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Hojo H, Ohba S. Runt-related Transcription Factors and Gene Regulatory Mechanisms in Skeletal Development and Diseases. Curr Osteoporos Rep 2023; 21:485-492. [PMID: 37436583 PMCID: PMC10543954 DOI: 10.1007/s11914-023-00808-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/13/2023]
Abstract
PURPOSE OF REVIEW Runt-related transcription factors (RUNX) play critical roles in skeletal development, metabolism, and diseases. In mammals, three RUNX members, namely RUNX1, RUNX2, and RUNX3, play distinct and redundant roles, although RUNX2 is a dominant factor in skeletal development and several skeletal diseases. This review is to provide an overview of the current understanding of RUNX-mediated transcriptional regulation in different skeletal cell types. RECENT FINDINGS Advances in chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) have revealed genome-wide RUNX-mediated gene regulatory mechanisms, including their association with cis-regulatory elements and putative target genes. Further studies with genome-wide analysis and biochemical assays have shed light on RUNX-mediated pioneering action and involvements of RUNX2 in lipid-lipid phase separation. Emerging multi-layered mechanisms of RUNX-mediated gene regulations help us better understanding of skeletal development and diseases, which also provides clues to think how genome-wide studies can help develop therapeutic strategies for skeletal diseases.
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Affiliation(s)
- Hironori Hojo
- Division of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655 Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo, 113-8655 Japan
| | - Shinsuke Ohba
- Department of Tissue and Developmental Biology, Graduate School of Dentistry, Osaka University, 1-8 Yamadaoka, Suita, Osaka 565-0871 Japan
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Meyer MB, Pike JW. Genomic mechanisms controlling renal vitamin D metabolism. J Steroid Biochem Mol Biol 2023; 228:106252. [PMID: 36657729 PMCID: PMC10006327 DOI: 10.1016/j.jsbmb.2023.106252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023]
Abstract
Vitamin D metabolism centers on regulation in the kidney of CYP27B1 induction by PTH, suppression by FGF23 and 1,25(OH)2D3, and reciprocal CYP24A1 suppression by PTH, and induction by FGF23 and 1,25(OH)2D3. This coordinated genomic regulation through enhancer modules results in the production and dynamic maintenance of circulating endocrine 1,25(OH)2D3 which, together with PTH and FGF23, controls mineral homeostasis. We discovered enhancers near Cyp27b1 in the mouse kidney located within intronic regions of Mettl1 and Mettl21b genes. These kidney-specific enhancers ("M1", "M21") control Cyp27b1. Through CRISPR/Cas deletion, we found that PTH activation of Cyp27b1 is lost with deletion of M1, whereas FGF23 suppression is lost with deletion of M21. The combination of both deletions (M1/M21-DIKO) eliminated the suppression by 1,25(OH)2D3. Cyp24a1 activation by 1,25(OH)2D3 is controlled by a promoter proximal pair of VDREs as well as a distal region - 35 to - 37 kb (DS2). We also found that FGF23 activation and PTH suppression of Cyp24a1 was located in a region - 21 to - 37 kb downstream (DS1). More recently, using in vivo ChIP-seq in mouse kidney, we demonstrate that PTH activation rapidly induces increased recruitment of pCREB and its coactivators, CBP and CRTC2, to the M1 and M21 enhancers near the Cyp27b1 gene. At distal enhancers of the Cyp24a1 gene, PTH suppression promotes dismisses CBP with only minor changes in pCREB and CRTC2 occupancy, all of which correlate with a suppression of basal histone acetylation across this locus and reduced transcripts. Surprisingly, we find that 1,25(OH)2D3 suppression increases the occupancy of CRTC2 in the M1 enhancer, a novel observation for CRTC2 and/or 1,25(OH)2D3 action. The suppressive actions of 1,25(OH)2D3 and FGF23 at the Cyp27b1 gene are associated with a reduction in CBP recruitment at these enhancers. Although FGF23-regulated transcription factors remain unknown, we hypothesize that VDR occupancy induced at the M1 and M21 enhancers by 1,25(OH)2D3 likely disrupts or competes with the active conformation of these CREB modules thereby preventing full induction by PTH. Our findings show coactivators such as CRTC2 and CBP contribute to Cyp27b1 and Cyp24a1 transcription and provide molecular insight into the coordinated mechanistic actions of PTH, FGF23, and 1,25(OH)2D3 in the kidney that regulate mineral homeostasis.
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Affiliation(s)
- Mark B Meyer
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - J Wesley Pike
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Pike JW, Meyer MB. New Approaches to Assess Mechanisms of Action of Selective Vitamin D Analogues. Int J Mol Sci 2021; 22:ijms222212352. [PMID: 34830234 PMCID: PMC8619157 DOI: 10.3390/ijms222212352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 12/28/2022] Open
Abstract
Recent studies of transcription have revealed an advanced set of overarching principles that govern vitamin D action on a genome-wide scale. These tenets of vitamin D transcription have emerged as a result of the application of now well-established techniques of chromatin immunoprecipitation coupled to next-generation DNA sequencing that have now been linked directly to CRISPR-Cas9 genomic editing in culture cells and in mouse tissues in vivo. Accordingly, these techniques have established that the vitamin D hormone modulates sets of cell-type specific genes via an initial action that involves rapid binding of the VDR-ligand complex to multiple enhancer elements at open chromatin sites that drive the expression of individual genes. Importantly, a sequential set of downstream events follows this initial binding that results in rapid histone acetylation at these sites, the recruitment of additional histone modifiers across the gene locus, and in many cases, the appearance of H3K36me3 and RNA polymerase II across gene bodies. The measured recruitment of these factors and/or activities and their presence at specific regions in the gene locus correlate with the emerging presence of cognate transcripts, thereby highlighting sequential molecular events that occur during activation of most genes both in vitro and in vivo. These features provide a novel approach to the study of vitamin D analogs and their actions in vivo and suggest that they can be used for synthetic compound evaluation and to select for novel tissue- and gene-specific features. This may be particularly useful for ligand activation of nuclear receptors given the targeting of these factors directly to genetic sites in the nucleus.
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Affiliation(s)
- John Wesley Pike
- Correspondence: ; Tel.: +1-(608)-262-8229; Fax: +1-(608)-263-7609
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Haussler MR, Livingston S, Sabir ZL, Haussler CA, Jurutka PW. Vitamin D Receptor Mediates a Myriad of Biological Actions Dependent on Its 1,25-Dihydroxyvitamin D Ligand: Distinct Regulatory Themes Revealed by Induction of Klotho and Fibroblast Growth Factor-23. JBMR Plus 2021; 5:e10432. [PMID: 33553988 PMCID: PMC7839824 DOI: 10.1002/jbm4.10432] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/01/2020] [Indexed: 11/21/2022] Open
Abstract
The hormonal vitamin D metabolite, 1,25‐dihydroxyvitamin D [1,25(OH)2D], produced in kidney, acts in numerous end organs via the nuclear vitamin D receptor (VDR) to trigger molecular events that orchestrate bone mineral homeostasis. VDR is a ligand‐controlled transcription factor that obligatorily heterodimerizes with retinoid X receptor (RXR) to target vitamin D responsive elements (VDREs) in the vicinity of vitamin D‐regulated genes. Circulating 1,25(OH)2D concentrations are governed by PTH, an inducer of renal D‐hormone biosynthesis catalyzed by CYP27B1 that functions as the key player in a calcemic endocrine circuit, and by fibroblast growth factor‐23 (FGF23), a repressor of the CYP27B1 renal enzyme, creating a hypophosphatemic endocrine loop. 1,25(OH)2D/VDR–RXR acts in kidney to induce Klotho (a phosphaturic coreceptor for FGF23) to correct hyperphosphatemia, NPT2a/c to correct hypophosphatemia, and TRPV5 and CaBP28k to enhance calcium reabsorption. 1,25(OH)2D‐liganded VDR–RXR functions in osteoblasts/osteocytes by augmenting RANK‐ligand expression to paracrine signal osteoclastic bone resorption, while simultaneously inducing FGF23, SPP1, BGLP, LRP5, ANK1, ENPP1, and TNAP, and conversely repressing RUNX2 and PHEX expression, effecting localized control of mineralization to sculpt the skeleton. Herein, we document the history of 1,25(OH)2D/VDR and summarize recent advances in characterizing their physiology, biochemistry, and mechanism of action by highlighting two examples of 1,25(OH)2D/VDR molecular function. The first is VDR‐mediated primary induction of Klotho mRNA by 1,25(OH)2D in kidney via a mechanism initiated by the docking of liganded VDR–RXR on a VDRE at −35 kb in the mouse Klotho gene. In contrast, the secondary induction of FGF23 by 1,25(OH)2D in bone is proposed to involve rapid nongenomic action of 1,25(OH)2D/VDR to acutely activate PI3K, in turn signaling the induction of MZF1, a transcription factor that, in cooperation with c‐ets1‐P, binds to an enhancer element centered at −263 bp in the promoter‐proximal region of the mouse fgf23 gene. Chronically, 1,25(OH)2D‐induced osteopontin apparently potentiates MZF1. © 2020 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research.
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Affiliation(s)
- Mark R Haussler
- Department of Basic Medical Sciences University of Arizona College of Medicine-Phoenix Phoenix AZ
| | - Sarah Livingston
- School of Mathematical and Natural Sciences Arizona State University Glendale AZ
| | - Zhela L Sabir
- School of Mathematical and Natural Sciences Arizona State University Glendale AZ
| | - Carol A Haussler
- Department of Basic Medical Sciences University of Arizona College of Medicine-Phoenix Phoenix AZ
| | - Peter W Jurutka
- Department of Basic Medical Sciences University of Arizona College of Medicine-Phoenix Phoenix AZ.,School of Mathematical and Natural Sciences Arizona State University Glendale AZ
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5
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Discover novel disease-associated genes based on regulatory networks of long-range chromatin interactions. Methods 2020; 189:22-33. [PMID: 33096239 DOI: 10.1016/j.ymeth.2020.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/29/2020] [Accepted: 10/18/2020] [Indexed: 02/01/2023] Open
Abstract
Identifying genes and non-coding genetic variants that are genetically associated with complex diseases and the underlying mechanisms is one of the most important questions in functional genomics. Due to the limited statistical power and the lack of mechanistic modeling, traditional genome-wide association studies (GWAS) is restricted to fully address this question. Based on multi-omics data integration, cell-type specific regulatory networks can be built to improve GWAS analysis. In this study, we developed a new computational infrastructure, APRIL, to incorporate 3D chromatin interactions into regulatory network construction, which can extend the networks to include long-range cis-regulatory links between non-coding GWAS SNPs and target genes. Combinatorial transcription factors that co-regulate groups of genes are also inferred to further expand the networks with trans-regulation. A suite of machine learning predictions and statistical tests are incorporated in APRIL to predict novel disease-associated genes based on the expanded regulatory networks. Important features of non-coding regulatory elements and genetic variants are prioritized in network-based predictions, providing systems-level insights on the mechanisms of transcriptional dysregulation associated with complex diseases.
