were shown to bind the FcRgamma gene with similar affinity in the context of chromatin, although Elf-1 exerted weaker enhancer activity for FcRgamma gene expression than did GABP. Both were thought to compete for binding to the element, because additional expression of Elf-1 in combination with Sp1 and GABP reduced FcRgamma promoter activity. Such functional and physical interactions among transcription factors involved in the cooperative regulation of FcRgamma gene expression as revealed in this study will become promising targets for medical applications against various immune diseases involving FcRgamma.
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Affiliation(s)
- Kyoko Takahashi
- Department of Molecular Cell Immunology and Allergology, Nihon University Graduate School of Medical Sciences, 30-1 Oyaguchi Kamima-chi, Itabashi-ku, Tokyo, Japan.
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23
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Abstract
The aim of this work was to examine the association between the polymorphisms in nuclear respiratory factor (NRF2) gene and endurance capacity measured prior to and after an 18-wk endurance training program in young Chinese men. The phenotypes measured were running economy (RE) and VO(2max). The RE was determined by measuring submaximal VO(2) for 5 min at a constant running speed of 12 km x h (-1) and VO(2max) was measured during an incremental test to volitional exhaustion. Genomic DNA was extracted from white cells of peripheral blood and the genotypes were examined in SNPrs12594956, rs8031031 and rs7181866 by PCR-RFLP. Genotype distributions were in Hardy-Weinberg equilibrium at three loci, and linkage disequilibrium was observed (LD D' = 1 and r (2) = 0.903) between rs8031031 and rs7181866. The VO(2max) was associated with rs12594956 at baseline while the training response of VO(2) at RE, was associated with rs12594956, rs8031031 and rs7181866. When the three SNPs were considered together, those carrying the ATG haplotype had 57.5 % higher training response in VO(2) at RE (p = 0.006) than non-carriers. In conclusion, polymorphisms in NRF2 gene may explain some of the between-person variance in endurance capacity.
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Affiliation(s)
- Z He
- Biology Center, China Institute of Sport Science, Beijing, China
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24
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Crook MF, Olive M, Xue HH, Langenickel TH, Boehm M, Leonard WJ, Nabel EG. GA-binding protein regulates KIS gene expression, cell migration, and cell cycle progression. FASEB J 2007; 22:225-35. [PMID: 17726090 DOI: 10.1096/fj.07-8573com] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [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: 12/26/2022]
Abstract
The cyclin-dependent kinase inhibitor p27(Kip1) arrests cell cycle progression through G1/S phases and is regulated by phosphorylation of serine/threonine residues. Recently, we identified the serine/threonine kinase, KIS, which phosphorylates p27(Kip1) on serine 10 leading to nuclear export of p27(Kip1) and protein degradation. However, the molecular mechanisms of transcriptional activation of the human KIS gene and its biological activity are not known. We mapped the transcription initiation site approximately 116 bp 5' to the translation start site, and sequences extending to -141 were sufficient for maximal promoter activity. Mutation in either of two Ets-binding sites in this region resulted in an approximately 75-80% decrease in promoter activity. These sites form at least 3 specific complexes, which contained GA-binding protein (GABP). Knocking down GABPalpha by siRNA in vascular smooth muscle cells (VSMCs) diminished KIS gene expression and reduced cell migration. Correspondingly, in serum stimulated GABPalpha-deficient mouse embryonic fibroblasts (MEFs), KIS gene expression was also significantly reduced, which was associated with an increase in p27(Kip1) protein levels and a decreased percentage of cells in S-phase. Consistent with these findings, following vascular injury in vivo, GABPalpha-heterozygous mice demonstrated reduced KIS gene expression within arterial lesions and these lesions were significantly smaller compared to GABP+/+ mice. In summary, serum-responsive GABP binding to Ets-binding sites activates the KIS promoter, leading to KIS gene expression, cell migration, and cell cycle progression.
