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Hayakawa A, Kurokawa T, Kanemoto Y, Sawada T, Mori J, Kato S. Skeletal and gene-regulatory functions of nuclear sex steroid hormone receptors. J Bone Miner Metab 2022; 40:361-374. [PMID: 35076781 DOI: 10.1007/s00774-021-01306-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/16/2021] [Indexed: 10/19/2022]
Abstract
The wide variety of sex hormone actions underlie bone growth and health, and their actions mediate gene regulation by the cognate nuclear receptors. Nuclear androgen and estrogen receptors (AR, and ERα/ERβ) are hormone-dependent and DNA binding- transcription regulatory factors, and gene regulation by sex hormones often accompany with chromatin remodeling under aid of a number of co-regulators. As sex hormone biosynthesis is under highly regulated systemic and local regulations, the skeletal actions of sex hormones could be inferred from only the phenotypic abnormalities in skeleton in mouse genetic models deficient of nuclear receptors selectively in specific types of bone cells as well as at specific cell differentiation stages. Anabolic androgen actions and anti-bone resorptive estrogen actions are discussed here from the phenotypic abnormalities in such model mice. Though rapid gene regulation by sex hormones may not require chromatin reorganization, dynamic chromatin reconfiguration looks to facilitate profound and long-term hormonal actions. In this review, we focus the recent findings in gene regulation at a chromatin level, particularly of the function of enhancer RNAs transcribed from strong enhancers, and in the role of liquid-liquid phase separation state in transcription initiation through chromatin reconfiguration.
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Affiliation(s)
- Akira Hayakawa
- Graduate School of Life Science and Engineering, Iryo Sosei University, 5-5-1, Iino, Chuo-dai, Iwaki, Fukushima, 9708551, Japan
- Research Institute of Innovative Medicine, Tokiwa Foundation, Iwaki, Fukushima, Japan
| | - Tomohiro Kurokawa
- Graduate School of Life Science and Engineering, Iryo Sosei University, 5-5-1, Iino, Chuo-dai, Iwaki, Fukushima, 9708551, Japan
- Research Institute of Innovative Medicine, Tokiwa Foundation, Iwaki, Fukushima, Japan
- School of Medicine, Fukushima Medical University, Fukushima, Fukushima, 960-1295, Japan
| | - Yoshiaki Kanemoto
- Graduate School of Life Science and Engineering, Iryo Sosei University, 5-5-1, Iino, Chuo-dai, Iwaki, Fukushima, 9708551, Japan
- Research Institute of Innovative Medicine, Tokiwa Foundation, Iwaki, Fukushima, Japan
| | - Takahiro Sawada
- Graduate School of Life Science and Engineering, Iryo Sosei University, 5-5-1, Iino, Chuo-dai, Iwaki, Fukushima, 9708551, Japan
- Research Institute of Innovative Medicine, Tokiwa Foundation, Iwaki, Fukushima, Japan
| | - Jinichi Mori
- Graduate School of Life Science and Engineering, Iryo Sosei University, 5-5-1, Iino, Chuo-dai, Iwaki, Fukushima, 9708551, Japan
- Research Institute of Innovative Medicine, Tokiwa Foundation, Iwaki, Fukushima, Japan
- Department of Hematology, Jyoban Hospital, Tokiwa Foundation, Iwaki, Fukushima, Japan
- School of Medicine, Fukushima Medical University, Fukushima, Fukushima, 960-1295, Japan
| | - Shigeaki Kato
- Graduate School of Life Science and Engineering, Iryo Sosei University, 5-5-1, Iino, Chuo-dai, Iwaki, Fukushima, 9708551, Japan.
- Research Institute of Innovative Medicine, Tokiwa Foundation, Iwaki, Fukushima, Japan.
- School of Medicine, Fukushima Medical University, Fukushima, Fukushima, 960-1295, Japan.
