1
|
Livne H, Avital T, Ruppo S, Harazi A, Mitrani-Rosenbaum S, Daya A. Generation and characterization of a novel gne Knockout Model in Zebrafish. Front Cell Dev Biol 2022; 10:976111. [PMID: 36353515 PMCID: PMC9637792 DOI: 10.3389/fcell.2022.976111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/14/2022] [Indexed: 12/04/2022] Open
Abstract
GNE Myopathy is a rare, recessively inherited neuromuscular worldwide disorder, caused by a spectrum of bi-allelic mutations in the human GNE gene. GNE encodes a bi-functional enzyme responsible for the rate-limiting step of sialic acid biosynthesis pathway. However, the process in which GNE mutations lead to the development of a muscle pathology is not clear yet. Cellular and mouse models for GNE Myopathy established to date have not been informative. Further, additional GNE functions in muscle have been hypothesized. In these studies, we aimed to investigate gne functions using zebrafish genetic and transgenic models, and characterized them using macroscopic, microscopic, and molecular approaches. We first established transgenic zebrafish lineages expressing the human GNE cDNA carrying the M743T mutation, driven by the zebrafish gne promoter. These fish developed entirely normally. Then, we generated a gne knocked-out (KO) fish using the CRISPR/Cas9 methodology. These fish died 8–10 days post-fertilization (dpf), but a phenotype appeared less than 24 h before death and included progressive body axis curving, deflation of the swim bladder and decreasing movement and heart rate. However, muscle histology uncovered severe defects, already at 5 dpf, with compromised fiber organization. Sialic acid supplementation did not rescue the larvae from this phenotype nor prolonged their lifespan. To have deeper insights into the potential functions of gne in zebrafish, RNA sequencing was performed at 3 time points (3, 5, and 7 dpf). Genotype clustering was progressive, with only 5 genes differentially expressed in gne KO compared to gne WT siblings at 3 dpf. Enrichment analyses of the primary processes affected by the lack of gne also at 5 and 7 dpf point to the involvement of cell cycle and DNA damage/repair processes in the gne KO zebrafish. Thus, we have established a gne KO zebrafish lineage and obtained new insights into gne functions. This is the only model where GNE can be related to clear muscle defects, thus the only animal model relevant to GNE Myopathy to date. Further elucidation of gne precise mechanism-of-action in these processes could be relevant to GNE Myopathy and allow the identification of novel therapeutic targets.
Collapse
Affiliation(s)
- Hagay Livne
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret, Israel
- Goldyne Savad Institute of Gene Therapy, Hadassah Medical Center, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tom Avital
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret, Israel
| | - Shmuel Ruppo
- Info-CORE, Bioinformatics Unit of the I-CORE, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avi Harazi
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret, Israel
- Goldyne Savad Institute of Gene Therapy, Hadassah Medical Center, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Stella Mitrani-Rosenbaum
- Goldyne Savad Institute of Gene Therapy, Hadassah Medical Center, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alon Daya
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret, Israel
- *Correspondence: Alon Daya,
| |
Collapse
|
2
|
Marchal C, Defossez PA, Miotto B. Context-dependent CpG methylation directs cell-specific binding of transcription factor ZBTB38. Epigenetics 2022; 17:2122-2143. [PMID: 36000449 DOI: 10.1080/15592294.2022.2111135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
DNA methylation on CpGs regulates transcription in mammals, both by decreasing the binding of methylation-repelled factors and by increasing the binding of methylation-attracted factors. Among the latter, zinc finger proteins have the potential to bind methylated CpGs in a sequence-specific context. The protein ZBTB38 is unique in that it has two independent sets of zinc fingers, which recognize two different methylated consensus sequences in vitro. Here, we identify the binding sites of ZBTB38 in a human cell line, and show that they contain the two methylated consensus sequences identified in vitro. In addition, we show that the distribution of ZBTB38 sites is highly unusual: while 10% of the ZBTB38 sites are also bound by CTCF, the other 90% of sites reside in closed chromatin and are not bound by any of the other factors mapped in our model cell line. Finally, a third of ZBTB38 sites are found upstream of long and active CpG islands. Our work therefore validates ZBTB38 as a methyl-DNA binder in vivo and identifies its unique distribution in the genome.
Collapse
Affiliation(s)
- Claire Marchal
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | | | - Benoit Miotto
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| |
Collapse
|
3
|
Vicente-García C, Hernández-Camacho JD, Carvajal JJ. Regulation of myogenic gene expression. Exp Cell Res 2022; 419:113299. [DOI: 10.1016/j.yexcr.2022.113299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 12/22/2022]
|
4
|
Promoter Methylation Changes in KRT17: A Novel Epigenetic Marker for Wool Production in Angora Rabbit. Int J Mol Sci 2022; 23:ijms23116077. [PMID: 35682756 PMCID: PMC9181683 DOI: 10.3390/ijms23116077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/04/2022] [Accepted: 05/09/2022] [Indexed: 11/17/2022] Open
Abstract
Wool production is an important economic trait of Angora rabbits. Exploring molecular markers related to wool production is one of the essentials of Angora rabbits’ breeding. KRT17 (Keratin 17) is an important gene of hair follicle development, which must be explored for genetic/epigenetic variation to assess its effect on wool production. Based on the effective wool production data of 217 Angora rabbits, the high and low yield groups were screened with 1.5 standard deviations of the population mean. The full-length sequence of KRT17 was obtained by rapid amplification of cDNA ends technology, and the polymorphism was analyzed in the promoter, exon, and intron regions by direct sequencing. KRT17, SP1 over-expression plasmids, and siRNA were constructed and transfected into dermal papilla cells. The mRNA expressions of relevant genes were analyzed by RT-qPCR. The methylation level of the KRT17 promoter was determined by Bisulfite Sequencing PCR. Dual-luciferase system, site-directed mutagenesis, and electrophoretic mobility shift assays were used to analyze the binding relationship between SP1 and the promoter of KRT17. The structure map of KRT17 was drawn, and no SNPs were found in the promoter, exon, and intron, indicating a relatively conserved structure of KRT17. Expression of KRT17 was significantly higher in cutaneous tissues than in other tissues and was significantly upregulated in the high-yield group compared to the low-yield group (p < 0.05). Furthermore, the overall high methylation levels of KRT17 CpG I and CpG III showed significant association with low wool yield; the methylation levels of 5 CpG locus (CpG I site 4 and CpG III site 2−5) were significantly different between the high and low yield groups (p < 0.05). The methylation levels of 3 CpG locus (CpG I site 4 and CpG III site 4, 14) showed a significant correlation with KRT17 expression (p < 0.05). Overall, CpG III site 4 significantly affects wool production and KRT17 expressions (p < 0.05). This site promotes SP1 binding to the KRT17 promoter region (CGCTACGCCC) to positively regulate the KRT17 expression. KRT17 CpG III site 4 can be used as candidate epigenetic markers for the breeding of high wool-producing Angora rabbits.
Collapse
|
5
|
Nishio M, Matsuura T, Hibi S, Ohta S, Oka C, Sasai N, Ishida Y, Matsuda E. Heterozygous loss of Zbtb38 leads to early embryonic lethality via the suppression of Nanog and Sox2 expression. Cell Prolif 2022; 55:e13215. [PMID: 35297517 PMCID: PMC9055898 DOI: 10.1111/cpr.13215] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 01/27/2023] Open
Abstract
Objectives Mammalian DNA methyltransferases are essential to re‐establish global DNA methylation patterns during implantation, which is critical for transmitting epigenetic information to the next generation. In contrast, the significance of methyl‐CpG binding proteins (MBPs) that bind methylated CpG remains almost unknown at this stage. We previously demonstrated that Zbtb38 (also known as CIBZ)—a zinc finger type of MBP—is required for mouse embryonic stem (ES) cell proliferation by positively regulating Nanog expression. However, the physiological function of Zbtb38 in vivo remains unclear. Materials and Methods This study used the Cre‐loxP system to generate conditional Zbtb38 knockout mice. Cell proliferation and apoptosis were studied by immunofluorescence staining. Quantitative real‐time PCR, immunoblotting and immunofluorescence were performed to investigate the molecular mechanisms. Results Germline loss of the Zbtb38 single allele resulted in decreased epiblast cell proliferation and increased apoptosis shortly after implantation, leading to early embryonic lethality. Heterozygous loss of Zbtb38 reduced the expression of Nanog, Sox2, and the genes responsible for epiblast proliferation, differentiation, and cell viability. Although this early lethal phenotype, Zbtb38 is dispensable for ES cell establishment and identity. Conclusions These findings indicate that Zbtb38 is essential for early embryonic development via the suppression of Nanog and Sox2 expression.
Collapse
Affiliation(s)
- Miki Nishio
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan.,Cosmo Bio Co., Ltd., Tokyo, Japan
| | - Takuya Matsuura
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shunya Hibi
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shiomi Ohta
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Chio Oka
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Noriaki Sasai
- Development Biomedical Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yasumasa Ishida
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| | - Eishou Matsuda
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, Japan
| |
Collapse
|
6
|
Muscle regeneration controlled by a designated DNA dioxygenase. Cell Death Dis 2021; 12:535. [PMID: 34035232 PMCID: PMC8149877 DOI: 10.1038/s41419-021-03817-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/27/2021] [Accepted: 05/07/2021] [Indexed: 12/27/2022]
Abstract
Tet dioxygenases are responsible for the active DNA demethylation. The functions of Tet proteins in muscle regeneration have not been well characterized. Here we find that Tet2, but not Tet1 and Tet3, is specifically required for muscle regeneration in vivo. Loss of Tet2 leads to severe muscle regeneration defects. Further analysis indicates that Tet2 regulates myoblast differentiation and fusion. Tet2 activates transcription of the key differentiation modulator Myogenin (MyoG) by actively demethylating its enhancer region. Re-expressing of MyoG in Tet2 KO myoblasts rescues the differentiation and fusion defects. Further mechanistic analysis reveals that Tet2 enhances MyoD binding by demethylating the flanking CpG sites of E boxes to facilitate the recruitment of active histone modifications and increase chromatin accessibility and activate its transcription. These findings shed new lights on DNA methylation and pioneer transcription factor activity regulation.