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Affiliation(s)
- Martin F Crook
- Cardiovascular Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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25
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Xue HH, Bollenbacher-Reilley J, Wu Z, Spolski R, Jing X, Zhang YC, McCoy JP, Leonard WJ. The transcription factor GABP is a critical regulator of B lymphocyte development. Immunity 2007; 26:421-31. [PMID: 17442597 DOI: 10.1016/j.immuni.2007.03.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [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] [Received: 10/19/2006] [Revised: 01/09/2007] [Accepted: 03/16/2007] [Indexed: 12/19/2022]
Abstract
GA binding protein (GABP) is a ubiquitously expressed Ets-family transcription factor that critically regulates the expression of the interleukin-7 receptor alpha chain (IL-7Ralpha) in T cells, whereas it is dispensable for IL-7Ralpha expression in fetal liver B cells. Here we showed that deficiency of GABPalpha, the DNA-binding subunit of GABP, resulted in profoundly defective B cell development and a compromised humoral immune response, in addition to thymic developmental defects. Furthermore, the expression of Pax5 and Pax5 target genes such as Cd79a was greatly diminished in GABPalpha-deficient B cell progenitors, pro-B, and mature B cells. GABP could bind to the regulatory regions of Pax5 and Cd79a in vivo. Thus, GABP is a key regulator of B cell development, maturation, and function.
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Affiliation(s)
- Hai-Hui Xue
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892-1674, USA
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26
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Handschin C, Kobayashi YM, Chin S, Seale P, Campbell KP, Spiegelman BM. PGC-1alpha regulates the neuromuscular junction program and ameliorates Duchenne muscular dystrophy. Genes Dev 2007; 21:770-83. [PMID: 17403779 PMCID: PMC1838529 DOI: 10.1101/gad.1525107] [Citation(s) in RCA: 274] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The coactivator PGC-1alpha mediates key responses of skeletal muscle to motor nerve activity. We show here that neuregulin-stimulated phosphorylation of PGC-1alpha and GA-binding protein (GABP) allows recruitment of PGC-1alpha to the GABP complex and enhances transcription of a broad neuromuscular junction gene program. Since a subset of genes controlled by PGC-1alpha and GABP is dysregulated in Duchenne muscular dystrophy (DMD), we examined the effects of transgenic PGC-1alpha in muscle of mdx mice. These animals show improvement in parameters characteristic of DMD, including muscle histology, running performance, and plasma creatine kinase levels. Thus, control of PGC-1alpha levels in skeletal muscle could represent a novel avenue to prevent or treat DMD.
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Affiliation(s)
- Christoph Handschin
- Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Institute of Physiology and Zurich Center for Integrative Human Physiology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Yvonne M. Kobayashi
- Howard Hughes Medical Institute and Departments of Molecular Physiology and Biophysics, Neurology, and Internal Medicine, University of Iowa, Roy J. and Lucille A. Carver College of Medicine, Iowa City, Iowa 52242, USA
| | - Sherry Chin
- Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Patrick Seale
- Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kevin P. Campbell
- Howard Hughes Medical Institute and Departments of Molecular Physiology and Biophysics, Neurology, and Internal Medicine, University of Iowa, Roy J. and Lucille A. Carver College of Medicine, Iowa City, Iowa 52242, USA
| | - Bruce M. Spiegelman
- Dana-Farber Cancer Institute and Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Corresponding author.E-MAIL ; FAX (617) 632-4655
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27
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Abstract
The mRNAs encoding postsynaptic components at the neuromuscular junction are concentrated in the synaptic region of muscle fibers. Accumulation of these RNAs in the synaptic region is mediated, at least in part, by selective transcription of the corresponding genes in synaptic myofiber nuclei. The transcriptional mechanisms that are responsible for synapse-specific gene expression are largely unknown, but an Ets site in the promoter regions of acetylcholine receptor (AChR) subunit genes and other "synaptic" genes is required for synapse-specific transcription. The Ets domain transcription factor GA-binding protein (GABP) has been implicated to mediate synapse-specific gene expression. Inactivation of GABPalpha, the DNA-binding subunit of GABP, leads to early embryonic lethality, preventing analysis of synapse formation in gabpalpha mutant mice. To study the role of GABP at neuromuscular synapses, we conditionally inactivated gabpalpha in skeletal muscle and studied synaptic differentiation and muscle gene expression. Although expression of rb, a target of GABP, is elevated in muscle tissue deficient in GABPalpha, clustering of synaptic AChRs at synapses and synapse-specific gene expression are normal in these mice. These data indicate that GABP is dispensable for synapse-specific transcription and maintenance of normal AChR expression at synapses.