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6
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Barter MJ, Cheung K, Falk J, Panagiotopoulos AC, Cosimini C, O'Brien S, Teja-Putri K, Neill G, Deehan DJ, Young DA. Dynamic chromatin accessibility landscape changes following interleukin-1 stimulation. Epigenetics 2020; 16:106-119. [PMID: 32741307 PMCID: PMC7889151 DOI: 10.1080/15592294.2020.1789266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Dynamic modifications of chromatin allow rapid access of the gene regulatory machinery to condensed genomic regions facilitating subsequent gene expression. Inflammatory cytokine stimulation of cells can cause rapid gene expression changes through direct signalling pathway-mediated transcription factor activation and regulatory element binding. Here we used the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) to assess regions of the genome that are differentially accessible following treatment of cells with interleukin-1 (IL-1). We identified 126,483 open chromatin regions, with 241 regions significantly differentially accessible following stimulation, with 64 and 177 more or less accessible, respectively. These differentially accessible regions predominantly correspond to regions of the genome marked as enhancers. Motif searching identified an overrepresentation of a number of transcription factors, most notably RelA, in the regions becoming more accessible, with analysis of ChIP-seq data confirmed RelA binding to these regions. A significant correlation in differential chromatin accessibility and gene expression was also observed. Functionality in regulating gene expression was confirmed using CRISPR/Cas9 genome-editing to delete regions that became more accessible following stimulation in the genes MMP13, IKBKE and C1QTNF1. These same regions were also accessible for activation using a dCas9-transcriptional activator and showed enhancer activity in a cellular model. Together, these data describe and functionally validate a number of dynamically accessible chromatin regions involved in inflammatory signalling.
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Affiliation(s)
- Matt J Barter
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Kathleen Cheung
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK.,Faculty of Medical Sciences, Bioinformatics Support Unit, Newcastle University , Newcastle upon Tyne, UK
| | - Julia Falk
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Andreas C Panagiotopoulos
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Caitlin Cosimini
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Siobhan O'Brien
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Karina Teja-Putri
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - Graham Neill
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
| | - David J Deehan
- Department of Orthopaedics, Freeman Hospital, Orthopaedics , UK
| | - David A Young
- Faculty of Medical Sciences, Skeletal Research Group, Biosciences Institute, Newcastle University , Newcastle upon Tyne, UK
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7
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Hojo H, Ohba S. Gene regulatory landscape in osteoblast differentiation. Bone 2020; 137:115458. [PMID: 32474244 DOI: 10.1016/j.bone.2020.115458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 12/29/2022]
Abstract
The development of osteoblasts, a bone-forming cell population, occurs in conjunction with development of the skeleton, which creates our physical framework and shapes the body. In the past two decades, genetic studies have uncovered the molecular framework of this process-namely, transcriptional regulators and signaling pathways coordinate the cell fate determination and differentiation of osteoblasts in a spatial and temporal manner. Recently emerging genome-wide studies provide additional layers of understanding of the gene regulatory landscape during osteoblast differentiation, allowing us to gain novel insight into the modes of action of the key regulators, functional interaction among the regulator-bound enhancers, epigenetic regulations, and the complex nature of regulatory inputs. In this review, we summarize current understanding of the transcriptional regulation in osteoblasts, in terms of the gene regulatory landscape.
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Affiliation(s)
- Hironori Hojo
- Department of Clinical Biotechnology, Center for Disease Biology and Integrative Medicine, The University of Tokyo Graduate School of Medicine, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Shinsuke Ohba
- Department of Cell Biology, Institute of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8588, Japan.
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8
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Mizuno-Iijima S, Ayabe S, Kato K, Matoba S, Ikeda Y, Dinh TTH, Le HT, Suzuki H, Nakashima K, Hasegawa Y, Hamada Y, Tanimoto Y, Daitoku Y, Iki N, Ishida M, Ibrahim EAE, Nakashiba T, Hamada M, Murata K, Miwa Y, Okada-Iwabu M, Iwabu M, Yagami KI, Ogura A, Obata Y, Takahashi S, Mizuno S, Yoshiki A, Sugiyama F. Efficient production of large deletion and gene fragment knock-in mice mediated by genome editing with Cas9-mouse Cdt1 in mouse zygotes. Methods 2020; 191:23-31. [PMID: 32334080 DOI: 10.1016/j.ymeth.2020.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/10/2020] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Genetically modified mouse models are essential for in vivo investigation of gene function and human disease research. Targeted mutations can be introduced into mouse embryos using genome editing technology such as CRISPR-Cas. Although mice with small indel mutations can be produced, the production of mice carrying large deletions or gene fragment knock-in alleles remains inefficient. We introduced the nuclear localisation property of Cdt1 protein into the CRISPR-Cas system for efficient production of genetically engineered mice. Mouse Cdt1-connected Cas9 (Cas9-mC) was present in the nucleus of HEK293T cells and mouse embryos. Cas9-mC induced a bi-allelic full deletion of Dmd, GC-rich fragment knock-in, and floxed allele knock-in with high efficiency compared to standard Cas9. These results indicate that Cas9-mC is a useful tool for producing mouse models carrying targeted mutations.
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Affiliation(s)
- Saori Mizuno-Iijima
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Shinya Ayabe
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan.
| | - Kanako Kato
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Shogo Matoba
- Bioresource Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yoshihisa Ikeda
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Charles River Laboratories Japan, Inc., 955 Kamibayashi, Ishioka 315-0138, Japan
| | - Tra Thi Huong Dinh
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Hoai Thu Le
- Ph.D Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Hayate Suzuki
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Science, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kenichi Nakashima
- Gene Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yoshikazu Hasegawa
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yuko Hamada
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Tanimoto
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Daitoku
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Natsumi Iki
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Miyuki Ishida
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Elzeftawy Abdelaziz Elsayed Ibrahim
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Toshiaki Nakashiba
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Michito Hamada
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Kazuya Murata
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoshihiro Miwa
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Miki Okada-Iwabu
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Laboratory for Advanced Research on Pathophysiology of Metabolic Diseases, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masato Iwabu
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Laboratory for Advanced Research on Pathophysiology of Metabolic Diseases, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ken-Ichi Yagami
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Yuichi Obata
- Gene Engineering Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Satoru Takahashi
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan; Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Seiya Mizuno
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.
| | - Atsushi Yoshiki
- Experimental Animal Division, RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Fumihiro Sugiyama
- Laborarory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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Bikle DD. Vitamin D: Newer Concepts of Its Metabolism and Function at the Basic and Clinical Level. J Endocr Soc 2020; 4:bvz038. [PMID: 32051922 PMCID: PMC7007804 DOI: 10.1210/jendso/bvz038] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/06/2020] [Indexed: 02/08/2023] Open
Abstract
The interest in vitamin D continues unabated with thousands of publications contributing to a vast and growing literature each year. It is widely recognized that the vitamin D receptor (VDR) and the enzymes that metabolize vitamin D are found in many cells, not just those involved with calcium and phosphate homeostasis. In this mini review I have focused primarily on recent studies that provide new insights into vitamin D metabolism, mechanisms of action, and clinical applications. In particular, I examine how mutations in vitamin D metabolizing enzymes—and new information on their regulation—links vitamin D metabolism into areas such as metabolism and diseases outside that of the musculoskeletal system. New information regarding the mechanisms governing the function of the VDR elucidates how this molecule can be so multifunctional in a cell-specific fashion. Clinically, the difficulty in determining vitamin D sufficiency for all groups is addressed, including a discussion of whether the standard measure of vitamin D sufficiency, total 25OHD (25 hydroxyvitamin) levels, may not be the best measure—at least by itself. Finally, several recent large clinical trials exploring the role of vitamin D supplementation in nonskeletal diseases are briefly reviewed, with an eye toward what questions they answered and what new questions they raised.
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Affiliation(s)
- Daniel D Bikle
- Department of Medicine and Endocrine Research Unit, Veterans Affairs Medical Center and University of California, San Francisco, California
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10
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Meyer MB, Pike JW. Mechanistic homeostasis of vitamin D metabolism in the kidney through reciprocal modulation of Cyp27b1 and Cyp24a1 expression. J Steroid Biochem Mol Biol 2020; 196:105500. [PMID: 31629064 PMCID: PMC6954286 DOI: 10.1016/j.jsbmb.2019.105500] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/07/2019] [Accepted: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Cyp27b1 and Cyp24a1 are reciprocally regulated in the kidney by the key hormones PTH, FGF23, and 1,25(OH)2D3. Our recent genomic studies in mice identified a complex kidney-specific enhancer module located within the introns of adjacent Mettl1 (M1) and Mettl21b (M21) genes that mediate basal and PTH induction of Cyp27b1 as well as suppression by FGF23 and 1,25(OH)2D3. Gross deletion of these segments in mice has severe consequences on skeletal health, and directly affects Cyp27b1 expression in the kidney. Deletion of both M1 and M21 submodules together fully eliminates basal Cyp27b1 expression in the kidney, leading to a systemic and skeletal phenotype similar to that of the Cyp27b1-KO mouse due to depletion of 1,25(OH)2D3 and high PTH. Cyp24a1 levels in the double KO mouse were low due to compensatory regulation by elevated PTH and reduced FGF23. However, expression of Cyp27b1 and retention of its regulation by inflammation (LPS) in the NRTCs remained unperturbed. Dietary normalization of calcium, phosphate, PTH, and FGF23 rescues this aberrant phenotype and normalizes the skeletal issues. Cyp24a1 is controlled by its own unique enhancers for 1,25(OH)2D3, FGF23, and PTH. We were also able to eliminate these activities in mice. Collectively, the hormone-mediated enhancer regulation of both Cyp27b1 and Cyp24a1 in the kidney is responsible for the circulating levels of 1,25(OH)2D3 in the blood which in turn primarily affects calcium and phosphate regulation. Importantly, we can now manipulate this system with our enhancer deletion animal models to study 1,25(OH)2D3 production in non-renal target cells and tissues not only in disease, where it is known to affect the immune system, but also in healthy individuals. Here we will review our studies that have defined a finely balanced homeostatic control mechanism employed by PTH and FGF23 with catastrophic toxicity protection from 1,25(OH)2D3 in the genomic regulation of vitamin D metabolism and its accompanied control of mineral maintenance.