Collapse
|
7
|
Diniz WJS, Crouse MS, Cushman RA, McLean KJ, Caton JS, Dahlen CR, Reynolds LP, Ward AK. Cerebrum, liver, and muscle regulatory networks uncover maternal nutrition effects in developmental programming of beef cattle during early pregnancy. Sci Rep 2021; 11:2771. [PMID: 33531552 PMCID: PMC7854659 DOI: 10.1038/s41598-021-82156-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
The molecular basis underlying fetal programming in response to maternal nutrition remains unclear. Herein, we investigated the regulatory relationships between genes in fetal cerebrum, liver, and muscle tissues to shed light on the putative mechanisms that underlie the effects of early maternal nutrient restriction on bovine developmental programming. To this end, cerebrum, liver, and muscle gene expression were measured with RNA-Seq in 14 fetuses collected on day 50 of gestation from dams fed a diet initiated at breeding to either achieve 60% (RES, n = 7) or 100% (CON, n = 7) of energy requirements. To build a tissue-to-tissue gene network, we prioritized tissue-specific genes, transcription factors, and differentially expressed genes. Furthermore, we built condition-specific networks to identify differentially co-expressed or connected genes. Nutrient restriction led to differential tissue regulation between the treatments. Myogenic factors differentially regulated by ZBTB33 and ZNF131 may negatively affect myogenesis. Additionally, nutrient-sensing pathways, such as mTOR and PI3K/Akt, were affected by gene expression changes in response to nutrient restriction. By unveiling the network properties, we identified major regulators driving gene expression. However, further research is still needed to determine the impact of early maternal nutrition and strategic supplementation on pre- and post-natal performance.
Collapse
Affiliation(s)
- Wellison J. S. Diniz
- grid.261055.50000 0001 2293 4611Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND USA
| | - Matthew S. Crouse
- grid.463419.d0000 0001 0946 3608USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Robert A. Cushman
- grid.463419.d0000 0001 0946 3608USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE USA
| | - Kyle J. McLean
- grid.411461.70000 0001 2315 1184Department of Animal Science, University of Tennessee, Knoxville, TN USA
| | - Joel S. Caton
- grid.261055.50000 0001 2293 4611Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND USA
| | - Carl R. Dahlen
- grid.261055.50000 0001 2293 4611Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND USA
| | - Lawrence P. Reynolds
- grid.261055.50000 0001 2293 4611Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND USA
| | - Alison K. Ward
- grid.261055.50000 0001 2293 4611Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, Fargo, ND USA
| |
Collapse
|
8
|
Jones G, Trajanoska K, Santanasto AJ, Stringa N, Kuo CL, Atkins JL, Lewis JR, Duong T, Hong S, Biggs ML, Luan J, Sarnowski C, Lunetta KL, Tanaka T, Wojczynski MK, Cvejkus R, Nethander M, Ghasemi S, Yang J, Zillikens MC, Walter S, Sicinski K, Kague E, Ackert-Bicknell CL, Arking DE, Windham BG, Boerwinkle E, Grove ML, Graff M, Spira D, Demuth I, van der Velde N, de Groot LCPGM, Psaty BM, Odden MC, Fohner AE, Langenberg C, Wareham NJ, Bandinelli S, van Schoor NM, Huisman M, Tan Q, Zmuda J, Mellström D, Karlsson M, Bennett DA, Buchman AS, De Jager PL, Uitterlinden AG, Völker U, Kocher T, Teumer A, Rodriguéz-Mañas L, García FJ, Carnicero JA, Herd P, Bertram L, Ohlsson C, Murabito JM, Melzer D, Kuchel GA, Ferrucci L, Karasik D, Rivadeneira F, Kiel DP, Pilling LC. Genome-wide meta-analysis of muscle weakness identifies 15 susceptibility loci in older men and women. Nat Commun 2021; 12:654. [PMID: 33510174 PMCID: PMC7844411 DOI: 10.1038/s41467-021-20918-w] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023] Open
Abstract
Low muscle strength is an important heritable indicator of poor health linked to morbidity and mortality in older people. In a genome-wide association study meta-analysis of 256,523 Europeans aged 60 years and over from 22 cohorts we identify 15 loci associated with muscle weakness (European Working Group on Sarcopenia in Older People definition: n = 48,596 cases, 18.9% of total), including 12 loci not implicated in previous analyses of continuous measures of grip strength. Loci include genes reportedly involved in autoimmune disease (HLA-DQA1 p = 4 × 10-17), arthritis (GDF5 p = 4 × 10-13), cell cycle control and cancer protection, regulation of transcription, and others involved in the development and maintenance of the musculoskeletal system. Using Mendelian randomization we report possible overlapping causal pathways, including diabetes susceptibility, haematological parameters, and the immune system. We conclude that muscle weakness in older adults has distinct mechanisms from continuous strength, including several pathways considered to be hallmarks of ageing.
Collapse
Affiliation(s)
- Garan Jones
- Epidemiology and Public Health Group, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adam J Santanasto
- University of Pittsburgh, Department of Epidemiology, Pittsburgh, PA, USA
| | - Najada Stringa
- Department of Epidemiology and Biostatistics, Amsterdam UMC- Vrije Universiteit, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Chia-Ling Kuo
- Biostatistics Center, Connecticut Convergence Institute for Translation in Regenerative Engineering, UConn Health, Farmington, CT, USA
| | - Janice L Atkins
- Epidemiology and Public Health Group, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Joshua R Lewis
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- School fo Public Health University of Sydney, Sydney, NSW, Australia
- Medical School, University of Western Australia, Crawley, WA, Australia
| | - ThuyVy Duong
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shengjun Hong
- Lübeck Interdisciplinary Plattform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Mary L Biggs
- Cardiovascular Health Research Unit, Department of Medicine, and Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jian'an Luan
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Chloe Sarnowski
- Biostatistics Department, Boston University School of Public Health, Boston, MA, USA
| | - Kathryn L Lunetta
- Biostatistics Department, Boston University School of Public Health, Boston, MA, USA
| | - Toshiko Tanaka
- Longitudinal Study Section, Translational Gerontology branch, National Institute on Aging, Baltimore, MD, USA
| | - Mary K Wojczynski
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ryan Cvejkus
- University of Pittsburgh, Department of Epidemiology, Pittsburgh, PA, USA
| | - Maria Nethander
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sahar Ghasemi
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Jingyun Yang
- Rush Alzheimer's Disease Center & Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Stefan Walter
- Department of Medicine and Public Health, Rey Juan Carlos University, Madrid, Spain
- CIBER of Frailty and Healthy Aging (CIBERFES), Madrid, Spain
| | - Kamil Sicinski
- Center for Demography of Health and Aging, University of Wisconsin-Madison, Madison, WI, USA
| | - Erika Kague
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK
| | | | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - B Gwen Windham
- Department of Medicine/Geriatrics, University of Mississippi School of Medicine, Jackson, MS, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Megan L Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Misa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27516, USA
| | - Dominik Spira
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Department of Endocrinology and Metabolism, Berlin, Germany
| | - Ilja Demuth
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Department of Endocrinology and Metabolism, Berlin, Germany
- Charité - Universitätsmedizin Berlin, BCRT - Berlin Institute of Health Center for Regenerative Therapies, Berlin, Germany
| | - Nathalie van der Velde
- Department of Internal Medicine, Section of Geriatric Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Lisette C P G M de Groot
- Wageningen University, Division of Human Nutrition, PO-box 17, 6700 AA, Wageningen, The Netherlands
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health services, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Michelle C Odden
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Alison E Fohner
- Department of Epidemiology and Institute of Public Genetics, University of Washington, Seattle, WA, USA
| | - Claudia Langenberg
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | | | - Natasja M van Schoor
- Department of Epidemiology and Biostatistics, Amsterdam UMC- Vrije Universiteit, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Martijn Huisman
- Department of Epidemiology and Biostatistics, Amsterdam UMC- Vrije Universiteit, Amsterdam Public Health Research Institute, Amsterdam, The Netherlands
| | - Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, Faculty of Health Science, University of Southern Denmark, Odense, Denmark
| | - Joseph Zmuda
- University of Pittsburgh, Department of Epidemiology, Pittsburgh, PA, USA
| | - Dan Mellström
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Geriatric Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Karlsson
- Clinical and Molecular Osteoporosis Research Unit, Department of Orthopedics and Clinical Sciences, Lund University, Skåne University Hospital, Malmö, Sweden
| | - David A Bennett
- Rush Alzheimer's Disease Center & Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Aron S Buchman
- Rush Alzheimer's Disease Center & Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Center for Translational and Systems Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Thomas Kocher
- Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, University Medicine Greifswald, Greifswald, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Leocadio Rodriguéz-Mañas
- CIBER of Frailty and Healthy Aging (CIBERFES), Madrid, Spain
- Department of Geriatrics, Getafe University Hospital, Getafe, Spain
| | - Francisco J García
- CIBER of Frailty and Healthy Aging (CIBERFES), Madrid, Spain
- Department of Geriatrics, Hospital Virgen del Valle, Complejo Hospitalario de Toledo, Toledo, Spain
| | | | - Pamela Herd
- Professor of Public Policy, Georgetown University, Washington, DC, USA
| | - Lars Bertram
- Lübeck Interdisciplinary Plattform for Genome Analytics, Institutes of Neurogenetics and Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Claes Ohlsson
- Centre for Bone and Arthritis Research, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Sahlgrenska University Hospital, Department of Drug Treatment, Gothenburg, Sweden
| | - Joanne M Murabito
- Section of General Internal Medicine, Boston University School of Medicine, Boston, MA, USA
| | - David Melzer
- Epidemiology and Public Health Group, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - George A Kuchel
- Center on Aging, University of Connecticut Health, 263 Farmington Avenue, Farmington, CT, 06030, USA
| | | | - David Karasik
- Marcus Institute for Aging Research, Hebrew SeniorLife, Boston, MA, USA
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Douglas P Kiel
- Marcus Institute for Aging Research, Hebrew SeniorLife and Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Broad Institute of MIT & Harvard, Boston, MA, USA
| | - Luke C Pilling
- Epidemiology and Public Health Group, Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
| |
Collapse
|
9
|
Massenet J, Gardner E, Chazaud B, Dilworth FJ. Epigenetic regulation of satellite cell fate during skeletal muscle regeneration. Skelet Muscle 2021; 11:4. [PMID: 33431060 PMCID: PMC7798257 DOI: 10.1186/s13395-020-00259-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/20/2020] [Indexed: 12/13/2022] Open
Abstract
In response to muscle injury, muscle stem cells integrate environmental cues in the damaged tissue to mediate regeneration. These environmental cues are tightly regulated to ensure expansion of muscle stem cell population to repair the damaged myofibers while allowing repopulation of the stem cell niche. These changes in muscle stem cell fate result from changes in gene expression that occur in response to cell signaling from the muscle environment. Integration of signals from the muscle environment leads to changes in gene expression through epigenetic mechanisms. Such mechanisms, including post-translational modification of chromatin and nucleosome repositioning, act to make specific gene loci more, or less, accessible to the transcriptional machinery. In youth, the muscle environment is ideally structured to allow for coordinated signaling that mediates efficient regeneration. Both age and disease alter the muscle environment such that the signaling pathways that shape the healthy muscle stem cell epigenome are altered. Altered epigenome reduces the efficiency of cell fate transitions required for muscle repair and contributes to muscle pathology. However, the reversible nature of epigenetic changes holds out potential for restoring cell fate potential to improve muscle repair in myopathies. In this review, we will describe the current knowledge of the mechanisms allowing muscle stem cell fate transitions during regeneration and how it is altered in muscle disease. In addition, we provide some examples of how epigenetics could be harnessed therapeutically to improve regeneration in various muscle pathologies.