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Affiliation(s)
- Alexander Jaworski
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine, Skirball Institute of Biomoledular Medicine, NYU School of Medicine, New York, NY 10016, USA
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28
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O'Leary DA, Noakes PG, Lavidis NA, Kola I, Hertzog PJ, Ristevski S. Targeting of the ETS factor GABPalpha disrupts neuromuscular junction synaptic function. Mol Cell Biol 2007; 27:3470-80. [PMID: 17325042 PMCID: PMC1899955 DOI: 10.1128/mcb.00659-06] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [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: 01/20/2023] Open
Abstract
The GA-binding protein (GABP) transcription factor has been shown in vitro to regulate the expression of the neuromuscular proteins utrophin, acetylcholine esterase, and acetylcholine receptor subunits delta and epsilon through the N-box promoter motif (5'-CCGGAA-3'), but its in vivo function remains unknown. A single point mutation within the N-box of the gene encoding the acetylcholine receptor epsilon subunit has been identified in several patients suffering from postsynaptic congenital myasthenic syndrome, implicating the GA-binding protein in neuromuscular function and disease. Since conventional gene targeting results in an embryonic-lethal phenotype, we used conditional targeting to investigate the role of GABPalpha in neuromuscular junction and skeletal muscle development. The diaphragm and soleus muscles from mutant mice display alterations in morphology and distribution of acetylcholine receptor clusters at the neuromuscular junction and neurotransmission properties consistent with reduced receptor function. Furthermore, we confirmed decreased expression of the acetylcholine receptor epsilon subunit and increased expression of the gamma subunit in skeletal muscle tissues. Therefore, the GABP transcription factor aids in the structural formation and function of neuromuscular junctions by regulating the expression of postsynaptic genes.
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Affiliation(s)
- Debra A O'Leary
- Monash Institute of Medical Research, Monash University, Clayton, Victoria 3168, Australia
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Yang ZF, Mott S, Rosmarin AG. The Ets transcription factor GABP is required for cell-cycle progression. Nat Cell Biol 2007; 9:339-46. [PMID: 17277770 DOI: 10.1038/ncb1548] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [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] [Received: 11/03/2006] [Accepted: 01/10/2007] [Indexed: 11/09/2022]
Abstract
The transition from cellular quiescence (G0) into S phase is regulated by the mitogenic-activation of D-type cyclins and cyclin-dependent kinases (Cdks), the sequestration of the Cdk inhibitors (CDKIs), p21 and p27, and the hyperphosphorylation of Rb with release of E2F transcription factors. However, fibroblasts that lack all D-type cyclins can still undergo serum-induced proliferation and key E2F targets are expressed at stable levels despite cyclical Rb-E2F activity. Here, we show that serum induces expression of the Ets transcription factor, Gabpalpha, and that its ectopic expression induces quiescent cells to re-enter the cell cycle. Genetic disruption of Gabpalpha prevents entry into S phase, and selectively reduces expression of genes that are required for DNA synthesis and degradation of CDKIs, yet does not alter expression of D-type cyclins, Cdks, Rb or E2Fs. Thus, GABP is necessary and sufficient for re-entry into the cell cycle and it regulates a pathway that is distinct from that of D-type cyclins and CDKs.