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Affiliation(s)
- Mark B Meyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - J Wesley Pike
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
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11
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Gong Y, Tian S, Xuan Y, Zhang S. Lipid and polymer mediated CRISPR/Cas9 gene editing. J Mater Chem B 2020; 8:4369-4386. [DOI: 10.1039/d0tb00207k] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein 9 (CRISPR/Cas9) system is the most widely used tool for gene editing.
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Affiliation(s)
- Yan Gong
- Key Lab of Biotechnology and Bioresources Utilization of Ministry of Education
- College of Life Science
- Dalian Minzu University
- Dalian
- China
| | - Siyu Tian
- Key Lab of Biotechnology and Bioresources Utilization of Ministry of Education
- College of Life Science
- Dalian Minzu University
- Dalian
- China
| | - Yang Xuan
- Key Lab of Biotechnology and Bioresources Utilization of Ministry of Education
- College of Life Science
- Dalian Minzu University
- Dalian
- China
| | - Shubiao Zhang
- Key Lab of Biotechnology and Bioresources Utilization of Ministry of Education
- College of Life Science
- Dalian Minzu University
- Dalian
- China
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12
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Moena D, Merino P, Lian JB, Stein GS, Stein JL, Montecino M. Switches in histone modifications epigenetically control vitamin D3-dependent transcriptional upregulation of the CYP24A1 gene in osteoblastic cells. J Cell Physiol 2019; 235:5328-5339. [PMID: 31868234 DOI: 10.1002/jcp.29420] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 12/16/2019] [Indexed: 01/17/2023]
Abstract
In bone cells vitamin D dependent regulation of gene expression principally occurs through modulation of gene transcription. Binding of the active vitamin D metabolite, 1,25-dihydroxy vitamin D3 (1,25(OH)2 D3 ) to the vitamin D receptor (VDR) induces conformational changes in its C-terminal domain enabling competency for interaction with physiologically relevant coactivators, including SRC-1. Consequently, regulatory complexes can be assembled that support intrinsic enzymatic activities with competency to posttranslationally modify chromatin histones at target genomic sequences to epigenetically alter transcription. Here we examine specific transitions in representation and/or enrichment of epigenetic histone marks during 1,25(OH)2 D3 mediated upregulation of CYP24A1 gene expression in osteoblastic cells. This gene encodes the 24-hydroxylase enzyme, essential for biological control of vitamin D levels. We demonstrate that as the CYP24A1 gene promoter remains transcriptionally silent, there is enrichment of H4R3me2s together with its "writing" enzyme PRMT5 and decreased abundance of the istone H3 and H4 acetylation, H3R17me2a, and H4R3me2a marks as well as of their corresponding "writers." Exposure of osteoblastic cells to 1,25(OH)2 D3 stimulates the recruitment of a VDR/SRC-1 containing complex to the CYP24A1 promoter to mediate increased H3/H4 acetylation. VDR/SRC-1 binding occurs concomitant with the release of PRMT5 and the recruitment of the arginine methyltransferases CARM1 and PRMT1 to catalyze the deposition of the H3R17me2a and H4R3me2a marks, respectively. Our results indicate that these dynamic transitions of histone marks at the CYP24A1 promoter, provide a "chromatin context" that is transcriptionally competent for activation of the CYP24A1 gene in osteoblastic cells in response to 1,25(OH)2 D3 .
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Affiliation(s)
- Daniel Moena
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences and FONDAP Center for Genome Regulation, Universidad Andres Bello-Santiago, Santiago, Chile.,Department of Biological Sciences, Faculty of Life Sciences, Universidad Andres Bello-Concepcion, Santiago, Chile
| | - Paola Merino
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences and FONDAP Center for Genome Regulation, Universidad Andres Bello-Santiago, Santiago, Chile
| | - Jane B Lian
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont
| | - Gary S Stein
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont
| | - Janet L Stein
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont
| | - Martin Montecino
- Faculty of Medicine and Faculty of Life Sciences, Institute of Biomedical Sciences and FONDAP Center for Genome Regulation, Universidad Andres Bello-Santiago, Santiago, Chile
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13
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Chen D, Kim DJ, Shen J, Zou Z, O'Keefe RJ. Runx2 plays a central role in Osteoarthritis development. J Orthop Translat 2019; 23:132-139. [PMID: 32913706 PMCID: PMC7452174 DOI: 10.1016/j.jot.2019.11.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
Osteoarthritis (OA) is the most common form of arthritis, is the leading cause of impaired mobility in the elderly, and accounts for more than a third of chronic moderate to severe pain. As a degenerative joint disorder, OA affects the whole joint and results in synovial hyperplasia, degradation of articular cartilage, subchondral sclerosis, osteophyte formation, and chronic pain. Currently, there is no effective drug to decelerate OA progression and molecular targets for drug development have been insufficiently investigated. Anti-OA drug development can benefit from more and precise knowledge of molecular targets for drug development. Runt-related transcription factor 2 (Runx2) is a key transcription factor controlling osteoblast and chondrocyte differentiation and is among the most promising potential therapeutic targets. Notably, Runx2 expression is upregulated in several murine OA models, suggesting a role in disease pathogenesis. In this review article, we summarized recent findings on Runx2 related to OA development and evaluated its potential as a therapeutic target. The translational potential of this article A better understanding of the role of Runx2 in osteoarthritis pathogenesis will contribute to the development of novel intervention of osteoarthritis disease.
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Affiliation(s)
- Di Chen
- Research Center for Human Tissues and Organs Degeneration, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dongyeon J Kim
- Department of Orthopedic Surgery, Washington University at St. Louis, MO, USA
| | - Jie Shen
- Department of Orthopedic Surgery, Washington University at St. Louis, MO, USA
| | - Zhen Zou
- Department of Orthopedic Surgery, Washington University at St. Louis, MO, USA
| | - Regis J O'Keefe
- Department of Orthopedic Surgery, Washington University at St. Louis, MO, USA
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14
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Meyer MB, Lee SM, Carlson AH, Benkusky NA, Kaufmann M, Jones G, Pike JW. A chromatin-based mechanism controls differential regulation of the cytochrome P450 gene Cyp24a1 in renal and non-renal tissues. J Biol Chem 2019; 294:14467-14481. [PMID: 31439663 DOI: 10.1074/jbc.ra119.010173] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/08/2019] [Indexed: 12/18/2022] Open
Abstract
Cytochrome P450 family 27 subfamily B member 1 (CYP27B1) and CYP24A1 function to maintain physiological levels of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) in the kidney. Renal Cyp27b1 and Cyp24a1 expression levels are transcriptionally regulated in a highly reciprocal manner by parathyroid hormone (PTH), fibroblast growth factor 23 (FGF23), and 1,25(OH)2D3 In contrast, Cyp24a1 regulation in nonrenal target cells (NRTCs) is limited to induction by 1,25(OH)2D3 Herein, we used ChIP-Seq analyses of mouse tissues to identify regulatory regions within the Cyp24a1 gene locus. We found an extended region downstream of Cyp24a1 containing a cluster of sites, termed C24-DS1, binding PTH-sensitive cAMP-responsive element-binding protein (CREB) and a cluster termed C24-DS2 binding the vitamin D receptor (VDR). VDR-occupied sites were present in both the kidney and NRTCs, but pCREB sites were occupied only in the kidney. We deleted each segment in the mouse and observed that although the overt phenotypes of both cluster deletions were unremarkable, RNA analysis in the C24-DS1-deleted strain revealed a loss of basal renal Cyp24a1 expression, total resistance to FGF23 and PTH regulation, and secondary suppression of renal Cyp27b1; 1,25(OH)2D3 induction remained unaffected in all tissues. In contrast, loss of the VDR cluster in the C24-DS2-deleted strain did not affect 1,25(OH)2D3 induction of renal Cyp24a1 expression yet reduced but did not eliminate Cyp24a1 responses in NRTCs. We conclude that a chromatin-based mechanism differentially regulates Cyp24a1 in the kidney and NRTCs and is essential for the specific functions of Cyp24a1 in these two tissue types.
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Affiliation(s)
- Mark B Meyer
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Seong Min Lee
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Alex H Carlson
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Nancy A Benkusky
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Martin Kaufmann
- Department of Biomedical and Molecular Sciences, Queens University, Kingston, Ontario K7L 3N6, Canada.,Department of Surgery, Queens University, Kingston, Ontario K7L 3N6, Canada
| | - Glenville Jones
- Department of Biomedical and Molecular Sciences, Queens University, Kingston, Ontario K7L 3N6, Canada
| | - J Wesley Pike
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
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15
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Meyer MB, Benkusky NA, Kaufmann M, Lee SM, Redfield RR, Jones G, Pike JW. Targeted genomic deletions identify diverse enhancer functions and generate a kidney-specific, endocrine-deficient Cyp27b1 pseudo-null mouse. J Biol Chem 2019; 294:9518-9535. [PMID: 31053643 DOI: 10.1074/jbc.ra119.008760] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 04/26/2019] [Indexed: 12/19/2022] Open
Abstract
Vitamin D3 is terminally bioactivated in the kidney to 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) via cytochrome P450 family 27 subfamily B member 1 (CYP27B1), whose gene is regulated by parathyroid hormone (PTH), fibroblast growth factor 23 (FGF23), and 1,25(OH)2D3 Our recent genomic studies in the mouse have revealed a complex kidney-specific enhancer module within the introns of adjacent methyltransferase-like 1 (Mettl1) and Mettl21b that mediate basal and PTH-induced expression of Cyp27b1 and FGF23- and 1,25(OH)2D3-mediated repression. Gross deletion of these segments in mice has severe effects on Cyp27b1 regulation and skeletal phenotype but does not affect Cyp27b1 expression in nonrenal target cells (NRTCs). Here, we report a bimodal activity in the Mettl1 intronic enhancer with components responsible for PTH-mediated Cyp27b1 induction and 1,25(OH)2D3-mediated repression and additional activities, including FGF23 repression, within the Mettl21b enhancers. Deletion of both submodules eliminated basal Cyp27b1 expression and regulation in the kidney, leading to systemic and skeletal phenotypes similar to those of Cyp27b1-null mice. However, basal expression and lipopolysaccharide-induced regulation of Cyp27b1 in NRTCs was unperturbed. Importantly, dietary normalization of calcium, phosphate, PTH, and FGF23 rescued the skeletal phenotype of this mutant mouse, creating an ideal in vivo model to study nonrenal 1,25(OH)2D3 production in health and disease. Finally, we confirmed a conserved chromatin landscape in human kidney that is similar to that in mouse. These findings define a finely balanced homeostatic mechanism involving PTH and FGF23 together with protection from 1,25(OH)2D3 toxicity that is responsible for both adaptive vitamin D metabolism and mineral regulation.