Collapse
Affiliation(s)
- Jimmy Massenet
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Rd, Mailbox 511, Ottawa, ON, K1H 8L6, Canada.,Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS 5310, INSERM U1217, 8 Rockefeller Ave, 69008, Lyon, France
| | - Edward Gardner
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Rd, Mailbox 511, Ottawa, ON, K1H 8L6, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8L6, Canada
| | - Bénédicte Chazaud
- Institut NeuroMyoGène, Université Claude Bernard Lyon 1, CNRS 5310, INSERM U1217, 8 Rockefeller Ave, 69008, Lyon, France
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Rd, Mailbox 511, Ottawa, ON, K1H 8L6, Canada. .,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8L6, Canada. .,LIFE Research Institute, University of Ottawa, Ottawa, ON, K1H 8L6, Canada.
| |
Collapse
|
10
|
Wong R, Bhattacharya D. ZBTB38 is dispensable for antibody responses. PLoS One 2020; 15:e0235183. [PMID: 32956421 PMCID: PMC7505459 DOI: 10.1371/journal.pone.0235183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/07/2020] [Indexed: 12/19/2022] Open
Abstract
Members of the broad complex, tram track, bric-a-brac and zinc finger (BTB-ZF) family of transcription factors, such as BCL-6, ZBTB20, and ZBTB32, regulate antigen-specific B cell differentiation, plasma cell longevity, and the duration of antibody production. We found that ZBTB38, a different member of the BTB-ZF family that binds methylated DNA at CpG motifs, is highly expressed by germinal center B cells and plasma cells. To define the functional role of ZBTB38 in B cell responses, we generated mice conditionally deficient in this transcription factor. Germinal center B cells lacking ZBTB38 dysregulated very few genes relative to wild-type and heterozygous littermate controls. Accordingly, mice with hematopoietic-specific deletion of Zbtb38 showed normal germinal center B cell numbers and antibody responses following immunization with hapten-protein conjugates. Memory B cells from these animals functioned normally in secondary recall responses. Despite expression of ZBTB38 in hematopoietic stem cells, progenitors and mature myeloid and lymphoid lineages were also present in normal numbers in mutant mice. These data demonstrate that ZBTB38 is dispensable for hematopoiesis and antibody responses. These conditional knockout mice may instead be useful in defining the functional importance of ZBTB38 in other cell types and contexts.
Collapse
Affiliation(s)
- Rachel Wong
- Division of Biological and Biomedical Sciences, Washington University in St. Louis, Saint Louis, MO, United States of America
- Department of Immunobiology, University of Arizona, Tucson, AZ, United States of America
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona, Tucson, AZ, United States of America
- * E-mail:
| |
Collapse
|
11
|
Li M, Shen Y, Chen Y, Gao H, Zhou J, Wang Q, Fan C, Zhang W, Li J, Cong H, Gu J, Gan Y, Tu H. Characterization of hepatitis B virus infection and viral DNA integration in non-Hodgkin lymphoma. Int J Cancer 2020; 147:2199-2209. [PMID: 32350851 DOI: 10.1002/ijc.33027] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/02/2020] [Accepted: 04/17/2020] [Indexed: 12/12/2022]
Abstract
Hepatitis B virus (HBV) infection has been reported to be associated with non-Hodgkin lymphoma (NHL). However, the evidence is limited to the seroepidemiological study. There is a lack of evidence showing the HBV infection and integration in NHL cells. Here, we reported that in the Shanghai area, the positive rates of serum HBsAg (OR: 3.11; 95% CI: 2.20-4.41) and HBeAg (OR: 3.99; 95% CI: 1.73-9.91) were significantly higher in patients with NHL. HBsAg, HBcAg and HBV DNA were detected in 34.4%, 45.2% and 47.0% of the NHL tissues, respectively. Furthermore, by using a high-throughput viral integration detection approach (HIVID), integrated HBV DNA was identified from 50% (6/12) HBV-related NHL tissues. There were a total of 313 HBV integration sites isolated from the NHL tissues, among which four protein-coding genes (FAT2, SETX, ITGA10 and CD63) were interrupted by HBV DNA in their exons. Seven HBV preferential target genes (ANKS1B, HDAC4, EGFLAM, MAN1C1, XKR6, ZBTB38 and CCDC91) showed significantly altered expression levels in NHL, suggesting a potential role of these genes in NHL development. Taken together, HBV integration is a common phenomenon in NHL. This finding opens up a new direction of research into the mechanistic link between HBV infection and NHL.
Collapse
Affiliation(s)
- Mengge Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuling Shen
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Head and Neck Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiming Chen
- Department of Pathology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haifeng Gao
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jiaqin Zhou
- Department of Head and Neck Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing Wang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunsun Fan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of etiology, Qidong People's Hospital/Qidong Liver Cancer Institute, Qidong, China
| | - Wei Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Cong
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinyang Gu
- Department of Transplantation, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Gan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Tu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
12
|
Molecular and Clinical Relevance of ZBTB38 Expression Levels in Prostate Cancer. Cancers (Basel) 2020; 12:cancers12051106. [PMID: 32365491 PMCID: PMC7281456 DOI: 10.3390/cancers12051106] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/12/2020] [Accepted: 04/23/2020] [Indexed: 12/18/2022] Open
Abstract
Prostate cancer is one of the most commonly diagnosed cancers in men. A number of genomic and clinical studies have led to a better understanding of prostate cancer biology. Still, the care of patients as well as the prediction of disease aggressiveness, recurrence and outcome remain challenging. Here, we showed that expression of the gene ZBTB38 is associated with poor prognosis in localised prostate cancer and could help discriminate aggressive localised prostate tumours from those who can benefit only from observation. Analysis of different prostate cancer cohorts indicates that low expression levels of ZBTB38 associate with increased levels of chromosomal abnormalities and more aggressive pathological features, including higher rate of biochemical recurrence of the disease. Importantly, gene expression profiling of these tumours, complemented with cellular assays on prostate cancer cell lines, unveiled that tumours with low levels of ZBTB38 expression might be targeted by doxorubicin, a compound generating reactive oxygen species. Our study shows that ZBTB38 is involved in prostate cancer pathogenesis and may represent a useful marker to identify high risk and highly rearranged localised prostate cancer susceptible to doxorubicin.
Collapse
|
13
|
Hodges AJ, Hudson NO, Buck-Koehntop BA. Cys 2His 2 Zinc Finger Methyl-CpG Binding Proteins: Getting a Handle on Methylated DNA. J Mol Biol 2019:S0022-2836(19)30567-4. [PMID: 31628952 DOI: 10.1016/j.jmb.2019.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
DNA methylation is an essential epigenetic modification involved in the maintenance of genomic stability, preservation of cellular identity, and regulation of the transcriptional landscape needed to maintain cellular function. In an increasing number of disease conditions, DNA methylation patterns are inappropriately distributed in a manner that supports the disease phenotype. Methyl-CpG binding proteins (MBPs) are specialized transcription factors that read and translate methylated DNA signals into recruitment of protein assemblies that can alter local chromatin architecture and transcription. MBPs thus play a key intermediary role in gene regulation for both normal and diseased cells. Here, we highlight established and potential structure-function relationships for the best characterized members of the zinc finger (ZF) family of MBPs in propagating DNA methylation signals into downstream cellular responses. Current and future investigations aimed toward expanding our understanding of ZF MBP cellular roles will provide needed mechanistic insight into normal and disease state functions, as well as afford evaluation for the potential of these proteins as epigenetic-based therapeutic targets.
Collapse
Affiliation(s)
- Amelia J Hodges
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Nicholas O Hudson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Bethany A Buck-Koehntop
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA.
| |
Collapse
|
14
|
Mahmood N, Rabbani SA. DNA Methylation Readers and Cancer: Mechanistic and Therapeutic Applications. Front Oncol 2019; 9:489. [PMID: 31245293 PMCID: PMC6579900 DOI: 10.3389/fonc.2019.00489] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/23/2019] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is a major epigenetic process that regulates chromatin structure which causes transcriptional activation or repression of genes in a context-dependent manner. In general, DNA methylation takes place when methyl groups are added to the appropriate bases on the genome by the action of "writer" molecules known as DNA methyltransferases. How these methylation marks are read and interpreted into different functionalities represents one of the main mechanisms through which the genes are switched "ON" or "OFF" and typically involves different types of "reader" proteins that can recognize and bind to the methylated regions. A tightly balanced regulation exists between the "writers" and "readers" in order to mediate normal cellular functions. However, alterations in normal methylation pattern is a typical hallmark of cancer which alters the way methylation marks are written, read and interpreted in different disease states. This unique characteristic of DNA methylation "readers" has identified them as attractive therapeutic targets. In this review, we describe the current state of knowledge on the different classes of DNA methylation "readers" identified thus far along with their normal biological functions, describe how they are dysregulated in cancer, and discuss the various anti-cancer therapies that are currently being developed and evaluated for targeting these proteins.