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Affiliation(s)
- Zhong-Fa Yang
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
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Abstract
To investigate a possible new physiological role of carbon monoxide (CO), an endogenous gas involved in cell signaling and cytotoxicity, we tested the hypothesis that the mitochondrial generation of reactive oxygen species by CO activates mitochondrial biogenesis in the heart. In mice, transient elevations of cellular CO by five- to 20-fold increased the copy number of cardiac mitochondrial DNA, the content of respiratory complex I-V and interfibrillar mitochondrial density within 24 hours. Mitochondrial biogenesis is activated by gene and protein expression of the nuclear respiratory factor 1 (NRF1) and NRF2, of peroxisome proliferator-activated receptor gamma co-activator-1α, and of mitochondrial transcription factor A (TFAM), which augmented the copy number of mitochondrial DNA (mtDNA). This is independent of nitric oxide synthase (NOS), as demonstrated by the identical responses in wild-type and endothelial NOS (eNOS)-deficient mice, and by the inhibition of inducible NOS (iNOS). In the heart and in isolated cardiomyocytes, CO activation involved both guanylate cyclase and the pro-survival kinase Akt/PKB. Akt activation was facilitated by mitochondrial binding of CO and by production of hydrogen peroxide (H2O2). Interference with Akt activity by blocking PI 3-kinase and by mitochondrial targeting of catalase to scavenge H2O2 prevented binding of NRF1 to the Tfam promoter, thereby connecting mitochondrial H2O2 to the pathway leading to mtDNA replication. The findings disclose mitochondrial CO and H2O2 as new activating factors in cardiac mitochondrial biogenesis.
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Affiliation(s)
- Hagit B Suliman
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
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Zoll J, Monassier L, Garnier A, N'Guessan B, Mettauer B, Veksler V, Piquard F, Ventura-Clapier R, Geny B. ACE inhibition prevents myocardial infarction-induced skeletal muscle mitochondrial dysfunction. J Appl Physiol (1985) 2006; 101:385-91. [PMID: 16614354 DOI: 10.1152/japplphysiol.01486.2005] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [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: 11/22/2022] Open
Abstract
Heart failure is associated with alterations in cardiac and skeletal muscle energy metabolism resulting in a generalized myopathy. We investigated the molecular and cellular effects of angiotensin-converting enzyme inhibition (ACEi) on skeletal muscle metabolism in infarcted animals. Myocardial infarction (MI) was obtained by left descending coronary artery ligation. Sham, MI, and MI-treated rats (perindopril, 2 mg·kg−1·day−1 given 7 days after MI) were studied 1 and 4 mo after surgery. Oxygen consumption of white gastrocnemius (Gas) muscle was studied in saponin-permeabilized fibers, using the main substrates of mitochondrial respiration. mRNA expression of nuclear factors (PGC-1α, NRF-2α, and mtTFA), involved in the transcription of mitochondrial proteins, and of MCIP1, a marker of calcineurin activation, were also determined. Echocardiographic left ventricular fractional shortening was reduced in both MI and perindopril group after 1 and 4 mo, whereas systemic blood pressure was reduced by 16% only in the MI group after 4 mo. The capacity of Gas to oxidize glutamate-malate, glycerol-triphosphate, or pyruvate (−30%, P < 0.01; −32%, P < 0.05; −33%, P < 0.01, respectively), was greatly decreased. Furthermore, PGC-1α (−54%), NRF-2α (−45%), and MCIP1 (−84%) gene expression were significantly downregulated. ACEi improved survival, left ventricular function, and blood pressure. Perindopril protected also totally the Gas mitochondrial function and preserved the mRNAs concentration of the mitochondrial transcriptional factors. Moreover, PGC-1α correlated with Gas oxidative capacity ( r = 0.48), mitochondrial cytochrome- c oxidase ( r = 0.65), citrate synthase ( r = 0.45) activities, and MCIP1 expression ( r = 0.44). Thus ACEi totally prevented MI-induced alterations of skeletal muscle mitochondrial function and protein expression, halting the development of this metabolic myopathy.
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Affiliation(s)
- Joffrey Zoll
- Département de Physiologie, Faculté de Médecine, 11, rue Humann, 67000 Strasbourg, France.