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Affiliation(s)
- Mark B Meyer
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706,
| | - Nancy A Benkusky
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Martin Kaufmann
- the Departments of Biomedical and Molecular Sciences and.,Surgery, Queen's University, Kingston, Ontario K7L 3N6, Canada, and
| | - Seong Min Lee
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Robert R Redfield
- the Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | | | - J Wesley Pike
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
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16
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Abstract
Metalloproteinases remain important players in arthritic disease, in part because members of this large enzymatic family, namely matrix metalloproteinase-1 (MMP-1) and MMP-13, are responsible for the irreversible degradation of articular cartilage collagen. Although direct inhibition of MMPs fell out of vogue with the initial clinical disappointment of the first generation of compounds, interest in other mechanisms that control these important enzymes has always been maintained. Since these enzymes are critically important for tissue homeostasis, their expression and activity are tightly regulated at many levels, not just by direct inhibition by their endogenous inhibitors the tissue inhibitors of metalloproteinases (TIMPs). Focussing on MMP-13, we discuss recent work that highlights new discoveries in the transcriptional regulation of this enzyme, from defined promoter functional analysis to how more global technologies can provide insight into the enzyme’s regulation, especially by epigenetic mechanisms, including non-coding RNAs. In terms of protein regulation, we highlight recent findings into enzymatic cascades involved in MMP-13 regulation and activation. Importantly, we highlight a series of recent studies that describe how MMP-13 activity, and in fact that of other metalloproteinases, is in part controlled by receptor-mediated endocytosis. Together, these new discoveries provide a plethora of novel regulatory mechanisms, besides direct inhibition, which with renewed vigour could provide further therapeutic opportunities for regulating the activity of this class of important enzymes.
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Affiliation(s)
- David A Young
- Skeletal Research Group, Institute of Genetic Medicine, Central Parkway, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Matt J Barter
- Skeletal Research Group, Institute of Genetic Medicine, Central Parkway, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - David J Wilkinson
- Skeletal Research Group, Institute of Genetic Medicine, Central Parkway, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
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17
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Park CY. Vitamin D in the Prevention and Treatment of Osteoarthritis: From Clinical Interventions to Cellular Evidence. Nutrients 2019; 11:E243. [PMID: 30678273 PMCID: PMC6413222 DOI: 10.3390/nu11020243] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/03/2019] [Accepted: 01/06/2019] [Indexed: 12/11/2022] Open
Abstract
Older adults are recommended vitamin D to prevent fractures. Though this population is also at risk of osteoarthritis (OA), the effect of vitamin D on OA is unclear and may differ by disease state. The relationship between vitamin D and OA during OA initiation and progression were considered in this narrative review of in vivo and in vitro studies. Regarding OA initiation in humans, the small number of published observational studies suggest a lack of association between induction of OA and vitamin D status. Most randomized controlled trials were performed in White OA patients with relatively high vitamin D status (>50 nmol/L). These studies found no benefit of vitamin D supplementation on OA progression. However, subset analyses and one randomized controlled pilot trial indicated that vitamin D supplementation may alleviate joint pain in OA patients with low vitamin D status (<50 nmol/L). As the etiology of OA is recently being more fully uncovered, better animal and cell models are needed. According to currently available clinical results, evidence is lacking to set a vitamin D level to prevent OA, and increasing vitamin D status above 50 nmol/L does not seem to benefit OA patients.
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18
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New Insights into the Runt Domain of RUNX2 in Melanoma Cell Proliferation and Migration. Cells 2018; 7:cells7110220. [PMID: 30463392 PMCID: PMC6262450 DOI: 10.3390/cells7110220] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 12/13/2022] Open
Abstract
The mortality rate for malignant melanoma (MM) is very high, since it is highly invasive and resistant to chemotherapeutic treatments. The modulation of some transcription factors affects cellular processes in MM. In particular, a higher expression of the osteogenic master gene RUNX2 has been reported in melanoma cells, compared to normal melanocytes. By analyzing public databases for recurrent RUNX2 genetic and epigenetic modifications in melanoma, we found that the most common RUNX2 genetic alteration that exists in transcription upregulation is, followed by genomic amplification, nucleotide substitution and multiple changes. Additionally, altered RUNX2 is involved in unchecked pathways promoting tumor progression, Epithelial Mesenchymal Transition (EMT), and metastasis. In order to investigate further the role of RUNX2 in melanoma development and to identify a therapeutic target, we applied the CRISPR/Cas9 technique to explore the role of the RUNT domain of RUNX2 in a melanoma cell line. RUNT-deleted cells showed reduced proliferation, increased apoptosis, and reduced EMT features, suggesting the involvement of the RUNT domain in different pathways. In addition, del-RUNT cells showed a downregulation of genes involved in migration ability. In an in vivo zebrafish model, we observed that wild-type melanoma cells migrated in 81% of transplanted fishes, while del-RUNT cells migrated in 58%. All these findings strongly suggest the involvement of the RUNT domain in melanoma metastasis and cell migration and indicate RUNX2 as a prospective target in MM therapy.
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19
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CRISPR-based strategies for studying regulatory elements and chromatin structure in mammalian gene control. Mamm Genome 2018; 29:205-228. [PMID: 29196861 PMCID: PMC9881389 DOI: 10.1007/s00335-017-9727-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/27/2017] [Indexed: 01/31/2023]
Abstract
The development of high-throughput methods has enabled the genome-wide identification of putative regulatory elements in a wide variety of mammalian cells at an unprecedented resolution. Extensive genomic studies have revealed the important role of regulatory elements and genetic variation therein in disease formation and risk. In most cases, there is only correlative evidence for the roles of these elements and non-coding changes within these elements in pathogenesis. With the advent of genome- and epigenome-editing tools based on the CRISPR technology, it is now possible to test the functional relevance of the regulatory elements and alterations on a genomic scale. Here, we review the various CRISPR-based strategies that have been developed to functionally validate the candidate regulatory elements in mammals as well as the non-coding genetic variants found to be associated with human disease. We also discuss how these synthetic biology tools have helped to elucidate the role of three-dimensional nuclear architecture and higher-order chromatin organization in shaping functional genome and controlling gene expression.
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20
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Tokarz D, Martins JS, Petit ET, Lin CP, Demay MB, Liu ES. Hormonal Regulation of Osteocyte Perilacunar and Canalicular Remodeling in the Hyp Mouse Model of X-Linked Hypophosphatemia. J Bone Miner Res 2018; 33:499-509. [PMID: 29083055 PMCID: PMC6005377 DOI: 10.1002/jbmr.3327] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/14/2017] [Accepted: 10/27/2017] [Indexed: 01/07/2023]
Abstract
Osteocytes remodel their surrounding perilacunar matrix and canalicular network to maintain skeletal homeostasis. Perilacunar/canalicular remodeling is also thought to play a role in determining bone quality. X-linked hypophosphatemia (XLH) is characterized by elevated serum fibroblast growth factor 23 (FGF23) levels, resulting in hypophosphatemia and decreased production of 1,25 dihydroxyvitamin D (1,25D). In addition to rickets and osteomalacia, long bones from mice with XLH (Hyp) have impaired whole-bone biomechanical integrity accompanied by increased osteocyte apoptosis. To address whether perilacunar/canalicular remodeling is altered in Hyp mice, histomorphometric analyses of tibia and 3D intravital microscopic analyses of calvaria were performed. These studies demonstrate that Hyp mice have larger osteocyte lacunae in both the tibia and calvaria, accompanied by enhanced osteocyte mRNA and protein expression of matrix metalloproteinase 13 (MMP13) and genes classically used by osteoclasts to resorb bone, such as cathepsin K (CTSK). Hyp mice also exhibit impaired canalicular organization, with a decrease in number and branching of canaliculi extending from tibial and calvarial lacunae. To determine whether improving mineral ion and hormone homeostasis attenuates the lacunocanalicular phenotype, Hyp mice were treated with 1,25D or FGF23 blocking antibody (FGF23Ab). Both therapies were shown to decrease osteocyte lacunar size and to improve canalicular organization in tibia and calvaria. 1,25D treatment of Hyp mice normalizes osteocyte expression of MMP13 and classic osteoclast markers, while FGF23Ab decreases expression of MMP13 and selected osteoclast markers. Taken together, these studies point to regulation of perilacunar/canalicular remodeling by physiologic stimuli including hypophosphatemia and 1,25D. © 2017 American Society for Bone and Mineral Research.
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Affiliation(s)
- Danielle Tokarz
- Advanced Microscopy Program, Center for Systems Biology and Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Janaina S Martins
- Harvard Medical School, Boston, MA, USA
- Endocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | | | - Charles P Lin
- Advanced Microscopy Program, Center for Systems Biology and Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Marie B Demay
- Harvard Medical School, Boston, MA, USA
- Endocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Eva S Liu
- Harvard Medical School, Boston, MA, USA
- Endocrine Unit, Massachusetts General Hospital, Boston, MA, USA
- Division of Endocrinology, Diabetes, and Hypertension, Brigham and Women's Hospital, Boston, MA, USA
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21
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Lee SM, Meyer MB, Benkusky NA, O'Brien CA, Pike JW. The impact of VDR expression and regulation in vivo. J Steroid Biochem Mol Biol 2018; 177:36-45. [PMID: 28602960 PMCID: PMC5723236 DOI: 10.1016/j.jsbmb.2017.06.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/02/2017] [Accepted: 06/05/2017] [Indexed: 12/23/2022]
Abstract
The vitamin D receptor (VDR) mediates the pleiotropic biological actions of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3). These actions include orchestration of mineral homeostasis which is coordinated by the kidney, intestine, bone and parathyroid gland wherein the VDR transcriptionally regulates expression of the genes involved in this complex process. Mutations in human VDR (hVDR) cause hereditary vitamin D resistant rickets, a genetic syndrome characterized by hypocalcemia, hyperparathyroidism and rickets resulting from dysregulation of mineral homeostasis. Expression of the VDR is regulated by external stimuli in a tissue-specific manner. However, the mechanisms of this tissue-specificity remain unclear. Studies also suggest that phosphorylation of hVDR at serine 208 impacts the receptor's transcriptional activity. These experiments were conducted in vitro, however, and therefore limited in their conclusions. In this report, we summarize (1) our most recently updated ChIP-seq data from mouse tissues to identify regulatory regions responsible for the tissues-specific regulation of the VDR and (2) our studies to understand the mechanism of hormonal regulation of Vdr expression in bone and kidney in vivo using transgenic mouse strains generated by mouse mini-genes that contain comprehensive genetic information capable of recapitulating endogenous Vdr gene regulation and expression. We also defined the functional human VDR gene locus in vivo by using a human mini-gene comparable to that in the mouse to generate a humanized VDR mouse strain in which the receptor is expressed at normal levels (normal expressor). The present report also shows that a humanized mouse model in which the VDR is expressed at levels about 10-fold lower than the normal expressor mouse rescued the VDR-null phenotype despite its reduced transcriptional activity relative to wildtype expression. We also generated an additional humanized mouse model expressing hVDR bearing a mutation converting serine 208 to alanine (hVDR-S208A). In spite of the mutation, target gene expression induced by the ligand was unchanged relative to a mouse strain expressing comparable levels of wildtype hVDR. Further characterization also showed that serum calcium and parathyroid hormone levels were normal and alopecia was not observed in this hVDR-S208A mouse strain as well. Taken together, our in vivo studies using ChIP-seq analyses and the mini-gene transgenic mice improve our understanding of the tissue-specific regulatory mechanisms of controlling VDR expression and the mechanisms of action of the VDR.