Collapse
Affiliation(s)
- Niaz Mahmood
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
| |
Collapse
|
15
|
Zhang W, Zhang S, Xu Y, Ma Y, Zhang D, Li X, Zhao S. The DNA Methylation Status of Wnt and Tgfβ Signals Is a Key Factor on Functional Regulation of Skeletal Muscle Satellite Cell Development. Front Genet 2019; 10:220. [PMID: 30949196 PMCID: PMC6437077 DOI: 10.3389/fgene.2019.00220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 02/28/2019] [Indexed: 12/16/2022] Open
Abstract
DNA methylation is an important form of epigenetic regulation that can regulate the expression of genes and the development of tissues. Muscle satellite cells play an important role in skeletal muscle development and regeneration. Therefore, the DNA methylation status of genes in satellite cells is important in the regulation of the development of skeletal muscle. This study systematically investigated the changes of genome-wide DNA methylation in satellite cells during skeletal muscle development. According to the MeDIP-Seq data, 52,809-123,317 peaks were obtained for each sample, covering 0.70-1.79% of the genome. The number of reads and peaks was highest in the intron regions followed by the CDS regions. A total of 96,609 DMRs were identified between any two time points. Among them 6198 DMRs were annotated into the gene promoter regions, corresponding to 4726 DMGs. By combining the MeDIP-Seq and RNA-Seq data, a total of 202 overlap genes were obtained between DMGs and DEGs. GO and Pathway analysis revealed that the overlap genes were mainly involved in 128 biological processes and 23 pathways. Among the biological processes, terms related to regulation of cell proliferation and Wnt signaling pathway were significantly different. Gene-gene interaction analysis showed that Wnt5a, Wnt9a, and Tgfβ1 were the key nodes in the network. Furthermore, the expression level of Wnt5a, Wnt9a, and Tgfβ1 genes could be influenced by the methylation status of promoter region during skeletal muscle development. These results indicated that the Wnt and Tgfβ signaling pathways may play an important role in functional regulation of satellite cells, and the DNA methylation status of Wnt and Tgfβ signals is a key regulatory factor during skeletal muscle development. This study provided new insights into the effects of genome-wide methylation on the function of satellite cells.
Collapse
Affiliation(s)
- Weiya Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Saixian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Yueyuan Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Dingxiao Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
| | - Xinyun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shuhong Zhao
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| |
Collapse
|
16
|
de Dieuleveult M, Miotto B. DNA Methylation and Chromatin: Role(s) of Methyl-CpG-Binding Protein ZBTB38. Epigenet Insights 2018; 11:2516865718811117. [PMID: 30480223 PMCID: PMC6243405 DOI: 10.1177/2516865718811117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 12/16/2022] Open
Abstract
DNA methylation plays an essential role in the control of gene expression during early stages of development as well as in disease. Although many transcription factors are sensitive to this modification of the DNA, we still do not clearly understand how it contributes to the establishment of proper gene expression patterns. We discuss here the recent findings regarding the biological and molecular function(s) of the transcription factor ZBTB38 that binds methylated DNA sequences in vitro and in cells. We speculate how these findings may help understand the role of DNA methylation and DNA methylation–sensitive transcription factors in mammalian cells.
Collapse
Affiliation(s)
- Maud de Dieuleveult
- Institut Cochin, INSERM U1016, Paris, France.,CNRS UMR8104, Paris, France.,Department of Development, Reproduction and Cancer, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Benoit Miotto
- Institut Cochin, INSERM U1016, Paris, France.,CNRS UMR8104, Paris, France.,Department of Development, Reproduction and Cancer, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| |
Collapse
|
17
|
Hudson NO, Whitby FG, Buck-Koehntop BA. Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38. J Biol Chem 2018; 293:19835-19843. [PMID: 30355731 DOI: 10.1074/jbc.ra118.005147] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/16/2018] [Indexed: 02/05/2023] Open
Abstract
Methyl-CpG-binding proteins (MBPs) are selective readers of DNA methylation that play an essential role in mediating cellular transcription processes in both normal and diseased cells. This physiological function of MBPs has generated significant interest in understanding the mechanisms by which these proteins read and interpret DNA methylation signals. Zinc finger and BTB domain-containing 38 (ZBTB38) represents one member of the zinc finger (ZF) family of MBPs. We recently demonstrated that the C-terminal ZFs of ZBTB38 exhibit methyl-selective DNA binding within the ((A/G)TmCG(G/A)(mC/T)(G/A)) context both in vitro and within cells. Here we report the crystal structure of the first four C-terminal ZBTB38 ZFs (ZFs 6-9) in complex with the previously identified methylated consensus sequence at 1.75 Å resolution. From the structure, methyl-selective binding is preferentially localized at the 5' mCpG site of the bound DNA, which is facilitated through a series of base-specific interactions from residues within the α-helices of ZF7 and ZF8. ZF6 and ZF9 primarily stabilize ZF7 and ZF8 to facilitate the core base-specific interactions. Further structural and biochemical analyses, including solution NMR spectroscopy and electrophoretic mobility gel shift assays, revealed that the C-terminal ZFs of ZBTB38 utilize an alternative mode of mCpG recognition from the ZF MBPs structurally evaluated to date. Combined, these findings provide insight into the mechanism by which this ZF domain of ZBTB38 selectively recognizes methylated CpG sites and expands our understanding of how ZF-containing proteins can interpret this essential epigenetic mark.
Collapse
Affiliation(s)
| | - Frank G Whitby
- Biochemistry, University of Utah, Salt Lake City, Utah 84112
| | | |
Collapse
|
18
|
Marchal C, de Dieuleveult M, Saint-Ruf C, Guinot N, Ferry L, Olalla Saad ST, Lazarini M, Defossez PA, Miotto B. Depletion of ZBTB38 potentiates the effects of DNA demethylating agents in cancer cells via CDKN1C mRNA up-regulation. Oncogenesis 2018; 7:82. [PMID: 30310057 PMCID: PMC6182000 DOI: 10.1038/s41389-018-0092-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 08/22/2018] [Indexed: 11/09/2022] Open
Abstract
DNA methyltransferase inhibitor (DNMTi) treatments have been used for patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), and have shown promising beneficial effects in some other types of cancers. Here, we demonstrate that the transcriptional repressor ZBTB38 is a critical regulator of the cellular response to DNMTi. Treatments with 5-azacytidine, or its derivatives decitabine and zebularine, lead to down-regulation of ZBTB38 protein expression in cancer cells, in parallel with cellular damage. The depletion of ZBTB38 by RNA interference enhances the toxicity of DNMTi in cell lines from leukemia and from various solid tumor types. Further we observed that inactivation of ZBTB38 causes the up-regulation of CDKN1C mRNA, a previously described indirect target of DNMTi. We show that CDKN1C is a key actor of DNMTi toxicity in cells lacking ZBTB38. Finally, in patients with MDS a high level of CDKN1C mRNA expression before treatment correlates with a better clinical response to a drug regimen combining 5-azacytidine and histone deacetylase inhibitors. Collectively, our results suggest that the ZBTB38 protein is a target of DNMTi and that its depletion potentiates the toxicity of DNMT inhibitors in cancer cells, providing new opportunities to enhance the response to DNMT inhibitor therapies in patients with MDS and other cancers.
Collapse
Affiliation(s)
- Claire Marchal
- INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Department of Biological Science, Florida State University, Tallahassee, FL, 32306-4295, USA
| | - Maud de Dieuleveult
- INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Claude Saint-Ruf
- INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Nadège Guinot
- INSERM, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Laure Ferry
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, 75013, Paris, France
| | - Sara T Olalla Saad
- Hematology and Blood Transfusion Center-University of Campinas/Hemocentro-Unicamp, Instituto Nacional de Ciência e Tecnologia do Sangue, Campinas, Brazil
| | - Mariana Lazarini
- Department of Biological Sciences, Federal University of São Paulo, Diadema, Brazil
| | - Pierre-Antoine Defossez
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, 75013, Paris, France
| | - Benoit Miotto
- INSERM, U1016, Institut Cochin, Paris, France. .,CNRS, UMR8104, Paris, France. .,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| |
Collapse
|
19
|
Hudson NO, Buck-Koehntop BA. Zinc Finger Readers of Methylated DNA. Molecules 2018; 23:E2555. [PMID: 30301273 PMCID: PMC6222495 DOI: 10.3390/molecules23102555] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/07/2023] Open
Abstract
DNA methylation is a prevalent epigenetic modification involved in regulating a number of essential cellular processes, including genomic accessibility and transcriptional outcomes. As such, aberrant alterations in global DNA methylation patterns have been associated with a growing number of disease conditions. Nevertheless, the full mechanisms by which DNA methylation information is interpreted and translated into genomic responses is not yet fully understood. Methyl-CpG binding proteins (MBPs) function as important mediators of this essential process by selectively reading DNA methylation signals and translating this information into down-stream cellular outcomes. The Cys₂His₂ zinc finger scaffold is one of the most abundant DNA binding motifs found within human transcription factors, yet only a few zinc finger containing proteins capable of conferring selectivity for mCpG over CpG sites have been characterized. This review summarizes our current structural understanding for the mechanisms by which the zinc finger MBPs evaluated to date read this essential epigenetic mark. Further, some of the biological implications for mCpG readout elicited by this family of MBPs are discussed.
