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Kawa Y, Shindo M, Ohgane J, Inui M. Epigenome editing revealed the role of DNA methylation of T-DMR/CpG island shore on Runx2 transcription. Biochem Biophys Rep 2024; 38:101733. [PMID: 38799114 PMCID: PMC11127475 DOI: 10.1016/j.bbrep.2024.101733] [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: 03/29/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
RUNX2 is a transcription factor crucial for bone formation. Mutant mice with varying levels of Runx2 expression display dosage-dependent skeletal abnormalities, underscoring the importance of Runx2 dosage control in skeletal formation. RUNX2 activity is regulated by several molecular mechanisms, including epigenetic modification such as DNA methylation. In this study, we investigated whether targeted repressive epigenome editing including hypermethylation to the Runx2-DMR/CpG island shore could influence Runx2 expression using Cas9-based epigenome-editing tools. Through the transient introduction of CRISPRoff-v2.1 and gRNAs targeting Runx2-DMR into MC3T3-E1 cells, we successfully induced hypermethylation of the region and concurrently reduced Runx2 expression during osteoblast differentiation. Although the epigenome editing of Runx2-DMR did not impact the expression of RUNX2 downstream target genes, these results indicate a causal relationship between the epigenetic status of the Runx2-DMR and Runx2 transcription. Additionally, we observed that hypermethylation of the Runx2-DMR persisted for at least 24 days under growth conditions but decreased during osteogenic differentiation, highlighting an endogenous DNA demethylation activity targeting the Runx2-DMR during the differentiation process. In summary, our study underscore the usefulness of the epigenome editing technology to evaluate the function of endogenous genetic elements and revealed that the Runx2-DMR methylation is actively regulated during osteoblast differentiation, subsequently could influence Runx2 expression.
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Affiliation(s)
- Yutaro Kawa
- Laboratory of Animal Regeneration Systemology, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa, 214-8571, Japan
| | - Miyuki Shindo
- Division of Laboratory Animal Resources, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Jun Ohgane
- Laboratory of Genomic Function Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa, 214-8571, Japan
| | - Masafumi Inui
- Laboratory of Animal Regeneration Systemology, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa, 214-8571, Japan
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2
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Scott CA, Duryea JD, MacKay H, Baker MS, Laritsky E, Gunasekara CJ, Coarfa C, Waterland RA. Identification of cell type-specific methylation signals in bulk whole genome bisulfite sequencing data. Genome Biol 2020; 21:156. [PMID: 32605651 PMCID: PMC7329512 DOI: 10.1186/s13059-020-02065-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/29/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The traditional approach to studying the epigenetic mechanism CpG methylation in tissue samples is to identify regions of concordant differential methylation spanning multiple CpG sites (differentially methylated regions). Variation limited to single or small numbers of CpGs has been assumed to reflect stochastic processes. To test this, we developed software, Cluster-Based analysis of CpG methylation (CluBCpG), and explored variation in read-level CpG methylation patterns in whole genome bisulfite sequencing data. RESULTS Analysis of both human and mouse whole genome bisulfite sequencing datasets reveals read-level signatures associated with cell type and cell type-specific biological processes. These signatures, which are mostly orthogonal to classical differentially methylated regions, are enriched at cell type-specific enhancers and allow estimation of proportional cell composition in synthetic mixtures and improved prediction of gene expression. In tandem, we developed a machine learning algorithm, Precise Read-Level Imputation of Methylation (PReLIM), to increase coverage of existing whole genome bisulfite sequencing datasets by imputing CpG methylation states on individual sequencing reads. PReLIM both improves CluBCpG coverage and performance and enables identification of novel differentially methylated regions, which we independently validate. CONCLUSIONS Our data indicate that, rather than stochastic variation, read-level CpG methylation patterns in tissue whole genome bisulfite sequencing libraries reflect cell type. Accordingly, these new computational tools should lead to an improved understanding of epigenetic regulation by DNA methylation.