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Affiliation(s)
- Seong Min Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Mark B Meyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Nancy A Benkusky
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States
| | - Charles A O'Brien
- University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - J Wesley Pike
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, United States.
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22
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Krupkova O, Cambria E, Besse L, Besse A, Bowles R, Wuertz‐Kozak K. The potential of CRISPR/Cas9 genome editing for the study and treatment of intervertebral disc pathologies. JOR Spine 2018; 1:e1003. [PMID: 31463435 PMCID: PMC6686831 DOI: 10.1002/jsp2.1003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/09/2018] [Accepted: 02/12/2018] [Indexed: 12/11/2022] Open
Abstract
The CRISPR/Cas9 system has emerged as a powerful tool for mammalian genome engineering. In basic and translational intervertebral disc (IVD) research, this technique has remarkable potential to answer fundamental questions on pathway interactions, to simulate IVD pathologies, and to promote drug development. Furthermore, the precisely targeted CRISPR/Cas9 gene therapy holds promise for the effective and targeted treatment of degenerative disc disease and low back pain. In this perspective, we provide an overview of recent CRISPR/Cas9 advances stemming from/with transferability to IVD research, outline possible treatment approaches for degenerative disc disease, and discuss current limitations that may hinder clinical translation.
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Affiliation(s)
- Olga Krupkova
- Department of Health Sciences and TechnologyInstitute for BiomechanicsETH ZurichSwitzerland
| | - Elena Cambria
- Department of Health Sciences and TechnologyInstitute for BiomechanicsETH ZurichSwitzerland
| | - Lenka Besse
- Department of Oncology and HematologyCantonal Hospital St GallenSt GallenSwitzerland
| | - Andrej Besse
- Department of Oncology and HematologyCantonal Hospital St GallenSt GallenSwitzerland
| | - Robert Bowles
- Department of BioengineeringUniversity of UtahSalt Lake CityUtah
- Department of OrthopaedicsUniversity of UtahSalt Lake CityUtah
| | - Karin Wuertz‐Kozak
- Department of Health Sciences and TechnologyInstitute for BiomechanicsETH ZurichSwitzerland
- Spine CenterSchön Klinik München HarlachingMunichGermany
- Academic Teaching Hospital and Spine Research InstituteParacelsus Private Medical University SalzburgSalzburgAustria
- Department of Health SciencesUniversity of PotsdamPotsdamGermany
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23
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Abstract
The central role of hormonal 1,25-dihydroxyvitamin D3 [1,25(OH)2D3] is to regulate calcium and phosphorus homeostasis via actions in intestine, kidney, and bone. These and other actions in many cell types not involved in mineral metabolism are mediated by the vitamin D receptor. Recent studies using genome-wide scale techniques have extended fundamental ideas regarding vitamin D-mediated control of gene expression while simultaneously revealing a series of new concepts. This article summarizes the current view of the biological actions of the vitamin D hormone and focuses on new concepts that drive the understanding of the mechanisms through which vitamin D operates.
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Affiliation(s)
- J Wesley Pike
- Department of Biochemistry, University of Wisconsin-Madison, Biochem Addition, Room 543D, 433 Babcock Drive, Madison, WI 53706, USA.
| | - Sylvia Christakos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, 185 South Orange Avenue, Newark, NJ 07103, USA
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24
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Onal M, Carlson AH, Thostenson JD, Benkusky NA, Meyer MB, Lee SM, Pike JW. A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene. JBMR Plus 2017. [PMID: 29527594 PMCID: PMC5842943 DOI: 10.1002/jbm4.10023] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Fibroblast growth factor 23 (FGF23) production is regulated by both calciotropic hormones and inflammation. Consistent with this, elevated FGF23 levels are associated with inflammatory markers as well as parathyroid hormone (PTH) in various disease states, including chronic kidney disease (CKD). However, the molecular mechanisms underpinning Fgf23 transcription in response to these regulators are largely unknown. We therefore utilized chromatin immunoprecipitation followed by DNA sequencing (ChIP‐seq) data from an osteocyte cell line to identify potential regulatory regions of the Fgf23 gene. Based on ChIP‐seq analysis of enhancer‐associated histone modifications, including H3K4 methylation and H3K9 acetylation, we discovered several potential enhancers for Fgf23, one of which was located 16kb upstream of the gene's transcriptional start site. Deletion of this putative enhancer from the mouse genome using CRISPR‐Cas9 technology led to lower bone, thymus, and spleen expression of Fgf23 mRNA without altering circulating levels of the intact hormone, although as previously reported, only bone displayed significant basal expression. Nevertheless, lack of the −16kb enhancer blunted FGF23 upregulation in a tissue‐specific manner by the acute inflammatory inducers lipopolysaccharide (LPS), interleukin‐1‐beta (IL‐1β), and tumor necrosis factor‐alpha (TNFα) in bone, non‐osseous tissues, and in circulation. Lack of the −16kb enhancer also inhibited PTH‐induced bone Fgf23 mRNA. Moreover, the absence of this Fgf23 enhancer in an oxalate diet‐induced murine CKD model prevented the early onset induction of osseous, renal, and thymic Fgf23 mRNA levels and led to a significant blunting of elevated circulating intact FGF23 levels. These results suggest that −16kb enhancer mediates the induction of Fgf23 by inflammation and PTH and facilitates the increase in FGF23 expression in a murine model of CKD. As exemplified herein, these Fgf23 enhancer‐deleted mice will provide a unique model in which to study the role of FGF23 expression in inflammatory diseases. © 2017 The Authors. JBMR Plus is published by Wiley Periodicals, Inc. on behalf of the American Society for Bone and Mineral Research.
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Affiliation(s)
- Melda Onal
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.,Department of Physiology and Biophysics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Alex H Carlson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jeff D Thostenson
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Nancy A Benkusky
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Mark B Meyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Seong M Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - J Wesley Pike
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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25
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Hojo H, Chung UI, Ohba S. Identification of the gene-regulatory landscape in skeletal development and potential links to skeletal regeneration. Regen Ther 2017; 6:100-107. [PMID: 30271844 PMCID: PMC6134913 DOI: 10.1016/j.reth.2017.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/03/2017] [Accepted: 04/06/2017] [Indexed: 12/21/2022] Open
Abstract
A class of gene-regulatory elements called enhancers are the main mediators controlling quantitative, temporal and spatial gene expressions. In the course of evolution, the enhancer landscape of higher organisms such as mammals has become quite complex, exerting biological functions precisely and coordinately. In mammalian skeletal development, the master transcription factors Sox9, Runx2 and Sp7/Osterix function primarily through enhancers on the genome to achieve specification and differentiation of skeletal cells. Recently developed genome-scale analyses have shed light on multiple layers of gene regulations, uncovering not only the primary mode of actions of these transcription factors on skeletal enhancers, but also the relation of the epigenetic landscape to three-dimensional chromatin architecture. Here, we review findings on the emerging framework of gene-regulatory networks involved in skeletal development. We further discuss the power of genome-scale analyses to provide new insights into genetic diseases and regenerative medicine in skeletal tissues. Skeletal development is coordinated by master transcription factors. ChIP-seq analyses for the skeletal regulators identified their modes of actions. Analyses of epigenetic landscape features distinct cell types in skeletal tissues. Integrated analyses of the gene regulatory networks link to skeletal regeneration.
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Affiliation(s)
- Hironori Hojo
- Department of Bioengineering, The University of Tokyo Graduate School of Engineering, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ung-Il Chung
- Department of Bioengineering, The University of Tokyo Graduate School of Engineering, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Shinsuke Ohba
- Department of Bioengineering, The University of Tokyo Graduate School of Engineering, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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26
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Abstract
CRISPR/Cas9 genome editing technology has taken the research world by storm since its use in eukaryotes was first proposed in 2012. Publications describing advances in technology and new applications have continued at an unrelenting pace since that time. In this Review, we discuss the application of CRISPR/Cas9 for creating gene mutations - the application that initiated the current avalanche of interest - and new developments that have largely answered initial concerns about its specificity and ability to introduce new gene sequences. We discuss the new, diverse and rapidly growing adaptations of the CRISPR/Cas9 technique that enable activation, repression, multiplexing and gene screening. These developments have enabled researchers to create sophisticated tools for dissecting the function and inter-relatedness of genes, as well as noncoding regions of the genome, and to identify gene networks and noncoding regions that promote disease or confer disease susceptibility. These approaches are beginning to be used to interrogate complex and multilayered biological systems and to produce complex animal models of disease. CRISPR/Cas9 technology has enabled the application of new therapeutic approaches to treating disease in animal models, some of which are beginning to be seen in the first human clinical trials. We discuss the direct application of these techniques to rheumatic diseases, which are currently limited but are sure to increase rapidly in the near future.
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Affiliation(s)
- Gary J Gibson
- Henry Ford Hospital, Bone and Joint Center, 6135 Woodward Avenue, Detroit, Michigan 48202, USA
| | - Maozhou Yang
- Henry Ford Hospital, Bone and Joint Center, 6135 Woodward Avenue, Detroit, Michigan 48202, USA
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27
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Pike JW, Meyer MB, Lee SM, Onal M, Benkusky NA. The vitamin D receptor: contemporary genomic approaches reveal new basic and translational insights. J Clin Invest 2017; 127:1146-1154. [PMID: 28240603 DOI: 10.1172/jci88887] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The vitamin D receptor (VDR) is the single known regulatory mediator of hormonal 1,25-dihydroxyvitamin D3 [1,25(OH)2D3] in higher vertebrates. It acts in the nucleus of vitamin D target cells to regulate the expression of genes whose products control diverse, cell type-specific biological functions that include mineral homeostasis. In this Review we describe progress that has been made in defining new cellular sites of action of this receptor, the mechanisms through which this mediator controls the expression of genes, the biology that ensues, and the translational impact of this receptor on human health and disease. We conclude with a brief discussion of what comes next in understanding vitamin D biology and the mechanisms that underlie its actions.