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Lagrutta LC, Layerenza JP, Bronsoms S, Trejo SA, Ves-Losada A. Nuclear-lipid-droplet proteome: carboxylesterase as a nuclear lipase involved in lipid-droplet homeostasis. Heliyon 2021; 7:e06539. [PMID: 33817385 PMCID: PMC8010399 DOI: 10.1016/j.heliyon.2021.e06539] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/11/2019] [Accepted: 03/12/2021] [Indexed: 11/20/2022] Open
Abstract
Nuclear-lipid droplets (nLD)—a dynamic cellular organelle that stores neutral lipids, within the nucleus of eukaryotic cells—consists of a hydrophobic triacylglycerol –cholesterol-ester core enriched in oleic acid (OA) surrounded by a monolayer of polar lipids, cholesterol, and proteins. nLD are probably involved in nuclear-lipid homeostasis serving as an endonuclear buffer that provides or incorporates lipids and proteins participating in signaling pathways, as transcription factors and enzymes of lipid metabolism and nuclear processes. In the present work, we analyzed the nLD proteome and hypothesized that nLD-monolayer proteins could be involved in processes similar as the ones occurring in the cLD including lipid metabolism and other cellular functions. We evaluated the rat-liver–nLD proteome under physiological and nonpathological conditions by GeLC-MS2. Since isolated nLD are highly diluted, a protein-concentrating isolation protocol was designed. Thirty-five proteins were identified within the functional categories: cytoskeleton and structural, transcription and translation, histones, protein-folding and posttranslational modification, cellular proliferation and/or cancer, lipid metabolism, and transport. Purified nLD contained an enzyme from the lipid-metabolism pathway, carboxylesterase 1d (Ces1d/Ces3). Nuclear Carboxylesterase localization was confirmed by Western blotting. By in-silico analyses rat Ces1d/Ces3 secondary and tertiary structure predicted would be equivalent to human CES1. These results—the first nLD proteome—demonstrate that a tandem-GeLC-MS2-analysis protocol facilitates studies like these on rat-liver nuclei. A diversity of cellular-protein function was identified indicating the direct or indirect nLD participation and involving Ces1d/Ces3 in the LD-population homeostasis.
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Affiliation(s)
- Lucía C. Lagrutta
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP-CCT-La Plata-CONICET-UNLP), La Plata, Argentina
| | - Juan P. Layerenza
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP-CCT-La Plata-CONICET-UNLP), La Plata, Argentina
| | - Silvia Bronsoms
- Servei de Proteómica i Biología Estructural de la Universitat Autonma de Barcelona, Barcelona, Spain
| | - Sebastián A. Trejo
- Servei de Proteómica i Biología Estructural de la Universitat Autonma de Barcelona, Barcelona, Spain
- Corresponding author.
| | - Ana Ves-Losada
- Instituto de Investigaciones Bioquímicas de La Plata “Profesor Doctor Rodolfo R. Brenner” (INIBIOLP-CCT-La Plata-CONICET-UNLP), La Plata, Argentina
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
- Corresponding author.
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Sawatsubashi S, Nishimura K, Mori J, Kouzmenko A, Kato S. The Function of the Vitamin D Receptor and a Possible Role of Enhancer RNA in Epigenomic Regulation of Target Genes: Implications for Bone Metabolism. J Bone Metab 2019; 26:3-12. [PMID: 30899718 PMCID: PMC6416145 DOI: 10.11005/jbm.2019.26.1.3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/18/2018] [Accepted: 01/15/2019] [Indexed: 12/15/2022] Open
Abstract
Vitamin D (VD) is essential for bone health, and VD or its analogues are widely used in clinics to ameliorate bone loss. The targets and mode of VD anti-osteoporotic actions appear to be different from those of other classes of drugs modulating bone remodeling. VD exerts its biological activities through the nuclear VD receptor (VDR)-mediated transcriptional regulation of target mRNA and non-coding RNA genes. VD-induced gene regulation involves epigenetic modifications of chromatin conformation at the target loci as well as reconfiguration of higher-order chromosomal organization through VDR-mediated recruitment of various regulatory factors. Enhancer RNAs (eRNA), a class of non-coding enhancer-derived RNAs, have recently emerged as VDR target gene candidates that act through reorganization of chromatin looping to induce enhancer-promoter interaction in activation of mRNA-encoding genes. This review outlines the molecular mechanisms of VD actions mediated by the VDR and suggests novel function of eRNAs in VDR transactivation.