Collapse
Affiliation(s)
- Nicholas O Hudson
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA.
| | | |
Collapse
|
20
|
Chen J, Yan L, Wang H, Zhang Z, Yu D, Xing C, Li J, Li H, Li J, Cai Y. ZBTB38, a novel regulator of autophagy initiation targeted by RB1CC1/FIP200 in spinal cord injury. Gene 2018; 678:8-16. [PMID: 30075197 DOI: 10.1016/j.gene.2018.07.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/03/2018] [Accepted: 07/29/2018] [Indexed: 12/22/2022]
Abstract
Apoptosis is an important contributing factor in spinal cord injury (SCI). ZBTB38 is involved in the transcriptional regulation of multiple signaling pathways, is differentially expressed at different SCI stages, and may provide a therapeutic strategy for the treatment of patients with SCI. In this study, we found that autophagy is blocked in ZBTB38 knockdown SH-SY5Y cells and that the expression levels of LC3B II/I decreased and P62 increased. We used transcriptome high-throughput sequencing to identify the target in ZBTB38 knockdown cells. From the transcriptome profile, RB1CC1 (i.e., FIP200), a key component of the initiation machinery of autophagy (FIP200-ATG13-ULK1-ATG101), was found to decrease 4.2-fold following ZBTB38 knockdown. When RB1CC1-overexpressed plasmids were transfected into ZBTB38 knockdown cells, they rescued the phenotype of ZBTB38 knockdown cells. Cell proliferation and viability were significantly enhanced by RB1CC1 overexpression, and LC3B and P62 expression returned to their original levels. We also injected ZBTB38-overexpressed lentivirus into the injured center of the spinal cord and detected significant upregulation of RB1CC1 in the spinal cord. ZBTB38 overexpression can promote autophagy and partly rescue the secondary damage of SCI. Therefore, our findings provide a new strategy for the treatment of SCI.
Collapse
Affiliation(s)
- Jie Chen
- College of Life Sciences, Anhui Provincial Key Lab of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China; College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; The Secondary Hospital of Wuhu, Wuhu 241000, China
| | - Li Yan
- Department of Radiation Oncology, Linyi People Hospital, 276003, China
| | | | - Zengmeng Zhang
- College of Life Sciences, Anhui Provincial Key Lab of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Daolun Yu
- College of Life Sciences, Anhui Provincial Key Lab of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Chaofeng Xing
- College of Life Sciences, Anhui Provincial Key Lab of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Jie Li
- College of Life Sciences, Anhui Provincial Key Lab of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China
| | - Honglin Li
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Jun Li
- College of Life Sciences, Anhui Provincial Key Lab of the Conservation and Exploitation of Biological Resources, Anhui Normal University, Wuhu 241000, China.
| | - Yafei Cai
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
21
|
Miotto B, Marchal C, Adelmant G, Guinot N, Xie P, Marto JA, Zhang L, Defossez PA. Stabilization of the methyl-CpG binding protein ZBTB38 by the deubiquitinase USP9X limits the occurrence and toxicity of oxidative stress in human cells. Nucleic Acids Res 2018; 46:4392-4404. [PMID: 29490077 PMCID: PMC5961141 DOI: 10.1093/nar/gky149] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 02/05/2018] [Accepted: 02/16/2018] [Indexed: 12/29/2022] Open
Abstract
Reactive oxygen species (ROS) are a byproduct of cell metabolism, and can also arise from environmental sources, such as toxins or radiation. Depending on dose and context, ROS have both beneficial and deleterious roles in mammalian development and disease, therefore it is crucial to understand how these molecules are generated, sensed, and detoxified. The question of how oxidative stress connects to the epigenome, in particular, is important yet incompletely understood. Here we show that an epigenetic regulator, the methyl-CpG-binding protein ZBTB38, limits the basal cellular production of ROS, is induced by ROS, and is required to mount a proper response to oxidative stress. Molecularly, these functions depend on a deubiquitinase, USP9X, which interacts with ZBTB38, deubiquitinates it, and stabilizes it. We find that USP9X is itself stabilized by oxidative stress, and is required together with ZBTB38 to limit the basal generation of ROS, as well as the toxicity of an acute oxidative stress. Our data uncover a new nuclear target of USP9X, show that the USP9X/ZBTB38 axis limits, senses and detoxifies ROS, and provide a molecular link between oxidative stress and the epigenome.
Collapse
Affiliation(s)
- Benoit Miotto
- Univ. Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, 75013 Paris, France
- Institut Cochin, Sorbonne Paris Cité, 75014 Paris, France
| | - Claire Marchal
- Univ. Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, 75013 Paris, France
- Institut Cochin, Sorbonne Paris Cité, 75014 Paris, France
| | - Guillaume Adelmant
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Nadège Guinot
- Institut Cochin, Sorbonne Paris Cité, 75014 Paris, France
| | - Ping Xie
- State Key Laboratory of Proteomics, National Center of Protein Science (Beijing), Beijing Institute of Lifeomics, Beijing 100850, China
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Lingqiang Zhang
- State Key Laboratory of Proteomics, National Center of Protein Science (Beijing), Beijing Institute of Lifeomics, Beijing 100850, China
| | - Pierre-Antoine Defossez
- Univ. Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, 75013 Paris, France
| |
Collapse
|
22
|
The C-Terminal Zinc Fingers of ZBTB38 are Novel Selective Readers of DNA Methylation. J Mol Biol 2017; 430:258-271. [PMID: 29287967 DOI: 10.1016/j.jmb.2017.12.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 12/09/2017] [Accepted: 12/19/2017] [Indexed: 11/22/2022]
Abstract
Methyl-CpG binding proteins play an essential role in translating DNA methylation marks into a downstream transcriptional response, which has implications for both normal cell function as well as disease. Although for many of these proteins, a detailed mechanistic understanding for how this cellular process is mediated remains to be determined. ZBTB38 is an under-characterized member of the zinc finger (ZF) family of methyl-CpG binding proteins. Functional knowledge has been gained for its conserved methylated DNA binding N-terminal ZF region; however, a specific role for the C-terminal set of five ZFs remains to be elucidated. Here we demonstrate for the first time that a subset of the C-terminal ZBTB38 ZFs exhibit high-affinity DNA interactions and that preferential targeting of the consensus DNA site is methyl specific. Utilizing a hybrid approach, a model for the C-terminal ZBTB38 ZFs in complex with its cognate DNA target is proposed, providing insight into a possible novel mode of methylated DNA recognition. Furthermore, it is shown that the C-terminal ZFs of ZBTB38 can directly occupy promoters harboring the newly identified sequence motif in cell in a methyl-dependent manner and, depending on the gene context, contribute to modulating transcriptional response. Combined, these findings provide evidence for a key and novel physiological function for the C-terminal ZF domain of ZBTB38.
Collapse
|
23
|
Abstract
Skeletal muscle regeneration is an efficient stem cell-based repair system that ensures healthy musculature. For this repair system to function continuously throughout life, muscle stem cells must contribute to the process of myofiber repair as well as repopulation of the stem cell niche. The decision made by the muscle stem cells to commit to the muscle repair or to remain a stem cell depends upon patterns of gene expression, a process regulated at the epigenetic level. Indeed, it is well accepted that dynamic changes in epigenetic landscapes to control DNA accessibility and expression is a critical component during myogenesis for the effective repair of damaged muscle. Changes in the epigenetic landscape are governed by various posttranslational histone tail modifications, nucleosome repositioning, and DNA methylation events which collectively allow the control of changes in transcription networks during transitions of satellite cells from a dormant quiescent state toward terminal differentiation. This chapter focuses upon the specific epigenetic changes that occur during muscle stem cell-mediated regeneration to ensure myofiber repair and continuity of the stem cell compartment. Furthermore, we explore open questions in the field that are expected to be important areas of exploration as we move toward a more thorough understanding of the epigenetic mechanism regulating muscle regeneration.
Collapse
Affiliation(s)
- Daniel C L Robinson
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada; University of Ottawa, Ottawa, ON, Canada
| | - Francis J Dilworth
- Sprott Centre for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada; University of Ottawa, Ottawa, ON, Canada.
| |
Collapse
|
24
|
Zhu M, Liu J, Xiao J, Yang L, Cai M, Shen H, Chen X, Ma Y, Hu S, Wang Z, Hong A, Li Y, Sun Y, Wang X. Lnc-mg is a long non-coding RNA that promotes myogenesis. Nat Commun 2017; 8:14718. [PMID: 28281528 PMCID: PMC5353601 DOI: 10.1038/ncomms14718] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 01/25/2017] [Indexed: 12/11/2022] Open
Abstract
Recent studies indicate important roles for long noncoding RNAs (lncRNAs) as essential regulators of myogenesis and adult skeletal muscle regeneration. However, the specific roles of lncRNAs in myogenic differentiation of adult skeletal muscle stem cells and myogenesis are still largely unknown. Here we identify a lncRNA that is specifically enriched in skeletal muscle (myogenesis-associated lncRNA, in short, lnc-mg). In mice, conditional knockout of lnc-mg in skeletal muscle results in muscle atrophy and the loss of muscular endurance during exercise. Alternatively, skeletal muscle-specific overexpression of lnc-mg promotes muscle hypertrophy. In vitro analysis of primary skeletal muscle cells shows that lnc-mg increases gradually during myogenic differentiation and its overexpression improves cell differentiation. Mechanistically, lnc-mg promotes myogenesis, by functioning as a competing endogenous RNA (ceRNA) for microRNA-125b to control protein abundance of insulin-like growth factor 2. These findings identify lnc-mg as a novel noncoding regulator for muscle cell differentiation and skeletal muscle development.