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28
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Yang MG, West AE. Editing the Neuronal Genome: a CRISPR View of Chromatin Regulation in Neuronal Development, Function, and Plasticity. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2016; 89:457-470. [PMID: 28018138 PMCID: PMC5168825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dynamic orchestration of gene expression is crucial for the proper differentiation, function, and adaptation of cells. In the brain, transcriptional regulation underlies the incredible diversity of neuronal cell types and contributes to the ability of neurons to adapt their function to the environment. Recently, novel methods for genome and epigenome editing have begun to revolutionize our understanding of gene regulatory mechanisms. In particular, the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has proven to be a particularly accessible and adaptable technique for genome engineering. Here, we review the use of CRISPR/Cas9 in neurobiology and discuss how these studies have advanced understanding of nervous system development and plasticity. We cover four especially salient applications of CRISPR/Cas9: testing the consequences of enhancer mutations, tagging genes and gene products for visualization in live cells, directly activating or repressing enhancers in vivo, and manipulating the epigenome. In each case, we summarize findings from recent studies and discuss evolving adaptations of the method.
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Affiliation(s)
| | - Anne E. West
- Anne West, Department of Neurobiology, DUMC Box 3209, 311 Research Drive, Bryan Research 301D, Durham, NC 27710, Phone: 919-681-1909, Fax: 919-668-4431,
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29
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An Emerging Regulatory Landscape for Skeletal Development. Trends Genet 2016; 32:774-787. [PMID: 27814929 DOI: 10.1016/j.tig.2016.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/21/2016] [Accepted: 10/04/2016] [Indexed: 02/02/2023]
Abstract
Skeletal development creates the physical framework that shapes our body and its actions. In the past two decades, genetic studies have provided important insights into the molecular processes at play, including the roles of signaling pathways and transcriptional effectors that coordinate an orderly, progressive emergence and expansion of distinct cartilage and bone cell fates in an invariant temporal and spatial pattern for any given skeletal element within that specific vertebrate species. Genome-scale studies have provided additional layers of understanding, moving from individual genes to the gene regulatory landscape, integrating regulatory information through cis-regulatory modules into cell type-specific gene regulatory programs. This review discusses our current understanding of the transcriptional control of mammalian skeletal development, focusing on recent genome-scale studies.
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30
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Meyer MB, Benkusky NA, Onal M, Pike JW. Selective regulation of Mmp13 by 1,25(OH) 2D 3, PTH, and Osterix through distal enhancers. J Steroid Biochem Mol Biol 2016; 164:258-264. [PMID: 26348136 PMCID: PMC4779429 DOI: 10.1016/j.jsbmb.2015.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/21/2015] [Accepted: 09/03/2015] [Indexed: 11/24/2022]
Abstract
Matrix metalloproteinase 13 (MMP13, collagenase-3) is a vital component for chondrocyte and osteoblast maturation, and is aberrantly expressed in numerous disease states. At the transcriptional level, Mmp13 is controlled by many different growth factors and hormones. Most notably, Mmp13 is regulated by the vitamin D hormone (1,25(OH)2D3), parathyroid hormone (PTH), and several cytokines. These activities occur through participation by the transcription factors VDR, RUNX2, FOS, JUN, and Osterix (OSX), respectively. Recently, we discovered that Mmp13 is regulated by elements quite distal to the transcriptional start site -10, -20, and -30kb upstream. These enhancers, along with minor contributions from the region proximal to the promoter, are responsible for the ligand inducible and, most strikingly, the basal activities of Mmp13 gene regulation. Here, we found that the actions of PTH and OSX do not occur through the -10kb VDR bound enhancer. Rather, the -30kb RUNX2 bound enhancer and the promoter proximal regions were essential for activity. Through RUNX2 deletion and OSX overexpression in cells, we showed a specific role for OSX in Mmp13 regulation. Finally, we created an in vivo CRISPR deleted -10kb enhancer mouse model. Despite normal bone density and growth, they fail to up-regulate Mmp13 in response to 1,25(OH)2D3. These data are consistent with those obtained through UAMS osteoblast cell culture and further define the specific roles of distal enhancers in the regulation of Mmp13.
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Affiliation(s)
- Mark B Meyer
- University of Wisconsin at Madison, Madison, WI 53706, USA.
| | | | - Melda Onal
- University of Wisconsin at Madison, Madison, WI 53706, USA
| | - J Wesley Pike
- University of Wisconsin at Madison, Madison, WI 53706, USA
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31
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Wang S, Zang C, Xiao T, Fan J, Mei S, Qin Q, Wu Q, Li X, Xu K, He HH, Brown M, Meyer CA, Liu XS. Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles. Genome Res 2016; 26:1417-1429. [PMID: 27466232 PMCID: PMC5052056 DOI: 10.1101/gr.201574.115] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 07/21/2016] [Indexed: 01/01/2023]
Abstract
Model-based analysis of regulation of gene expression (MARGE) is a framework for interpreting the relationship between the H3K27ac chromatin environment and differentially expressed gene sets. The framework has three main functions: MARGE-potential, MARGE-express, and MARGE-cistrome. MARGE-potential defines a regulatory potential (RP) for each gene as the sum of H3K27ac ChIP-seq signals weighted by a function of genomic distance from the transcription start site. The MARGE framework includes a compendium of RPs derived from 365 human and 267 mouse H3K27ac ChIP-seq data sets. Relative RPs, scaled using this compendium, are superior to superenhancers in predicting BET (bromodomain and extraterminal domain) -inhibitor repressed genes. MARGE-express, which uses logistic regression to retrieve relevant H3K27ac profiles from the compendium to accurately model a query set of differentially expressed genes, was tested on 671 diverse gene sets from MSigDB. MARGE-cistrome adopts a novel semisupervised learning approach to identify cis-regulatory elements regulating a gene set. MARGE-cistrome exploits information from H3K27ac signal at DNase I hypersensitive sites identified from published human and mouse DNase-seq data. We tested the framework on newly generated RNA-seq and H3K27ac ChIP-seq profiles upon siRNA silencing of multiple transcriptional and epigenetic regulators in a prostate cancer cell line, LNCaP-abl. MARGE-cistrome can predict the binding sites of silenced transcription factors without matched H3K27ac ChIP-seq data. Even when the matching H3K27ac ChIP-seq profiles are available, MARGE leverages public H3K27ac profiles to enhance these data. This study demonstrates the advantage of integrating a large compendium of historical epigenetic data for genomic studies of transcriptional regulation.
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Affiliation(s)
- Su Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Shanghai, 200433, China; Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Chongzhi Zang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Tengfei Xiao
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Jingyu Fan
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Shenglin Mei
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Qian Qin
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Qiu Wu
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Xujuan Li
- Department of Bioinformatics, School of Life Science and Technology, Tongji University, Shanghai, 200092, China
| | - Kexin Xu
- Department of Molecular Medicine/Institute of Biotechnology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229-3900, USA
| | - Housheng Hansen He
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Myles Brown
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USA
| | - Clifford A Meyer
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
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32
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Meyer MB, Benkusky NA, Sen B, Rubin J, Pike JW. Epigenetic Plasticity Drives Adipogenic and Osteogenic Differentiation of Marrow-derived Mesenchymal Stem Cells. J Biol Chem 2016; 291:17829-47. [PMID: 27402842 DOI: 10.1074/jbc.m116.736538] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Indexed: 12/11/2022] Open
Abstract
Terminal differentiation of multipotent stem cells is achieved through a coordinated cascade of activated transcription factors and epigenetic modifications that drive gene transcription responsible for unique cell fate. Within the mesenchymal lineage, factors such as RUNX2 and PPARγ are indispensable for osteogenesis and adipogenesis, respectively. We therefore investigated genomic binding of transcription factors and accompanying epigenetic modifications that occur during osteogenic and adipogenic differentiation of mouse bone marrow-derived mesenchymal stem cells (MSCs). As assessed by ChIP-sequencing and RNA-sequencing analyses, we found that genes vital for osteogenic identity were linked to RUNX2, C/EBPβ, retinoid X receptor, and vitamin D receptor binding sites, whereas adipocyte differentiation favored PPARγ, retinoid X receptor, C/EBPα, and C/EBPβ binding sites. Epigenetic marks were clear predictors of active differentiation loci as well as enhancer activities and selective gene expression. These marrow-derived MSCs displayed an epigenetic pattern that suggested a default preference for the osteogenic pathway; however, these patterns were rapidly altered near the Adipoq, Cidec, Fabp4, Lipe, Plin1, Pparg, and Cebpa genes during adipogenic differentiation. Surprisingly, we found that these cells also exhibited an epigenetic plasticity that enabled them to trans-differentiate from adipocytes to osteoblasts (and vice versa) after commitment, as assessed by staining, gene expression, and ChIP-quantitative PCR analysis. The osteogenic default pathway may be subverted during pathological conditions, leading to skeletal fragility and increased marrow adiposity during aging, estrogen deficiency, and skeletal unloading. Taken together, our data provide an increased mechanistic understanding of the epigenetic programs necessary for multipotent differentiation of MSCs that may prove beneficial in the development of therapeutic strategies.
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Affiliation(s)
- Mark B Meyer
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 and
| | - Nancy A Benkusky
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 and
| | - Buer Sen
- the Department of Medicine, University of North Carolina, Chapel Hill, North Carolina 27514
| | - Janet Rubin
- the Department of Medicine, University of North Carolina, Chapel Hill, North Carolina 27514
| | - J Wesley Pike
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706 and
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33
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Ricarte F, Nakatani T, Partridge N. PTH Signaling and Epigenetic Control of Bone Remodeling. ACTA ACUST UNITED AC 2016; 2:55-61. [PMID: 27152252 DOI: 10.1007/s40610-016-0033-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
As our understanding of the mechanisms that govern bone development advance, the role of epigenetic modifications in these processes become increasingly evident. Interestingly, in parathyroid hormone (PTH)-induced bone metabolism and remodeling, recent evidence shows that PTH signaling employs a particular facet of the epigenetic machinery to elicit its desired effects. In this review, we briefly discuss the known epigenetic events occurring in cells of the osteoblast lineage. More specifically, we elaborate on current findings that reveal the utilization of histone deacetylating enzymes (HDACs) in PTH-regulated modulation of gene expression in bone.
