DNA methylation landscape of 16 canine somatic tissues by methylation-sensitive restriction enzyme-based next generation sequencing
Abstract DNA methylation plays important functions in gene expression regulation that is involved in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in companion animals like dog. Using methylation-sensitive...
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Nature Portfolio
2021-05-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-89279-0 |
| _version_ | 1818343592663449600 |
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| author | Jumpei Yamazaki Yuki Matsumoto Jaroslav Jelinek Teita Ishizaki Shingo Maeda Kei Watanabe Genki Ishihara Junya Yamagishi Mitsuyoshi Takiguchi |
| author_facet | Jumpei Yamazaki Yuki Matsumoto Jaroslav Jelinek Teita Ishizaki Shingo Maeda Kei Watanabe Genki Ishihara Junya Yamagishi Mitsuyoshi Takiguchi |
| author_sort | Jumpei Yamazaki |
| collection | DOAJ |
| description | Abstract DNA methylation plays important functions in gene expression regulation that is involved in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in companion animals like dog. Using methylation-sensitive restriction enzyme-based next generation sequencing (Canine DREAM), we obtained canine DNA methylation maps of 16 somatic tissues from two dogs. In total, we evaluated 130,861 CpG sites. The majority of CpG sites were either highly methylated (> 70%, 52.5–64.6% of all CpG sites analyzed) or unmethylated (< 30%, 22.5–28.0% of all CpG sites analyzed) which are methylation patterns similar to other species. The overall methylation status of CpG sites across the 32 methylomes were remarkably similar. However, the tissue types were clearly defined by principle component analysis and hierarchical clustering analysis with DNA methylome. We found 6416 CpG sites located closely at promoter region of genes and inverse correlation between DNA methylation and gene expression of these genes. Our study provides basic dataset for DNA methylation profiles in dogs. |
| first_indexed | 2024-12-13T16:33:02Z |
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| id | doaj.art-ed805d32d9d44ff9ae3bc26058b39e3f |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-13T16:33:02Z |
| publishDate | 2021-05-01 |
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| spelling | doaj.art-ed805d32d9d44ff9ae3bc26058b39e3f2022-12-21T23:38:28ZengNature PortfolioScientific Reports2045-23222021-05-0111111010.1038/s41598-021-89279-0DNA methylation landscape of 16 canine somatic tissues by methylation-sensitive restriction enzyme-based next generation sequencingJumpei Yamazaki0Yuki Matsumoto1Jaroslav Jelinek2Teita Ishizaki3Shingo Maeda4Kei Watanabe5Genki Ishihara6Junya Yamagishi7Mitsuyoshi Takiguchi8Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido UniversityResearch and Development Section, Anicom Specialty Medical Institute Inc.Coriell Institute for Medical ResearchLaboratory of Comparative Pathology, Graduate School of Veterinary Medicine, Hokkaido UniversityDepartment of Veterinary Clinical Pathobiology, Graduate School of Agricultural and Life Sciences, The University of TokyoResearch and Development Section, Anicom Specialty Medical Institute Inc.Research and Development Section, Anicom Specialty Medical Institute Inc.Division of Collaboration and Education, Research Center for Zoonosis Control, Hokkaido UniversityTranslational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary Medicine, Hokkaido UniversityAbstract DNA methylation plays important functions in gene expression regulation that is involved in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in companion animals like dog. Using methylation-sensitive restriction enzyme-based next generation sequencing (Canine DREAM), we obtained canine DNA methylation maps of 16 somatic tissues from two dogs. In total, we evaluated 130,861 CpG sites. The majority of CpG sites were either highly methylated (> 70%, 52.5–64.6% of all CpG sites analyzed) or unmethylated (< 30%, 22.5–28.0% of all CpG sites analyzed) which are methylation patterns similar to other species. The overall methylation status of CpG sites across the 32 methylomes were remarkably similar. However, the tissue types were clearly defined by principle component analysis and hierarchical clustering analysis with DNA methylome. We found 6416 CpG sites located closely at promoter region of genes and inverse correlation between DNA methylation and gene expression of these genes. Our study provides basic dataset for DNA methylation profiles in dogs.https://doi.org/10.1038/s41598-021-89279-0 |
| spellingShingle | Jumpei Yamazaki Yuki Matsumoto Jaroslav Jelinek Teita Ishizaki Shingo Maeda Kei Watanabe Genki Ishihara Junya Yamagishi Mitsuyoshi Takiguchi DNA methylation landscape of 16 canine somatic tissues by methylation-sensitive restriction enzyme-based next generation sequencing Scientific Reports |
| title | DNA methylation landscape of 16 canine somatic tissues by methylation-sensitive restriction enzyme-based next generation sequencing |
| title_full | DNA methylation landscape of 16 canine somatic tissues by methylation-sensitive restriction enzyme-based next generation sequencing |
| title_fullStr | DNA methylation landscape of 16 canine somatic tissues by methylation-sensitive restriction enzyme-based next generation sequencing |
| title_full_unstemmed | DNA methylation landscape of 16 canine somatic tissues by methylation-sensitive restriction enzyme-based next generation sequencing |
| title_short | DNA methylation landscape of 16 canine somatic tissues by methylation-sensitive restriction enzyme-based next generation sequencing |
| title_sort | dna methylation landscape of 16 canine somatic tissues by methylation sensitive restriction enzyme based next generation sequencing |
| url | https://doi.org/10.1038/s41598-021-89279-0 |
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