Collapse
Affiliation(s)
- Mu Zhu
- Guangdong Provincial Key Laboratory of Bioengineering Medicine &National Engineering Research Center of Genetic Medicine, Department of Cell Biology and Institute of Biomedicine, Jinan University, Huang-Pu Avenue West 601, Guangzhou 510632, China.,State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing 100094, China.,Preclinical Medical School, Beijing University of Chinese Medicine, Beijing 100019, China
| | - Jiafan Liu
- Guangdong Provincial Key Laboratory of Bioengineering Medicine &National Engineering Research Center of Genetic Medicine, Department of Cell Biology and Institute of Biomedicine, Jinan University, Huang-Pu Avenue West 601, Guangzhou 510632, China
| | - Jia Xiao
- State Key Discipline of Infectious Diseases, Shenzhen Third People's Hospital, Shenzhen 518116, China
| | - Li Yang
- Guangdong Provincial Key Laboratory of Bioengineering Medicine &National Engineering Research Center of Genetic Medicine, Department of Cell Biology and Institute of Biomedicine, Jinan University, Huang-Pu Avenue West 601, Guangzhou 510632, China
| | - Mingxiang Cai
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China
| | - Hongyu Shen
- Guangdong Provincial Key Laboratory of Bioengineering Medicine &National Engineering Research Center of Genetic Medicine, Department of Cell Biology and Institute of Biomedicine, Jinan University, Huang-Pu Avenue West 601, Guangzhou 510632, China
| | - Xiaojia Chen
- Guangdong Provincial Key Laboratory of Bioengineering Medicine &National Engineering Research Center of Genetic Medicine, Department of Cell Biology and Institute of Biomedicine, Jinan University, Huang-Pu Avenue West 601, Guangzhou 510632, China
| | - Yi Ma
- Guangdong Provincial Key Laboratory of Bioengineering Medicine &National Engineering Research Center of Genetic Medicine, Department of Cell Biology and Institute of Biomedicine, Jinan University, Huang-Pu Avenue West 601, Guangzhou 510632, China
| | - Sumin Hu
- Preclinical Medical School, Beijing University of Chinese Medicine, Beijing 100019, China
| | - Zuolin Wang
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China
| | - An Hong
- Guangdong Provincial Key Laboratory of Bioengineering Medicine &National Engineering Research Center of Genetic Medicine, Department of Cell Biology and Institute of Biomedicine, Jinan University, Huang-Pu Avenue West 601, Guangzhou 510632, China
| | - Yingxian Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing 100094, China
| | - Yao Sun
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, School and Hospital of Stomatology, Tongji University, Shanghai 200072, China
| | - Xiaogang Wang
- Guangdong Provincial Key Laboratory of Bioengineering Medicine &National Engineering Research Center of Genetic Medicine, Department of Cell Biology and Institute of Biomedicine, Jinan University, Huang-Pu Avenue West 601, Guangzhou 510632, China
| |
Collapse
|
25
|
Blondelle J, Shapiro P, Domenighetti AA, Lange S. Cullin E3 Ligase Activity Is Required for Myoblast Differentiation. J Mol Biol 2017; 429:1045-1066. [PMID: 28238764 DOI: 10.1016/j.jmb.2017.02.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/17/2017] [Accepted: 02/18/2017] [Indexed: 01/06/2023]
Abstract
The role of cullin E3-ubiquitin ligases for muscle homeostasis is best known during muscle atrophy, as the cullin-1 substrate adaptor atrogin-1 is among the most well-characterized muscle atrogins. We investigated whether cullin activity was also crucial during terminal myoblast differentiation and aggregation of acetylcholine receptors for the establishment of neuromuscular junctions in vitro. The activity of cullin E3-ligases is modulated through post-translational modification with the small ubiquitin-like modifier nedd8. Using either the Nae1 inhibitor MLN4924 (Pevonedistat) or siRNA against nedd8 in early or late stages of differentiation on C2C12 myoblasts, and primary satellite cells from mouse and human, we show that cullin E3-ligase activity is necessary for each step of the muscle cell differentiation program in vitro. We further investigate known transcriptional repressors for terminal muscle differentiation, namely ZBTB38, Bhlhe41, and Id1. Due to their identified roles for terminal muscle differentiation, we hypothesize that the accumulation of these potential cullin E3-ligase substrates may be partially responsible for the observed phenotype. MLN4924 is currently undergoing clinical trials in cancer patients, and our experiments highlight concerns on the homeostasis and regenerative capacity of muscles in these patients who often experience cachexia.
Collapse
Affiliation(s)
- Jordan Blondelle
- Division of Cardiology, University of California San Diego, La Jolla, CA-92093 USA
| | - Paige Shapiro
- Division of Cardiology, University of California San Diego, La Jolla, CA-92093 USA
| | - Andrea A Domenighetti
- Rehabilitation Institute of Chicago, Chicago, IL-60611 USA; Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL-60611, USA
| | - Stephan Lange
- Division of Cardiology, University of California San Diego, La Jolla, CA-92093 USA.
| |
Collapse
|
26
|
Megiorni F, Camero S, Ceccarelli S, McDowell HP, Mannarino O, Marampon F, Pizer B, Shukla R, Pizzuti A, Marchese C, Clerico A, Dominici C. DNMT3B in vitro knocking-down is able to reverse embryonal rhabdomyosarcoma cell phenotype through inhibition of proliferation and induction of myogenic differentiation. Oncotarget 2016; 7:79342-79356. [PMID: 27764816 PMCID: PMC5346718 DOI: 10.18632/oncotarget.12688] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/29/2016] [Indexed: 01/08/2023] Open
Abstract
Aberrant DNA methylation has been frequently observed in many human cancers, including rhabdomyosarcoma (RMS), the most common soft tissue sarcoma in children. To date, the expression and function of the de novo DNA methyltransferase (DNMT) 3B in RMS have not yet been investigated. Our study show for the first time a significant up-regulation of DNMT3B levels in 14 RMS tumour samples and 4 RMS cell lines in comparison to normal skeletal muscle. Transfection of RD and TE671 cells, two in vitro models of embryonal RMS (ERMS), with a synthetic DNMT3B siRNA decreased cell proliferation by arresting cell cycle at G1 phase, as demonstrated by the reduced expression of Cyclin B1, Cyclin D1 and Cyclin E2, and by the concomitant up-regulation of the checkpoint regulators p21 and p27. DNMT3B depletion also impaired RB phosphorylation status and decreased migratory capacity and clonogenic potential. Interestingly, DNMT3B knock-down was able to commit ERMS cells towards myogenic terminal differentiation, as confirmed by the acquisition of a myogenic-like phenotype and by the increased expression of the myogenic markers MYOD1, Myogenin and MyHC. Finally, inhibition of MEK/ERK signalling by U0126 resulted in a reduction of DNMT3B protein, giving evidence that DNMT3B is a down-stream molecule of this oncogenic pathway.Taken together, our data indicate that altered expression of DNMT3B plays a key role in ERMS development since its silencing is able to reverse cell cancer phenotype by rescuing myogenic program. Epigenetic therapy, by targeting the DNA methylation machinery, may represent a novel therapeutic strategy against RMS.
Collapse
Affiliation(s)
- Francesca Megiorni
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Simona Camero
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Simona Ceccarelli
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Heather P. McDowell
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
- Department of Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Olga Mannarino
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Francesco Marampon
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Barry Pizer
- Department of Oncology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Rajeev Shukla
- Department of Perinatal and Paediatric Pathology, Alder Hey Children's NHS Foundation Trust, Liverpool, United Kingdom
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Cinzia Marchese
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Anna Clerico
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| | - Carlo Dominici
- Department of Paediatrics and Infantile Neuropsychiatry, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
27
|
Kotoku T, Kosaka K, Nishio M, Ishida Y, Kawaichi M, Matsuda E. CIBZ Regulates Mesodermal and Cardiac Differentiation of by Suppressing T and Mesp1 Expression in Mouse Embryonic Stem Cells. Sci Rep 2016; 6:34188. [PMID: 27659197 PMCID: PMC5034229 DOI: 10.1038/srep34188] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/08/2016] [Indexed: 11/24/2022] Open
Abstract
The molecular mechanisms underlying mesodermal and cardiac specification from embryonic stem cells (ESCs) are not fully understood. Here, we showed that the BTB domain-containing zinc finger protein CIBZ is expressed in mouse ESCs but is dramatically downregulated during ESC differentiation. CIBZ deletion in ESCs induced specification toward mesoderm phenotypes and their differentiation into cardiomyocytes, whereas overexpression of CIBZ delayed these processes. During ESC differentiation, CIBZ loss-and-gain-of-function data indicate that CIBZ negatively regulates the expressions of Brachyury (T) and Mesp1, the key transcriptional factors responsible for the specification of mammalian mesoderm and cardiac progenitors, respectively. Chromatin immunoprecipitation assays showed that CIBZ binds to T and Mesp1 promoters in undifferentiated ESCs, and luciferase assays indicate that CIBZ suppresses T and Mesp1 promoters. These findings demonstrate that CIBZ is a novel regulator of mesodermal and cardiac differentiation of ESCs, and suggest that CIBZ-mediated cardiac differentiation depends on the regulation of these two genes.