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Affiliation(s)
- Florante Ricarte
- New York University School of Medicine, Sackler Institute of Graduate Biomedical Sciences, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016
| | - Teruyo Nakatani
- New York University College of Dentistry, Department of Basic Science and Craniofacial Biology, New York, NY 10010
| | - Nicola Partridge
- New York University School of Medicine, Sackler Institute of Graduate Biomedical Sciences, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016; New York University College of Dentistry, Department of Basic Science and Craniofacial Biology, New York, NY 10010
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34
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Onal M, St John HC, Danielson AL, Pike JW. Deletion of the Distal Tnfsf11 RL-D2 Enhancer That Contributes to PTH-Mediated RANKL Expression in Osteoblast Lineage Cells Results in a High Bone Mass Phenotype in Mice. J Bone Miner Res 2016; 31:416-29. [PMID: 26332516 PMCID: PMC4835217 DOI: 10.1002/jbmr.2698] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/24/2015] [Accepted: 08/27/2015] [Indexed: 12/24/2022]
Abstract
Receptor activator of nuclear factor-κB ligand (RANKL) is a tumor necrosis factor (TNF)-like cytokine that is necessary for osteoclast formation and survival. Elevated RANKL synthesis is associated with both increased osteoclast number and bone resorption. Earlier studies identified an enhancer 76 kb upstream of the Tnfsf11 transcriptional start site (TSS) termed RL-D5 or the distal control region (DCR) that modulates RANKL expression in response to PTH, 1,25(OH)2D3,, and an array of cytokines. Mice lacking RL-D5 exhibit high bone mass associated with decreased RANKL expression in bone, spleen, and thymus. In addition to RL-D5, genome-wide studies have identified 9 additional Tnfsf11 enhancers residing upstream of the gene's TSS, which provide RANKL cell type-specificity and responsiveness to local and systemic factors. ChIP-chip analyses has revealed inducible vitamin D receptor (VDR) and cAMP response element-binding protein (CREB) binding at an enhancer termed RL-D2 23 kb upstream of the Tnfsf11 TSS in osteoblastic ST2 cells. Herein, we use ChIP-seq analyses to confirm this finding and then delete this enhancer from the mouse genome to determine its physiological role in vivo. RL-D2(-/-) primary stromal cells showed decreased RANKL-induction by both forskolin and 1,25(OH)2D3 ex vivo. Consistent with this, the parathyroid hormone (PTH) induction of RANKL expression was significantly blunted in RL-D2(-/-) mice in vivo. In contrast, lack of RL-D2 had no effect on 1,25(OH)2D3 induction of RANKL in vivo. Similar to the results found in RL-D5(-/-) mice, lack of RL-D2 led to decreased skeletal RANKL expression, resulting in decreased osteoclast numbers and a progressive increase in bone mineral density. Lack of RL-D2 increased cancellous bone mass in femur and spine but did not alter femoral cortical bone thickness. These results highlight the role of distal enhancers in the regulation of RANKL expression by PTH and perhaps 1,25(OH)2D3 and suggest that the RL-D2 and RL-D5 enhancers contribute in either an additive or synergistic manner to regulate bone remodeling.
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Affiliation(s)
- Melda Onal
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Hillary C St John
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Allison L Danielson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - J Wesley Pike
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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35
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Genomic Views of Transcriptional Enhancers: Essential Determinants of Cellular Identity and Activity-Dependent Responses in the CNS. J Neurosci 2016; 35:13819-26. [PMID: 26468181 DOI: 10.1523/jneurosci.2622-15.2015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED Sprinkled throughout the genome are a million regulatory sequences called transcriptional enhancers that activate gene promoters in the right cells, at the right time. Enhancers endow the brain with its incredible diversity of cell types and also translate neural activity into gene induction. Thanks to rapid advances in genomic technologies, it is now possible to identify thousands of enhancers rapidly, test their transcriptional function en masse, and address their neurobiological functions via genome editing. Enhancers also promise to be a great technological opportunity for neuroscience, offering the potential for cell-type-specific genetic labeling and manipulation without the need for transgenesis. The objective of this review and the accompanying 2015 SfN mini-symposium is to highlight the use of new and emerging genomic technologies to probe enhancer function in the nervous system. SIGNIFICANCE STATEMENT Transcriptional enhancers turn on genes in the right cells, at the right time. Enhancers are also the genomic sequences that encode the incredible diversity of cell types in the brain and enable the brain to turn genes on in response to new experiences. New technology enables enhancers to be found and manipulated. The study of enhancers promises to inform our understanding of brain development and function. The application of enhancer technology holds promise in accelerating basic neuroscience research and enabling gene therapies to be targeted to specific cell types in the brain.
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36
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Haussler MR, Whitfield GK, Haussler CA, Sabir MS, Khan Z, Sandoval R, Jurutka PW. 1,25-Dihydroxyvitamin D and Klotho: A Tale of Two Renal Hormones Coming of Age. VITAMINS AND HORMONES 2016; 100:165-230. [PMID: 26827953 DOI: 10.1016/bs.vh.2015.11.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
1,25-Dihydroxyvitamin D3 (1,25D) is the renal metabolite of vitamin D that signals through binding to the nuclear vitamin D receptor (VDR). The ligand-receptor complex transcriptionally regulates genes encoding factors stimulating calcium and phosphate absorption plus bone remodeling, maintaining a skeleton with reduced risk of age-related osteoporotic fractures. 1,25D/VDR signaling exerts feedback control of Ca/PO4 via regulation of FGF23, klotho, and CYP24A1 to prevent age-related, ectopic calcification, fibrosis, and associated pathologies. Vitamin D also elicits xenobiotic detoxification, oxidative stress reduction, neuroprotective functions, antimicrobial defense, immunoregulation, anti-inflammatory/anticancer actions, and cardiovascular benefits. Many of the healthspan advantages conferred by 1,25D are promulgated by its induction of klotho, a renal hormone that is an anti-aging enzyme/coreceptor that protects against skin atrophy, osteopenia, hyperphosphatemia, endothelial dysfunction, cognitive defects, neurodegenerative disorders, and impaired hearing. In addition to the high-affinity 1,25D hormone, low-affinity nutritional VDR ligands including curcumin, polyunsaturated fatty acids, and anthocyanidins initiate VDR signaling, whereas the longevity principles resveratrol and SIRT1 potentiate VDR signaling. 1,25D exerts actions against neural excitotoxicity and induces serotonin mood elevation to support cognitive function and prosocial behavior. Together, 1,25D and klotho maintain the molecular signaling systems that promote growth (p21), development (Wnt), antioxidation (Nrf2/FOXO), and homeostasis (FGF23) in tissues crucial for normal physiology, while simultaneously guarding against malignancy and degeneration. Therefore, liganded-VDR modulates the expression of a "fountain of youth" array of genes, with the klotho target emerging as a major player in the facilitation of health span by delaying the chronic diseases of aging.
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Affiliation(s)
- Mark R Haussler
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona, USA.
| | - G Kerr Whitfield
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona, USA
| | - Carol A Haussler
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona, USA
| | - Marya S Sabir
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, Arizona, USA
| | - Zainab Khan
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, Arizona, USA
| | - Ruby Sandoval
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, Arizona, USA
| | - Peter W Jurutka
- Department of Basic Medical Sciences, University of Arizona College of Medicine, Phoenix, Arizona, USA; School of Mathematical and Natural Sciences, Arizona State University, Glendale, Arizona, USA
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Christakos S, Dhawan P, Verstuyf A, Verlinden L, Carmeliet G. Vitamin D: Metabolism, Molecular Mechanism of Action, and Pleiotropic Effects. Physiol Rev 2016; 96:365-408. [PMID: 26681795 PMCID: PMC4839493 DOI: 10.1152/physrev.00014.2015] [Citation(s) in RCA: 1055] [Impact Index Per Article: 131.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
1,25-Dihydroxvitamin D3 [1,25(OH)2D3] is the hormonally active form of vitamin D. The genomic mechanism of 1,25(OH)2D3 action involves the direct binding of the 1,25(OH)2D3 activated vitamin D receptor/retinoic X receptor (VDR/RXR) heterodimeric complex to specific DNA sequences. Numerous VDR co-regulatory proteins have been identified, and genome-wide studies have shown that the actions of 1,25(OH)2D3 involve regulation of gene activity at a range of locations many kilobases from the transcription start site. The structure of the liganded VDR/RXR complex was recently characterized using cryoelectron microscopy, X-ray scattering, and hydrogen deuterium exchange. These recent technological advances will result in a more complete understanding of VDR coactivator interactions, thus facilitating cell and gene specific clinical applications. Although the identification of mechanisms mediating VDR-regulated transcription has been one focus of recent research in the field, other topics of fundamental importance include the identification and functional significance of proteins involved in the metabolism of vitamin D. CYP2R1 has been identified as the most important 25-hydroxylase, and a critical role for CYP24A1 in humans was noted in studies showing that inactivating mutations in CYP24A1 are a probable cause of idiopathic infantile hypercalcemia. In addition, studies using knockout and transgenic mice have provided new insight on the physiological role of vitamin D in classical target tissues as well as evidence of extraskeletal effects of 1,25(OH)2D3 including inhibition of cancer progression, effects on the cardiovascular system, and immunomodulatory effects in certain autoimmune diseases. Some of the mechanistic findings in mouse models have also been observed in humans. The identification of similar pathways in humans could lead to the development of new therapies to prevent and treat disease.
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Affiliation(s)
- Sylvia Christakos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey; and Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Puneet Dhawan
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey; and Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Annemieke Verstuyf
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey; and Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Lieve Verlinden
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey; and Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
| | - Geert Carmeliet
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, New Jersey; and Laboratory of Clinical and Experimental Endocrinology, KU Leuven, Leuven, Belgium
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Tak YG, Farnham PJ. Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenetics Chromatin 2015; 8:57. [PMID: 26719772 PMCID: PMC4696349 DOI: 10.1186/s13072-015-0050-4] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022] Open
Abstract
Considerable progress towards an understanding of complex diseases has been made in recent years due to the development of high-throughput genotyping technologies. Using microarrays that contain millions of single-nucleotide polymorphisms (SNPs), Genome Wide Association Studies (GWASs) have identified SNPs that are associated with many complex diseases or traits. For example, as of February 2015, 2111 association studies have identified 15,396 SNPs for various diseases and traits, with the number of identified SNP-disease/trait associations increasing rapidly in recent years. However, it has been difficult for researchers to understand disease risk from GWAS results. This is because most GWAS-identified SNPs are located in non-coding regions of the genome. It is important to consider that the GWAS-identified SNPs serve only as representatives for all SNPs in the same haplotype block, and it is equally likely that other SNPs in high linkage disequilibrium (LD) with the array-identified SNPs are causal for the disease. Because it was hoped that disease-associated coding variants would be identified if the true casual SNPs were known, investigators have expanded their analyses using LD calculation and fine-mapping. However, such analyses also identified risk-associated SNPs located in non-coding regions. Thus, the GWAS field has been left with the conundrum as to how a single-nucleotide change in a non-coding region could confer increased risk for a specific disease. One possible answer to this puzzle is that the variant SNPs cause changes in gene expression levels rather than causing changes in protein function. This review provides a description of (1) advances in genomic and epigenomic approaches that incorporate functional annotation of regulatory elements to prioritize the disease risk-associated SNPs that are located in non-coding regions of the genome for follow-up studies, (2) various computational tools that aid in identifying gene expression changes caused by the non-coding disease-associated SNPs, and (3) experimental approaches to identify target genes of, and study the biological phenotypes conferred by, non-coding disease-associated SNPs.