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Affiliation(s)
- C. Anthony Scott
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children’s Nutrition Research Center, Houston, TX USA
| | - Jack D. Duryea
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children’s Nutrition Research Center, Houston, TX USA
| | - Harry MacKay
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children’s Nutrition Research Center, Houston, TX USA
| | - Maria S. Baker
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children’s Nutrition Research Center, Houston, TX USA
| | - Eleonora Laritsky
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children’s Nutrition Research Center, Houston, TX USA
| | - Chathura J. Gunasekara
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children’s Nutrition Research Center, Houston, TX USA
| | - Cristian Coarfa
- Department of Molecular & Cell Biology, Baylor College of Medicine, Houston, TX USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX USA
| | - Robert A. Waterland
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children’s Nutrition Research Center, Houston, TX USA
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX USA
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Arai Y, Umeyama K, Okazaki N, Nakano K, Nishino K, Nagashima H, Ohgane J. DNA methylation ambiguity in the Fibrillin-1 (FBN1) CpG island shore possibly involved in Marfan syndrome. Sci Rep 2020; 10:5287. [PMID: 32210272 PMCID: PMC7093481 DOI: 10.1038/s41598-020-62127-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 03/09/2020] [Indexed: 11/15/2022] Open
Abstract
Fibrillin-1 (FBN1) is responsible for haploinsufficient and autosomal dominant Marfan syndrome. Even in the same Marfan pedigree, penetrance and expressivity in heterozygous individuals can differ and result in variable disease onset and severity. Thus, other factors in addition to mutations in FBN1 are likely to contribute to the disease. In this study, we examined the regulation of FBN1 in porcine Marfan syndrome model, focusing on DNA methylation patterns distinguishable as wild-type (WT) and FBN1 null (KO) alleles in heterozygous cells. Most importantly, the ratio of the transcriptionally active hypomethylated WT allele was altered during cellular passage and highly correlated with FBN1 mRNA level compared with that in the KO allele. Transcribed FBN1 RNA from the KO allele was abolished after splicing coupled with translational initiation, suggesting that the functional FBN1 mRNA levels were affected by DNA methylation of the WT allele.
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Affiliation(s)
- Yoshikazu Arai
- Laboratory of Veterinary Biochemistry and Molecular Biology, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Kazuhiro Umeyama
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan.,Meiji University International Institute for Bio-Resource Research (MUIIBR), Kawasaki, 214-8571, Japan
| | - Natsumi Okazaki
- Laboratory of Genomic Function Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan
| | - Kazuaki Nakano
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan.,Meiji University International Institute for Bio-Resource Research (MUIIBR), Kawasaki, 214-8571, Japan
| | - Koichiro Nishino
- Laboratory of Veterinary Biochemistry and Molecular Biology, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192, Japan.,Center for Animal Disease Control, University of Miyazaki, Miyazaki, 889-2192, Japan
| | - Hiroshi Nagashima
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan.,Meiji University International Institute for Bio-Resource Research (MUIIBR), Kawasaki, 214-8571, Japan
| | - Jun Ohgane
- Laboratory of Genomic Function Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, 214-8571, Japan.
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MacKay H, Scott CA, Duryea JD, Baker MS, Laritsky E, Elson AE, Garland T, Fiorotto ML, Chen R, Li Y, Coarfa C, Simerly RB, Waterland RA. DNA methylation in AgRP neurons regulates voluntary exercise behavior in mice. Nat Commun 2019; 10:5364. [PMID: 31792207 PMCID: PMC6889160 DOI: 10.1038/s41467-019-13339-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 10/16/2019] [Indexed: 12/16/2022] Open
Abstract
DNA methylation regulates cell type-specific gene expression. Here, in a transgenic mouse model, we show that deletion of the gene encoding DNA methyltransferase Dnmt3a in hypothalamic AgRP neurons causes a sedentary phenotype characterized by reduced voluntary exercise and increased adiposity. Whole-genome bisulfite sequencing (WGBS) and transcriptional profiling in neuronal nuclei from the arcuate nucleus of the hypothalamus (ARH) reveal differentially methylated genomic regions and reduced expression of AgRP neuron-associated genes in knockout mice. We use read-level analysis of WGBS data to infer putative ARH neural cell types affected by the knockout, and to localize promoter hypomethylation and increased expression of the growth factor Bmp7 to AgRP neurons, suggesting a role for aberrant TGF-β signaling in the development of this phenotype. Together, these data demonstrate that DNA methylation in AgRP neurons is required for their normal epigenetic development and neuron-specific gene expression profiles, and regulates voluntary exercise behavior. AgRP neurons in the hypothalamic arcuate nucleus (ARH) are involved in regulating hunger and energy balance. Here the authors show that knockout of the DNA methyltransferase Dnmt3a in AgRP neurons of the ARH leads to a reduction in voluntary exercise along with numerous epigenetic and gene expression changes in ARH neurons.