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Affiliation(s)
- Shun Sawatsubashi
- Department of Molecular Endocrinology, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Koichi Nishimura
- Center for Regional Cooperation, Iwaki Meisei University, Iwaki, Japan.,Research Institute of Innovative Medicine, Tokiwa Foundation, Jyoban Kamiyunagayamachi, Iwaki, Japan
| | - Jinichi Mori
- Center for Regional Cooperation, Iwaki Meisei University, Iwaki, Japan.,Research Institute of Innovative Medicine, Tokiwa Foundation, Jyoban Kamiyunagayamachi, Iwaki, Japan
| | - Alexander Kouzmenko
- Research Institute of Innovative Medicine, Tokiwa Foundation, Jyoban Kamiyunagayamachi, Iwaki, Japan
| | - Shigeaki Kato
- Center for Regional Cooperation, Iwaki Meisei University, Iwaki, Japan.,Research Institute of Innovative Medicine, Tokiwa Foundation, Jyoban Kamiyunagayamachi, Iwaki, Japan
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Xia B, Li Y, Zhou J, Tian B, Feng L. Identification of potential pathogenic genes associated with osteoporosis. Bone Joint Res 2017; 6:640-648. [PMID: 29203636 PMCID: PMC5935809 DOI: 10.1302/2046-3758.612.bjr-2017-0102.r1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 08/24/2017] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVES Osteoporosis is a chronic disease. The aim of this study was to identify key genes in osteoporosis. METHODS Microarray data sets GSE56815 and GSE56814, comprising 67 osteoporosis blood samples and 62 control blood samples, were obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified in osteoporosis using Limma package (3.2.1) and Meta-MA packages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed to identify biological functions. Furthermore, the transcriptional regulatory network was established between the top 20 DEGs and transcriptional factors using the UCSC ENCODE Genome Browser. Receiver operating characteristic (ROC) analysis was applied to investigate the diagnostic value of several DEGs. RESULTS A total of 1320 DEGs were obtained, of which 855 were up-regulated and 465 were down-regulated. These differentially expressed genes were enriched in Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways, mainly associated with gene expression and osteoclast differentiation. In the transcriptional regulatory network, there were 6038 interactions pairs involving 88 transcriptional factors. In addition, the quantitative reverse transcriptase-polymerase chain reaction result validated the expression of several genes (VPS35, FCGR2A, TBCA, HIRA, TYROBP, and JUND). Finally, ROC analyses showed that VPS35, HIRA, PHF20 and NFKB2 had a significant diagnostic value for osteoporosis. CONCLUSION Genes such as VPS35, FCGR2A, TBCA, HIRA, TYROBP, JUND, PHF20, NFKB2, RPL35A and BICD2 may be considered to be potential pathogenic genes of osteoporosis and may be useful for further study of the mechanisms underlying osteoporosis.Cite this article: B. Xia, Y. Li, J. Zhou, B. Tian, L. Feng. Identification of potential pathogenic genes associated with osteoporosis. Bone Joint Res 2017;6:640-648. DOI: 10.1302/2046-3758.612.BJR-2017-0102.R1.
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Affiliation(s)
- B Xia
- Attending Doctor Department of Orthopedics, Jining No. 1 People's Hospital, 272011 Shandong Province, China
| | - Y Li
- Attending Doctor Department of Orthopedics, Jining No. 1 People's Hospital, 272011 Shandong Province, China
| | - J Zhou
- Attending Doctor Department of Gynecology, Jining No. 1 People's Hospital, 272011 Shandong Province, China
| | - B Tian
- Attending Doctor Department of Orthopedics, Jining No. 1 People's Hospital, 272011 Shandong Province, China
| | - L Feng
- Attending Doctor Department of Orthopedics, Jining No. 1 People's Hospital, 272011 Shandong Province, China
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Potential coordination role between O-GlcNAcylation and epigenetics. Protein Cell 2017; 8:713-723. [PMID: 28488246 PMCID: PMC5636747 DOI: 10.1007/s13238-017-0416-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/20/2017] [Indexed: 11/25/2022] Open
Abstract
Dynamic changes of the post-translational O-GlcNAc modification (O-GlcNAcylation) are controlled by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT) and the glycoside hydrolase O-GlcNAcase (OGA) in cells. O-GlcNAcylation often occurs on serine (Ser) and threonine (Thr) residues of the specific substrate proteins via the addition of O-GlcNAc group by OGT. It has been known that O-GlcNAcylation is not only involved in many fundamental cellular processes, but also plays an important role in cancer development through various mechanisms. Recently, accumulating data reveal that O-GlcNAcylation at histones or non-histone proteins can lead to the start of the subsequent biological processes, suggesting that O-GlcNAcylation as ‘protein code’ or ‘histone code’ may provide recognition platforms or executive instructions for subsequent recruitment of proteins to carry out the specific functions. In this review, we summarize the interaction of O-GlcNAcylation and epigenetic changes, introduce recent research findings that link crosstalk between O-GlcNAcylation and epigenetic changes, and speculate on the potential coordination role of O-GlcNAcylation with epigenetic changes in intracellular biological processes.
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