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Affiliation(s)
- Yu Gyoung Tak
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
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Lee SM, Meyer MB, Benkusky NA, O'Brien CA, Pike JW. Mechanisms of Enhancer-mediated Hormonal Control of Vitamin D Receptor Gene Expression in Target Cells. J Biol Chem 2015; 290:30573-86. [PMID: 26504088 PMCID: PMC4683277 DOI: 10.1074/jbc.m115.693614] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 10/14/2015] [Indexed: 12/18/2022] Open
Abstract
The biological actions of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) are mediated by the vitamin D receptor (VDR), whose expression in bone cells is regulated positively by 1,25(OH)2D3, retinoic acid, and parathyroid hormone through both intergenic and intronic enhancers. In this report, we used ChIP-sequencing analysis to confirm the presence of these Vdr gene enhancers in mesenchyme-derived bone cells and to describe the epigenetic histone landscape that spans the Vdr locus. Using bacterial artificial chromosome-minigene stable cell lines, CRISPR/Cas9 enhancer-deleted daughter cell lines, transient transfection/mutagenesis analyses, and transgenic mice, we confirmed the functionality of these bone cell enhancers in vivo as well as in vitro. We also identified VDR-binding sites across the Vdr gene locus in kidney and intestine using ChIP-sequencing analysis, revealing that only one of the bone cell-type enhancers bound VDR in kidney tissue, and none were occupied by the VDR in the intestine, consistent with weak or absent regulation by the 1,25(OH)2D3 hormone in these tissues, respectively. However, a number of additional sites of VDR binding unique to either kidney or intestine were present further upstream of the Vdr gene, suggesting the potential for alternative regulatory loci. Importantly, virtually all of these regions retained histone signatures consistent with those of enhancers and exhibited unique DNase I hypersensitivity profiles that reflected the potential for chromatin access. These studies define mechanisms associated with hormonal regulation of the Vdr and hint at the differential nature of VDR binding activity at the Vdr gene in different primary target tissues in vivo.
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Affiliation(s)
- Seong Min Lee
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and
| | - Mark B Meyer
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and
| | - Nancy A Benkusky
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and
| | - Charles A O'Brien
- the Department of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205
| | - J Wesley Pike
- From the Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and
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Pike JW, Meyer MB, Benkusky NA, Lee SM, St John H, Carlson A, Onal M, Shamsuzzaman S. Genomic Determinants of Vitamin D-Regulated Gene Expression. VITAMINS AND HORMONES 2015; 100:21-44. [PMID: 26827947 DOI: 10.1016/bs.vh.2015.10.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Insight into mechanisms that link the actions of 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) to the regulation of gene expression has evolved extensively since the initial discovery of a nuclear protein known as the vitamin D receptor (VDR). Perhaps most important was the molecular cloning of this receptor which enabled its inclusion within the nuclear receptor gene family and further studies of both its structure and regulatory function. Current studies are now refocused on the vitamin D hormone's action at the genome, where VDR together with other transcription factors coordinates the recruitment of chromatin active coregulatory complexes that participate directly in the modification of gene output. These studies highlight the role of chromatin in the expression of genes and the dynamic impact of the epigenetic landscape that contextualizes individual gene loci thus influencing the VDR's transcriptional actions. In this chapter, we summarize advances made over the past few years in understanding vitamin D action on a genome-wide scale, focusing on overarching principles that have emerged at this level. Of particular significance is the finding that dynamic changes that occur to the genome during cellular differentiation at both genetic and epigenetic levels profoundly alter the ability of 1,25(OH)2D3 and its receptor to regulate gene expression. We address the broad impact of differentiation on specific epigenetic histone modifications that occur across the genome and the ability of the VDR to influence this activity at selected gene loci as well. These studies advance our understanding of not only vitamin D action but also of the complex and dynamic role played by the genome itself as a major determinant of VDR activity.
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Affiliation(s)
- J Wesley Pike
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
| | - Mark B Meyer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nancy A Benkusky
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Seong Min Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Hillary St John
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alex Carlson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Melda Onal
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sohel Shamsuzzaman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Yao L, Berman BP, Farnham PJ. Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes. Crit Rev Biochem Mol Biol 2015; 50:550-73. [PMID: 26446758 PMCID: PMC4666684 DOI: 10.3109/10409238.2015.1087961] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Enhancers are short regulatory sequences bound by sequence-specific transcription factors and play a major role in the spatiotemporal specificity of gene expression patterns in development and disease. While it is now possible to identify enhancer regions genomewide in both cultured cells and primary tissues using epigenomic approaches, it has been more challenging to develop methods to understand the function of individual enhancers because enhancers are located far from the gene(s) that they regulate. However, it is essential to identify target genes of enhancers not only so that we can understand the role of enhancers in disease but also because this information will assist in the development of future therapeutic options. After reviewing models of enhancer function, we discuss recent methods for identifying target genes of enhancers. First, we describe chromatin structure-based approaches for directly mapping interactions between enhancers and promoters. Second, we describe the use of correlation-based approaches to link enhancer state with the activity of nearby promoters and/or gene expression. Third, we describe how to test the function of specific enhancers experimentally by perturbing enhancer–target relationships using high-throughput reporter assays and genome editing. Finally, we conclude by discussing as yet unanswered questions concerning how enhancers function, how target genes can be identified, and how to distinguish direct from indirect changes in gene expression mediated by individual enhancers.
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Affiliation(s)
- Lijing Yao
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
| | - Benjamin P Berman
- b Department of Biomedical Sciences , Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Peggy J Farnham
- a Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California , Los Angeles , CA , USA and
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Kaneko I, Saini RK, Griffin KP, Whitfield GK, Haussler MR, Jurutka PW. FGF23 gene regulation by 1,25-dihydroxyvitamin D: opposing effects in adipocytes and osteocytes. J Endocrinol 2015; 226:155-66. [PMID: 26148725 PMCID: PMC4560246 DOI: 10.1530/joe-15-0225] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/06/2015] [Indexed: 02/06/2023]
Abstract
In a closed endocrine loop, 1,25-dihydroxyvitamin D3 (1,25D) induces the expression of fibroblast growth factor 23 (FGF23) in bone, with the phosphaturic peptide in turn acting at kidney to feedback repress CYP27B1 and induce CYP24A1 to limit the levels of 1,25D. In 3T3-L1 differentiated adipocytes, 1,25D represses FGF23 and leptin expression and induces C/EBPβ, but does not affect leptin receptor transcription. Conversely, in UMR-106 osteoblast-like cells, FGF23 mRNA concentrations are upregulated by 1,25D, an effect that is blunted by lysophosphatidic acid, a cell-surface acting ligand. Progressive truncation of the mouse FGF23 proximal promoter linked in luciferase reporter constructs reveals a 1,25D-responsive region between -400 and -200 bp. A 0.6 kb fragment of the mouse FGF23 promoter, linked in a reporter construct, responds to 1,25D with a fourfold enhancement of transcription in transfected K562 cells. Mutation of either an ETS1 site at -346 bp, or an adjacent candidate vitamin D receptor (VDR)/Nurr1-element, in the 0.6 kb reporter construct reduces the transcriptional activity elicited by 1,25D to a level that is not significantly different from a minimal promoter. This composite ETS1-VDR/Nurr1 cis-element may function as a switch between induction (osteocytes) and repression (adipocytes) of FGF23, depending on the cellular setting of transcription factors. Moreover, experiments demonstrate that a 1 kb mouse FGF23 promoter-reporter construct, transfected into MC3T3-E1 osteoblast-like cells, responds to a high calcium challenge with a statistically significant 1.7- to 2.0-fold enhancement of transcription. Thus, the FGF23 proximal promoter harbors cis elements that drive responsiveness to 1,25D and calcium, agents that induce FGF23 to curtail the pathologic consequences of their excess.
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Affiliation(s)
- Ichiro Kaneko
- Department of Basic Medical SciencesUniversity of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USASchool of Mathematical and Natural SciencesArizona State University, 4701 W. Thunderbird Road, Phoenix, Arizona 85306, USA Department of Basic Medical SciencesUniversity of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USASchool of Mathematical and Natural SciencesArizona State University, 4701 W. Thunderbird Road, Phoenix, Arizona 85306, USA
| | - Rimpi K Saini
- Department of Basic Medical SciencesUniversity of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USASchool of Mathematical and Natural SciencesArizona State University, 4701 W. Thunderbird Road, Phoenix, Arizona 85306, USA
| | - Kristin P Griffin
- Department of Basic Medical SciencesUniversity of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USASchool of Mathematical and Natural SciencesArizona State University, 4701 W. Thunderbird Road, Phoenix, Arizona 85306, USA
| | - G Kerr Whitfield
- Department of Basic Medical SciencesUniversity of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USASchool of Mathematical and Natural SciencesArizona State University, 4701 W. Thunderbird Road, Phoenix, Arizona 85306, USA
| | - Mark R Haussler
- Department of Basic Medical SciencesUniversity of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USASchool of Mathematical and Natural SciencesArizona State University, 4701 W. Thunderbird Road, Phoenix, Arizona 85306, USA
| | - Peter W Jurutka
- Department of Basic Medical SciencesUniversity of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USASchool of Mathematical and Natural SciencesArizona State University, 4701 W. Thunderbird Road, Phoenix, Arizona 85306, USA Department of Basic Medical SciencesUniversity of Arizona College of Medicine, 425 N. Fifth Street, Phoenix, Arizona 85004, USASchool of Mathematical and Natural SciencesArizona State University, 4701 W. Thunderbird Road, Phoenix, Arizona 85306, USA
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