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Affiliation(s)
- Harry MacKay
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - C Anthony Scott
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - Jack D Duryea
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - Maria S Baker
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - Eleonora Laritsky
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA
| | - Amanda E Elson
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, CA, 92521, USA
| | - Marta L Fiorotto
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA.,Department of Molecular Physiology & Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Rui Chen
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yumei Li
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Cristian Coarfa
- Department of Molecular & Cell Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard B Simerly
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Robert A Waterland
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children's Nutrition Research Center, Houston, TX, 77030, USA. .,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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Yamada Y, Sasaki S. A method for identifying allele-specific hydroxymethylation. Epigenetics 2019; 15:231-250. [PMID: 31533538 DOI: 10.1080/15592294.2019.1664228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
We previously identified sequence-dependent allele-specific methylation (sd-ASM) in adult human peripheral blood leukocytes, in which ASM occurs in cis depending on adjacent polymorphic sequences. A number of groups have identified sd-ASM sites in the human and mouse genomes, illustrating the prevalence of sd-ASM in mammalian genomes. In addition, sd-ASM can lead to sequence-dependent allele-specific expression of neighbouring genes. Imprinted genes also often exhibit parent-of-origin-dependent allele-specific methylation (pd-ASM), which causes parent-of-origin-dependent allele-specific expression. However, whether most of the already known sd-ASM and pd-ASM sites are methylated or hydroxymethylated remains unclear due to technical restrictions. Accordingly, a novel method that enables examination of allelic methylation and hydroxymethylation status and also overcomes the drawbacks of conventional methods is needed. Such a method could also be used to elucidate the mechanisms underlying polymorphism-associated inter-individual differences in disease susceptibility and the mechanism of genomic imprinting. Here, we developed a simple method to determine allelic hydroxymethylation status and identified novel sequence- and parent-of-origin-dependent allele-specific hydroxymethylation sites. Correlation analyses of TF binding sequences and methylation or hydroxymethylation between three mouse strains revealed the involvement of Pax5 in strain-specific methylation and hydroxymethylation in exon 7 of Pdgfrb.
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Affiliation(s)
- Yoichi Yamada
- Faculty of Electrical and Computer Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Sho Sasaki
- Division of Electrical and Computer Engineering, Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
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Arai Y, Umeyama K, Takeuchi K, Okazaki N, Hichiwa N, Yashima S, Nakano K, Nagashima H, Ohgane J. Establishment of DNA methylation patterns of the Fibrillin1 (FBN1) gene in porcine embryos and tissues. J Reprod Dev 2017; 63:157-165. [PMID: 28111381 PMCID: PMC5401809 DOI: 10.1262/jrd.2016-158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
DNA methylation in transcriptional regulatory regions is crucial for gene expression. The DNA methylation status of the edges of CpG islands, called CpG island shore, is involved in tissue/cell-type-specific gene expression.
Haploinsufficiency diseases are caused by inheritance of one mutated null allele and are classified as autosomal dominant. However, in the same pedigree, phenotypic variances are observed despite the inheritance of the identical
mutated null allele, including Fibrillin1 (FBN1), which is responsible for development of the haploinsufficient Marfan disease. In this study, we examined the relationship between gene expression
and DNA methylation patterns of the FBN1 CpG island shore focusing on transcriptionally active hypomethylated alleles (Hypo-alleles). No difference in the DNA methylation level of FBN1 CpG island
shore was observed in porcine fetal fibroblast (PFF) and the liver, whereas FBN1 expression was higher in PFF than in the liver. However, Hypo-allele ratio of the FBN1 CpG island shore in PFF was
higher than that in the liver, indicating that Hypo-allele ratio of the FBN1 CpG island shore likely correlated with FBN1 expression level. In addition, oocyte-derived DNA hypermethylation in
preimplantation embryos was erased until the blastocyst stage, and re-methylation of the FBN1 CpG island shore was observed with prolonged in vitro culture of blastocysts. These results suggest
that the establishment of the DNA methylation pattern within the FBN1 CpG island shore occurs after the blastocyst stage, likely during organogenesis. In conclusion, Hypo-allele ratios of the FBN1
CpG island shore correlated with FBN1 expression levels in porcine tissues.
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Affiliation(s)
- Yoshikazu Arai
- Laboratory of Genomic Function Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan.,Laboratory of Veterinary Biochemistry and Molecular Biology, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan
| | - Kazuhiro Umeyama
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan.,Meiji University International Institute for Bio-Resource Research (MUIIBR), Kanagawa 214-8571, Japan
| | - Kenta Takeuchi
- Laboratory of Genomic Function Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| | - Natsumi Okazaki
- Laboratory of Genomic Function Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| | - Naomi Hichiwa
- Laboratory of Genomic Function Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| | - Sayaka Yashima
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| | - Kazuaki Nakano
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
| | - Hiroshi Nagashima
- Laboratory of Developmental Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan.,Meiji University International Institute for Bio-Resource Research (MUIIBR), Kanagawa 214-8571, Japan
| | - Jun Ohgane
- Laboratory of Genomic Function Engineering, Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa 214-8571, Japan
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