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Liang HL, Wong-Riley MTT. Activity-dependent regulation of nuclear respiratory factor-1, nuclear respiratory factor-2, and peroxisome proliferator-activated receptor gamma coactivator-1 in neurons. Neuroreport 2006; 17:401-5. [PMID: 16514366 DOI: 10.1097/01.wnr.0000204980.98876.11] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [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: 11/25/2022]
Abstract
Nuclear respiratory factor-1 and nuclear respiratory factor-2 activate the transcription of several respiratory chain enzymes and are prime candidates for bigenomic coordinated regulation of cytochrome oxidase subunit genes from the two genomes. Peroxisome proliferator-activated receptor gamma coactivator 1 is a proposed coactivator of nuclear respiratory factor-1 and nuclear respiratory factor-2-dependent transcription, but its significance and function in neurons are unknown. Our current study indicates that nuclear respiratory factor-1, nuclear respiratory factor-2, and peroxisome proliferator-activated receptor gamma coactivator-1 are expressed in rat visual cortical neurons, and that neuronal activity directly regulates the protein and mRNA expressions of these factors after functional inactivation in vivo and in vitro. Changes in peroxisome proliferator-activated receptor gamma coactivator-1 preceded those of nuclear respiratory factor-1 and nuclear respiratory factor-2, suggesting that it may be the prime sensor of neuronal activity and its energy demand.
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Affiliation(s)
- Huan Ling Liang
- Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA
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Abstract
Expression of CD18, the beta chain of the leukocyte integrins, is transcriptionally regulated by retinoic acid (RA) in myeloid cells. Full RA responsiveness of the CD18 gene requires its proximal promoter, which lacks a retinoic acid response element (RARE). Rather, RA responsiveness of the CD18 proximal promoter requires ets sites that are bound by GA-binding protein (GABP). The transcriptional coactivator, p300, further increases CD18 RA responsiveness. We demonstrate that GABPalpha, the ets DNA-binding subunit of GABP, physically interacts with p300 in myeloid cells. This interaction involves the GABPalpha pointed domain (PNT) and identifies p300 as the first known interaction partner of GABPalpha PNT. Expression of the PNT domain, alone, disrupts the GABPalpha-p300 interaction and decreases the RA responsiveness of the CD18 proximal promoter. Chromatin immunoprecipitation and chromosome conformation capture demonstrate that, in the presence of RA, GABPalpha and p300 at the proximal promoter recruit retinoic acid receptor/retinoid X receptor from a distal RARE to form an enhanceosome. A dominant negative p300 construct disrupts enhanceosome formation and reduces the RA responsiveness of CD18. Thus, proteins on the CD18 proximal promoter recruit the distal RARE in the presence of RA. This is the first description of an RA-induced enhanceosome and demonstrates that GABP and p300 are essential components of CD18 RA responsiveness in myeloid cells.
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Affiliation(s)
- Karen K Resendes
- Dept. of Molecular Biology, Brown University, Rhode Island Hospital, Providence, RI 02903, USA
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Jeong BC, Kim MY, Lee JH, Kee HJ, Kho DH, Han KE, Qian YR, Kim JK, Kim KK. Brain-specific angiogenesis inhibitor 2 regulates VEGF through GABP that acts as a transcriptional repressor. FEBS Lett 2006; 580:669-76. [PMID: 16412436 DOI: 10.1016/j.febslet.2005.12.086] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [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: 11/29/2005] [Revised: 12/28/2005] [Accepted: 12/29/2005] [Indexed: 10/25/2022]
Abstract
Previously, we reported that decreased brain-specific angiogenesis inhibitor 2 (BAI2) induced increased VEGF expression. The regulatory mechanisms for this process are not understood. Here we show that GA-binding protein gamma (GABPgamma) associates with the cytoplasmic domain of BAI2, and GABPalpha/gamma or GABPalpha/beta works as a transcriptional repressor of VEGF in SHSY5Y cells. Transcriptional activity of wild-type VEGF promoter was significantly increased in anti-sense BAI2-transfected cells, but not that of VEGF promoter harboring mutated GABP sites. In in vivo focal cerebral ischemia model, the decrease in BAI2 accompanied by decreased GABPalpha and GABPgamma elicited increased VEGF expression before the onset of HIF-1alpha. Our results point out that BAI2 controls VEGF transcription through GABP under normal conditions and cerebral ischemia.