Collapse
Affiliation(s)
| | - Koji Kosaka
- Division of Gene Function in Animals, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Miki Nishio
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Yasumasa Ishida
- Functional Genomics and Medicine, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Masashi Kawaichi
- Division of Gene Function in Animals, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Eishou Matsuda
- Division of Gene Function in Animals, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| |
Collapse
|
28
|
Carrió E, Magli A, Muñoz M, Peinado MA, Perlingeiro R, Suelves M. Muscle cell identity requires Pax7-mediated lineage-specific DNA demethylation. BMC Biol 2016; 14:30. [PMID: 27075038 PMCID: PMC4831197 DOI: 10.1186/s12915-016-0250-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/23/2016] [Indexed: 12/01/2022] Open
Abstract
Background Skeletal muscle stem cells enable the formation, growth, maintenance, and regeneration of skeletal muscle throughout life. The regeneration process is compromised in several pathological conditions, and muscle progenitors derived from pluripotent stem cells have been suggested as a potential therapeutic source for tissue replacement. DNA methylation is an important epigenetic mechanism in the setting and maintenance of cellular identity, but its role in stem cell determination towards the myogenic lineage is unknown. Here we addressed the DNA methylation dynamics of the major genes orchestrating the myogenic determination and differentiation programs in embryonic stem (ES) cells, their Pax7-induced myogenic derivatives, and muscle stem cells in proliferating and differentiating conditions. Results Our data showed a common muscle-specific DNA demethylation signature required to acquire and maintain the muscle-cell identity. This specific-DNA demethylation is Pax7-mediated, and it is a prime event in muscle stem cells gene activation. Notably, downregulation of the demethylation-related enzyme Apobec2 in ES-derived myogenic precursors reduced myogenin-associated DNA demethylation and dramatically impaired the expression of differentiation markers and, ultimately, muscle differentiation. Conclusions Our results underscore DNA demethylation as a key mechanism driving myogenesis and identify specific Pax7-mediated DNA demethylation signatures to acquire and maintain the muscle-cell identity. Additionally, we provide a panel of epigenetic markers for the efficient and safe generation of ES- and induced pluripotent stem cell (iPS)-derived myogenic progenitors for therapeutic applications. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0250-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Elvira Carrió
- Institut de Medicina Predictiva i Personalizada del Càncer (IMPPC) and Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Alessandro Magli
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, 55455, USA
| | - Mar Muñoz
- Institut de Medicina Predictiva i Personalizada del Càncer (IMPPC) and Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Miguel A Peinado
- Institut de Medicina Predictiva i Personalizada del Càncer (IMPPC) and Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Rita Perlingeiro
- Lillehei Heart Institute, Department of Medicine, University of Minnesota, Minneapolis, 55455, USA
| | - Mònica Suelves
- Institut de Medicina Predictiva i Personalizada del Càncer (IMPPC) and Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain.
| |
Collapse
|
29
|
Carrió E, Suelves M. DNA methylation dynamics in muscle development and disease. Front Aging Neurosci 2015; 7:19. [PMID: 25798107 PMCID: PMC4350440 DOI: 10.3389/fnagi.2015.00019] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/15/2015] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is an essential epigenetic modification for mammalian development and is crucial for the establishment and maintenance of cellular identity. Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of genome-wide approaches has allowed the analysis of DNA methylation in different genomic contexts revealing a more dynamic regulation than originally thought, since active DNA methylation and demethylation occur during cellular differentiation and tissue specification. Satellite cells are the primary stem cells in adult skeletal muscle and are responsible for postnatal muscle growth, hypertrophy, and muscle regeneration. This review outlines the published data regarding DNA methylation changes along the skeletal muscle program, in both physiological and pathological conditions, to better understand the epigenetic mechanisms that control myogenesis.
Collapse
Affiliation(s)
- Elvira Carrió
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) and Health Sciences Research Institute Germans Trias I Pujol (IGTP) Badalona, Spain
| | - Mònica Suelves
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) and Health Sciences Research Institute Germans Trias I Pujol (IGTP) Badalona, Spain
| |
Collapse
|
30
|
Marchal C, Miotto B. Emerging Concept in DNA Methylation: Role of Transcription Factors in Shaping DNA Methylation Patterns. J Cell Physiol 2014; 230:743-51. [DOI: 10.1002/jcp.24836] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/01/2014] [Indexed: 02/04/2023]
Affiliation(s)
- Claire Marchal
- Université Paris Diderot; Sorbonne Paris Cité; Epigenetics and Cell Fate; Paris France
| | - Benoit Miotto
- Université Paris Diderot; Sorbonne Paris Cité; Epigenetics and Cell Fate; Paris France
| |
Collapse
|
31
|
Segalés J, Perdiguero E, Muñoz-Cánoves P. Epigenetic control of adult skeletal muscle stem cell functions. FEBS J 2014; 282:1571-88. [PMID: 25251895 DOI: 10.1111/febs.13065] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 12/12/2022]
Abstract
Skeletal muscle regeneration in the adult (de novo myogenesis) depends on a resident population of muscle stem cells (satellite cells) that are normally quiescent. In response to injury or stress, satellite cells are activated and expand as myoblast cells that differentiate and fuse to form new muscle fibers or return to quiescence to maintain the stem cell pool (self-renewal). Satellite cell-dependent myogenesis is a well-characterized multi-step process orchestrated by muscle-specific transcription factors, such as Pax3/Pax7 and members of the MyoD family of muscle regulatory factors, and epigenetically controlled by mechanisms such as DNA methylation, covalent modification of histones and non-coding RNAs. Recent results from next-generation genome-wide sequencing have increased our understanding about the highly intricate layers of epigenetic regulation involved in satellite cell maintenance, activation, differentiation and self-renewal, and their cross-talk with the muscle-specific transcriptional machinery.
Collapse
Affiliation(s)
- Jessica Segalés
- Cell Biology Group, Department of Experimental and Health Sciences, Pompeu Fabra University, Center for Networked Biomedical Research on Neurodegenerative Diseases, Barcelona, Spain
| | | | | |
Collapse
|
32
|
Miyata K, Miyata T, Nakabayashi K, Okamura K, Naito M, Kawai T, Takada S, Kato K, Miyamoto S, Hata K, Asahara H. DNA methylation analysis of human myoblasts during in vitro myogenic differentiation: de novo methylation of promoters of muscle-related genes and its involvement in transcriptional down-regulation. Hum Mol Genet 2014; 24:410-23. [PMID: 25190712 DOI: 10.1093/hmg/ddu457] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Although DNA methylation is considered to play an important role during myogenic differentiation, chronological alterations in DNA methylation and gene expression patterns in this process have been poorly understood. Using the Infinium HumanMethylation450 BeadChip array, we obtained a chronological profile of the genome-wide DNA methylation status in a human myoblast differentiation model, where myoblasts were cultured in low-serum medium to stimulate myogenic differentiation. As the differentiation of the myoblasts proceeded, their global DNA methylation level increased and their methylation patterns became more distinct from those of mesenchymal stem cells. Gene ontology analysis revealed that genes whose promoter region was hypermethylated upon myoblast differentiation were highly significantly enriched with muscle-related terms such as 'muscle contraction' and 'muscle system process'. Sequence motif analysis identified 8-bp motifs somewhat similar to the binding motifs of ID4 and ZNF238 to be most significantly enriched in hypermethylated promoter regions. ID4 and ZNF238 have been shown to be critical transcriptional regulators of muscle-related genes during myogenic differentiation. An integrated analysis of DNA methylation and gene expression profiles revealed that de novo DNA methylation of non-CpG island (CGI) promoters was more often associated with transcriptional down-regulation than that of CGI promoters. These results strongly suggest the existence of an epigenetic mechanism in which DNA methylation modulates the functions of key transcriptional factors to coordinately regulate muscle-related genes during myogenic differentiation.
Collapse
Affiliation(s)
- Kohei Miyata
- Department of Systems BioMedicine and Department of Obstetrics and Gynecology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Tomoko Miyata
- Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazuhiko Nakabayashi
- Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | | | - Masashi Naito
- Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan and
| | - Tomoko Kawai
- Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | | | - Kiyoko Kato
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Shingo Miyamoto
- Department of Obstetrics and Gynecology, Faculty of Medicine, Fukuoka University, Fukuoka 814-0180, Japan
| | - Kenichiro Hata
- Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan
| | - Hiroshi Asahara
- Department of Systems BioMedicine and Department of Systems BioMedicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan and Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
33
|
Saini A, Mastana S, Myers F, Lewis MP. 'From death, lead me to immortality' - mantra of ageing skeletal muscle. Curr Genomics 2013; 14:256-67. [PMID: 24294106 PMCID: PMC3731816 DOI: 10.2174/1389202911314040004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/15/2013] [Accepted: 05/16/2013] [Indexed: 12/20/2022] Open
Abstract
Skeletal muscle is a post-mitotic tissue maintained by repair and regeneration through a population of stem cell-like satellite cells. Following muscle injury, satellite cell proliferation is mediated by local signals ensuring sufficient progeny for tissue repair. Age–related changes in satellite cells as well as to the local and systemic environment potentially impact on the capacity of satellite cells to generate sufficient progeny in an ageing organism resulting in diminished regeneration. ‘Rejuvenation’ of satellite cell progeny and regenerative capacity by environmental stimuli effectors suggest that a subset of age-dependent satellite cell changes may be reversible. Epigenetic regulation of satellite stem cells that include DNA methylation and histone modifications which regulate gene expression are potential mechanisms for such reversible changes and have been shown to control organismal longevity. The area of health and ageing that is likely to benefit soonest from advances in the biology of adult stem cells is the emerging field of regenerative medicine. Further studies are needed to elucidate the mechanisms by which epigenetic modifications regulate satellite stem cell function and will require an increased understanding of stem-cell biology, the environment of the aged tissue and the interaction between the two.
Collapse
Affiliation(s)
- Amarjit Saini
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | | | | | | |
Collapse
|
34
|
Ehrlich M, Lacey M. DNA methylation and differentiation: silencing, upregulation and modulation of gene expression. Epigenomics 2013; 5:553-68. [PMID: 24059801 PMCID: PMC3864898 DOI: 10.2217/epi.13.43] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Differentiation-related DNA methylation is receiving increasing attention, partly owing to new, whole-genome analyses. These revealed that cell type-specific differential methylation in gene bodies is more frequent than in promoters. We review new insights into the functionality of DNA methylation during differentiation, with emphasis on the methylomes of myoblasts, myotubes and skeletal muscle versus non-muscle samples. Biostatistical analyses of data from reduced representation bisulfite sequencing are discussed. Lastly, a model is presented for how promoter and intragenic DNA hypermethylation affect gene expression, including increasing the efficiency of polycomb silencing at some promoters, downmodulating other promoters rather than silencing them, counteracting enhancers with heterologous specificity, altering chromatin conformation by inhibiting the binding of CTCF, modulating mRNA transcript levels by inhibiting overlapping promoters of noncoding RNA genes or by regulating the use of alternative mRNA promoters, modulating transcription termination, regulating alternative splicing and acting as barriers to the spread of activating chromatin.