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Affiliation(s)
- Byung Chul Jeong
- Department of Pharmacology, Research Institute of Medical Sciences, Medical Research Center for Gene Regulation, Chonnam National University Medical School, Dong-Ku, Kwangju 501-190, Republic of Korea
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Lin JM, Weng Z. Systematic detection of statistically overrepresented DNA motif association rules. Genome Inform 2006; 17:124-33. [PMID: 17503362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
DNA motifs, or cis-elements, are short nucleotide sequence patterns recognized by various transcription factors (TFs). In promoters, these TFs bind in a complex combinatorial manner in order to regulate the expression of a downstream gene. The combinatorial space is frequently large and difficult to manage since vertebrates have thousands of transcription factors and more than 20,000 genes. We introduce a computer program called CAYCE (Combinatorial AnalYsis of Cis-Elements) that systematically detects statistically overrepresented DNA motif association rules independent of Microarray information. CAYCE is an adaptation of the apriori algorithm traditionally used for association rule mining, but offers three significant advancements. (1) It analyzes multiple occurrences of an item, corresponding to multiple TF binding sites, (2) It compares results with a biologically relevant background, and (3), it provides p-values for straightforward statistical interpretation. CAYCE can be easily applied to any item-set data where the investigator is also interested in multiple occurrences of a single item, and/or overrepresentation of association rules compared with a background. Applying CAYCE to human promoters in 1% of the human genome, we discover that motif clusters containing five repetitions of SP1 are the most statistically significant.
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Affiliation(s)
- Jane Marie Lin
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA.
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MacLean JA, Rao MK, Doyle KMH, Richards JS, Wilkinson MF. Regulation of the Rhox5 Homeobox Gene in Primary Granulosa Cells: Preovulatory Expression and Dependence on SP1/SP3 and GABP1. Biol Reprod 2005; 73:1126-34. [PMID: 16093360 DOI: 10.1095/biolreprod.105.042747] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [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: 01/06/2023] Open
Abstract
Homeobox genes encode transcription factors that regulate embryonic development and postnatal events. Rhox5 (previously called Pem), the founding member of a homeobox gene cluster that we recently identified on the X chromosome, is selectively expressed in granulosa cells in the ovary and other somatic-cell types in other reproductive organs. In this report, we investigate its regulation in granulosa cells in the rat ovary. We found that Rhox5 expression in the ovary is governed by the Rhox5 distal promoter and is expressed at least as early as Day 5 postpartum. Rhox5 mRNA levels are regulated during the ovarian cycle, peaking before ovulation. Deletion analysis revealed a 25-nt element essential for distal promoter transcription in primary granulosa cells. This distal promoter element contains two ETS and one SP1 transcription-factor family binding sites that mutagenesis analysis indicated were essential for high-level transcription. This element was both necessary and sufficient for transcription, because it activated transcription when placed upstream of a heterologous minimal promoter. Cold competition and electrophoretic mobility shift assay studies demonstrated that SP1, SP3, and the ETS family transcription factor GABP bound this element. Dominant-negative forms of GABP and SP3 repressed distal promoter expression in primary rat granulosa, showing that these factors are crucial for Rhox5 expression. Cotransfection of dominant-negative mutants indicated that Rhox5 expression in granulosa cells is regulated by the c-Jun N-terminal protein kinase (JNK, MAPK8) and RAS pathways, which are known to be upstream of ETS family transcription factors. The discovery that Rhox5 expression in granulosa cells is regulated by MAPK pathways and ETS and SP1 family members provides an opportunity to understand how these regulatory pathways and factors collaborate to regulate gene expression during the ovarian cycle.
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Affiliation(s)
- James A MacLean
- Department of Immunology, The University of Texas, M.D. Anderson Cancer Center, Houston, Texas 77030, USA
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Patton J, Block S, Coombs C, Martin ME. Identification of functional elements in the murine Gabp alpha/ATP synthase coupling factor 6 bi-directional promoter. Gene 2005; 369:35-44. [PMID: 16309857 DOI: 10.1016/j.gene.2005.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [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: 06/09/2005] [Revised: 09/26/2005] [Accepted: 10/10/2005] [Indexed: 11/19/2022]
Abstract
The GA-repeat binding protein (GABP) is a ubiquitous transcription factor involved in transcriptional regulation of genes encoding proteins involved in a variety of cellular processes including adipocyte differentiation, mitochondrial respiration, and neuromuscular signaling. GABP is composed of two subunits; the GABP alpha subunit is a member of the Ets-family of transcription factors, and the unrelated ankyrin repeat containing GABP beta subunit. We previously identified a bidirectional promoter directing the expression of Gabpa (GAA) gene in one direction and ATP Synthase Coupling Factor 6 (Atp5j) (CF6) gene in the other [Chinenov, Y., Coombs, C. and Martin, M. E., 2000a. "Isolation of a bi-directional promoter directing the expression of the mouse GABP alpha and ATP Synthase Coupling Factor 6 genes. Gene 261:311-320.]. In this study we characterize sequence elements and regulatory factors contributing to the promoter activities of the GAA/CF6 bidirectional promoter. The core of the GAA/CF6 bidirectional promoter is retained within a 400 bp sequence and contains four GABP binding sites, a Sp1/3 binding site and an YY1 binding site. Site-directed mutagenesis demonstrated that while no single factor binding site was essential for promoter activity in either direction, the GA1 site located proximal to the previously mapped transcription start sites functioned cooperatively with the other GABP binding sites and with the Sp1/3 and YY1 sites to provide transcriptional activation of the GAA and CF6 promoters. The other GABP sites and the Sp1/3 and YY1 binding sites were functionally redundant for basal promoter activities in both directions. Electrophoretic mobility shift assays identified multiple DNA-protein complexes containing GABP alpha, GABP beta, Sp1, Sp3 or YY1 proteins, including one ternary complex containing GABP alpha, GABP beta and Sp1 proteins. Binding of GABP to the GAA/CF6 bi-directional promoter provides the potential for autoregulation of GABP alpha expression and confirms the importance of GABP in the coordinate expression of respiratory chain components.
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Affiliation(s)
- John Patton
- Department of Biochemistry, University of Missouri, Columbia, MO 65212, USA
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Cho YM, Shin HD, Park BL, Kim JH, Park KS, Kim SY, Lee HK. Association between polymorphisms in the nuclear respiratory factor 1 gene and type 2 diabetes mellitus in the Korean population. Diabetologia 2005; 48:2033-8. [PMID: 16082529 DOI: 10.1007/s00125-005-1855-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Accepted: 04/02/2005] [Indexed: 01/07/2023]
Abstract
AIMS/HYPOTHESIS Dysfunction in mitochondrial oxidative phosphorylation plays a central role in insulin resistance and type 2 diabetes. Nuclear respiratory factor 1 (NRF1) is a transcription factor that acts on nuclear genes encoding respiratory subunits and components of the mitochondrial transcription and replication machinery. Thus, we investigated its genetic association with type 2 diabetes. METHODS The NRF1 gene was sequenced to identify polymorphisms in 24 Korean DNA samples and then common variants were genotyped in 766 patients with type 2 diabetes and 303 non-diabetic subjects. RESULTS Twelve single nucleotide polymorphisms and one insertion/deletion polymorphism were identified. Six common variants among them were genotyped in a larger study. Although three individual polymorphisms appeared to be associated with type 2 diabetes (g.-46350insdel A, g.+141G>T and g.+54529A>G), the effects were only marginal. However, a haplotype (H2) was associated with a decreased risk of type 2 diabetes and another haplotype (H4) was associated with an increased risk of type 2 diabetes (p values for the Haplo. Score test were 0.009 and 0.004, respectively). CONCLUSIONS/INTERPRETATION We demonstrated that two common haplotypes of NRF1 gene are associated with type 2 diabetes in the Korean population.
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Affiliation(s)
- Y M Cho
- Department of Internal Medicine, Seoul National University College of Medicine, 28 Yongon-dong, Chongno-gu, Seoul 110-744, South Korea
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