Collapse
Affiliation(s)
- Melanie Ehrlich
- Hayward Human Genetics Program, Tulane Cancer Center, and Center for Bioinformatics & Genomics, Tulane Health Sciences Center, New Orleans, LA 70112, USA.
| | | |
Collapse
|
35
|
Turning on myogenin in muscle: a paradigm for understanding mechanisms of tissue-specific gene expression. Comp Funct Genomics 2012; 2012:836374. [PMID: 22811619 PMCID: PMC3395204 DOI: 10.1155/2012/836374] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/23/2012] [Indexed: 11/21/2022] Open
Abstract
Expression of the myogenin (Myog) gene is restricted to skeletal muscle cells where the transcriptional activator turns on a gene expression program that permits the transition from proliferating myoblasts to differentiating myotubes. The strict temporal and spatial regulation on Myog expression in the embryo makes it an ideal gene to study the developmental regulation of tissue-specific expression. Over the last 20 years, our knowledge of the regulation of Myog expression has evolved from the identification of the minimal promoter elements necessary for the gene to be transcribed in muscle, to a mechanistic understanding of how the proteins that bind these DNA elements work together to establish transcriptional competence. Here we present our current understanding of the developmental regulation of gene expression gained from studies of the Myog gene.
Collapse
|
36
|
Liang QH, Jiang Y, Zhu X, Cui RR, Liu GY, Liu Y, Wu SS, Liao XB, Xie H, Zhou HD, Wu XP, Yuan LQ, Liao EY. Ghrelin attenuates the osteoblastic differentiation of vascular smooth muscle cells through the ERK pathway. PLoS One 2012; 7:e33126. [PMID: 22514603 PMCID: PMC3326017 DOI: 10.1371/journal.pone.0033126] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 02/06/2012] [Indexed: 11/21/2022] Open
Abstract
Vascular calcification results from osteoblastic differentiation of vascular smooth muscle cells (VSMCs) and is a major risk factor for cardiovascular events. Ghrelin is a newly discovered bioactive peptide that acts as a natural endogenous ligand of the growth hormone secretagog receptor (GHSR). Several studies have identified the protective effects of ghrelin on the cardiovascular system, however research on the effects and mechanisms of ghrelin on vascular calcification is still quite rare. In this study, we determined the effect of ghrelin on osteoblastic differentiation of VSMCs and investigated the mechanism involved using the two universally accepted calcifying models of calcifying vascular smooth muscle cells (CVSMCs) and beta-glycerophosphate (beta-GP)-induced VSMCs. Our data demonstrated that ghrelin inhibits osteoblastic differentiation and mineralization of VSMCs due to decreased alkaline phosphatase (ALP) activity, Runx2 expression, bone morphogenetic protein-2 (BMP-2) expression and calcium content. Further study demonstrated that ghrelin exerted this suppression effect via an extracellular signal-related kinase (ERK)-dependent pathway and that the suppression effect of ghrelin was time dependent and dose dependent. Furthermore, inhibition of the growth hormone secretagog receptor (GHSR), the ghrelin receptor, by siRNA significantly reversed the activation of ERK by ghrelin. In conclusion, our study suggests that ghrelin may inhibit osteoblastic differentiation of VSMCs through the GHSR/ERK pathway.
Collapse
Affiliation(s)
- Qiu-Hua Liang
- Institute of Metabolism and Endocrinology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
| | - Yi Jiang
- Department of Pathology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
| | - Xiao Zhu
- Institute of Metabolism and Endocrinology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
| | - Rong-Rong Cui
- Institute of Metabolism and Endocrinology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
- Department of Pediatrics, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
| | - Guan-Ying Liu
- Institute of Metabolism and Endocrinology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
| | - Yuan Liu
- Institute of Metabolism and Endocrinology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
| | - Shan-Shan Wu
- Institute of Metabolism and Endocrinology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
| | - Xiao-Bo Liao
- Department of Cardiothoracic Surgery, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
| | - Hui Xie
- Institute of Metabolism and Endocrinology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
| | - Hou-De Zhou
- Institute of Metabolism and Endocrinology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
| | - Xian-Ping Wu
- Institute of Metabolism and Endocrinology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
| | - Ling-Qing Yuan
- Institute of Metabolism and Endocrinology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
- * E-mail: (LQY); (EYL)
| | - Er-Yuan Liao
- Institute of Metabolism and Endocrinology, the Second Xiang-Ya Hospital, Central South University, Changsha, People's Republic of China
- * E-mail: (LQY); (EYL)
| |
Collapse
|
37
|
CIBZ, a novel BTB domain-containing protein, is involved in mouse spinal cord injury via mitochondrial pathway independent of p53 gene. PLoS One 2012; 7:e33156. [PMID: 22427977 PMCID: PMC3299754 DOI: 10.1371/journal.pone.0033156] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 02/10/2012] [Indexed: 12/22/2022] Open
Abstract
Spinal cord injury (SCI) induces both primary uncontrollable mechanical injury and secondary controllable degeneration, which further results in the activation of cell death cascades that mediate delayed tissue damage. To alleviate its impairments and seek for an effective remedy, mRNA differential display was used to investigate gene mRNA expression profiling in mice following SCI. A specific Zinc finger and BTB domain-containing protein, CIBZ, was discovered to implicate in the SCI process for the first time. Further researches indicated that CIBZ was extensively distributed in various tissues, and the expression level was highest in muscle, followed by spinal cord, large intestine, kidney, spleen, thymus, lung, cerebrum, stomach, ovary and heart, respectively. After injury, the CIBZ expression decreased dramatically and reached the lowest level at 8 h, but it gradually increased to the maximal level at 7 d. Caspase-3 and C-terminal-binding protein (CtBP), two CIBZ-related proteins, showed similar tendency. Interestingly, p53 expression remained constant in all groups. Via flow cytometry (FCM) analysis, it was found that the cell death rate in SCI group markedly increased and reached the highest value 1 d after surgery and the mitochondrial transmembrane potential (ΔΨm) at 1 d was the lowest in all groups. Taken together, it is suggested that: (i) in the presence of CtBP, CIBZ gene is involved in secondary injury process and trigger the activation of apoptotic caspase-3 and bax genes independent of p53; (ii) abrupt down-regulation of CtBP at 8 h is a sign of mitochondria dysfunction and the onset of cell death; (iii) it could be used as an inhibitor or target drug of caspase-3 gene to improve spinal cord function.
Collapse
|
38
|
Sodium arsenite represses the expression of myogenin in C2C12 mouse myoblast cells through histone modifications and altered expression of Ezh2, Glp, and Igf-1. Toxicol Appl Pharmacol 2012; 260:250-9. [PMID: 22426358 DOI: 10.1016/j.taap.2012.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/29/2012] [Accepted: 03/01/2012] [Indexed: 12/22/2022]
Abstract
Arsenic is a toxicant commonly found in water systems and chronic exposure can result in adverse developmental effects including increased neonatal death, stillbirths, and miscarriages, low birth weight, and altered locomotor activity. Previous studies indicate that 20 nM sodium arsenite exposure to C2C12 mouse myocyte cells delayed myoblast differentiation due to reduced myogenin expression, the transcription factor that differentiates myoblasts into myotubes. In this study, several mechanisms by which arsenic could alter myogenin expression were examined. Exposing differentiating C2C12 cells to 20 nM arsenic increased H3K9 dimethylation (H3K9me2) and H3K9 trimethylation (H3K9me3) by 3-fold near the transcription start site of myogenin, which is indicative of increased repressive marks, and reduced H3K9 acetylation (H3K9Ac) by 0.5-fold, indicative of reduced permissive marks. Protein expression of Glp or Ehmt1, a H3-K9 methyltransferase, was also increased by 1.6-fold in arsenic-exposed cells. In addition to the altered histone remodeling status on the myogenin promoter, protein and mRNA levels of Igf-1, a myogenic growth factor, were significantly repressed by arsenic exposure. Moreover, a 2-fold induction of Ezh2 expression, and an increased recruitment of Ezh2 (3.3-fold) and Dnmt3a (~2-fold) to the myogenin promoter at the transcription start site (-40 to +42), were detected in the arsenic-treated cells. Together, we conclude that the repressed myogenin expression in arsenic-exposed C2C12 cells was likely due to a combination of reduced expression of Igf-1, enhanced nuclear expression and promoter recruitment of Ezh2, and altered histone remodeling status on myogenin promoter (-40 to +42).
Collapse
|
39
|
Nishii T, Oikawa Y, Ishida Y, Kawaichi M, Matsuda E. CtBP-interacting BTB zinc finger protein (CIBZ) promotes proliferation and G1/S transition in embryonic stem cells via Nanog. J Biol Chem 2012; 287:12417-24. [PMID: 22315219 DOI: 10.1074/jbc.m111.333856] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mouse embryonic stem cells (ESCs) require transcriptional regulation to ensure rapid proliferation that allows for self-renewal. However, the molecular mechanism by which transcriptional factors regulate this rapid proliferation remains largely unknown. Here we present data showing that CIBZ, a BTB domain zinc finger transcriptional factor, is a key transcriptional regulator for regulation of ESC proliferation. Here we show that deletion or siRNA knockdown of CIBZ inhibits ESC proliferation. Cell cycle analysis shows that loss of CIBZ delays the progression of ESCs through the G1 to S phase transition. Conversely, constitutive ectopic expression of exogenous CIBZ in ESCs promotes proliferation and accelerates G1/S transition. These findings suggest that regulation of the G1/S transition explains, in part, CIBZ-associated ESC proliferation. Our data suggest that CIBZ acts through the post-transcriptionally regulates the expression of Nanog, a positive regulator of ESC proliferation and G1/S transition, but does not affect Oct3/4 and Sox2 protein expression. Notably, constitutive overexpression of Nanog partially rescued the proliferation defect caused by CIBZ knockdown, indicating the role of CIBZ in ESC proliferation and G1/S transition at least in part depends on the Nanog protein level.
Collapse
Affiliation(s)
- Tomonori Nishii
- Division of Gene Function in Animals, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | | | | | | | | |
Collapse
|
40
|
Reddington JP, Meehan RR. Putting muscle in DNA methylation. Cell Res 2011; 21:1531-3. [PMID: 21625268 DOI: 10.1038/cr.2011.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- James P Reddington
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh EH4 2XU, UK.
| | | |
Collapse
|