Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle
Abstract Background Skeletal muscles consist of fibers of differing contractility and metabolic properties, which are primarily determined by the content of myosin heavy chain (MYH) isoforms (MYH7, MYH2, MYH1, and MYH4). The regulation of Myh genes transcription depends on three-dimensional chromati...
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| Format: | Article |
| Language: | English |
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BMC
2022-07-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-022-08737-9 |
| _version_ | 1818474169747111936 |
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| author | Keren Long Duo Su Xiaokai Li Hengkuan Li Sha Zeng Yu Zhang Zhining Zhong Yu Lin Xuemin Li Lu Lu Long Jin Jideng Ma Qianzi Tang Mingzhou Li |
| author_facet | Keren Long Duo Su Xiaokai Li Hengkuan Li Sha Zeng Yu Zhang Zhining Zhong Yu Lin Xuemin Li Lu Lu Long Jin Jideng Ma Qianzi Tang Mingzhou Li |
| author_sort | Keren Long |
| collection | DOAJ |
| description | Abstract Background Skeletal muscles consist of fibers of differing contractility and metabolic properties, which are primarily determined by the content of myosin heavy chain (MYH) isoforms (MYH7, MYH2, MYH1, and MYH4). The regulation of Myh genes transcription depends on three-dimensional chromatin conformation interaction, but the mechanistic details remain to be determined. Results In this study, we characterized the interaction profiles of Myh genes using 4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing). The interaction profile of Myh genes changed between fast quadriceps and slow soleus muscles. Combining chromatin immunoprecipitation-sequencing (ChIP-seq) and transposase accessible chromatin with high-throughput sequencing (ATAC-seq), we found that a 38 kb intergenic region interacting simultaneously with fast Myh genes promoters controlled the coordinated expression of fast Myh genes. We also identified four active enhancers of Myh7, and revealed that binding of MYOG and MYOD increased the activity of Myh7 enhancers. Conclusions This study provides new insight into the chromatin interactions that regulate Myh genes expression. |
| first_indexed | 2024-04-14T04:33:24Z |
| format | Article |
| id | doaj.art-dcb30f9d54aa4a258fed783d6ba3da27 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-14T04:33:24Z |
| publishDate | 2022-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-dcb30f9d54aa4a258fed783d6ba3da272022-12-22T02:11:59ZengBMCBMC Genomics1471-21642022-07-0123111310.1186/s12864-022-08737-9Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscleKeren Long0Duo Su1Xiaokai Li2Hengkuan Li3Sha Zeng4Yu Zhang5Zhining Zhong6Yu Lin7Xuemin Li8Lu Lu9Long Jin10Jideng Ma11Qianzi Tang12Mingzhou Li13Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityInstitute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural UniversityAbstract Background Skeletal muscles consist of fibers of differing contractility and metabolic properties, which are primarily determined by the content of myosin heavy chain (MYH) isoforms (MYH7, MYH2, MYH1, and MYH4). The regulation of Myh genes transcription depends on three-dimensional chromatin conformation interaction, but the mechanistic details remain to be determined. Results In this study, we characterized the interaction profiles of Myh genes using 4C-seq (circular chromosome conformation capture coupled to high-throughput sequencing). The interaction profile of Myh genes changed between fast quadriceps and slow soleus muscles. Combining chromatin immunoprecipitation-sequencing (ChIP-seq) and transposase accessible chromatin with high-throughput sequencing (ATAC-seq), we found that a 38 kb intergenic region interacting simultaneously with fast Myh genes promoters controlled the coordinated expression of fast Myh genes. We also identified four active enhancers of Myh7, and revealed that binding of MYOG and MYOD increased the activity of Myh7 enhancers. Conclusions This study provides new insight into the chromatin interactions that regulate Myh genes expression.https://doi.org/10.1186/s12864-022-08737-9Myh genesChromatin interaction4C-seqEnhancer |
| spellingShingle | Keren Long Duo Su Xiaokai Li Hengkuan Li Sha Zeng Yu Zhang Zhining Zhong Yu Lin Xuemin Li Lu Lu Long Jin Jideng Ma Qianzi Tang Mingzhou Li Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle BMC Genomics Myh genes Chromatin interaction 4C-seq Enhancer |
| title | Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle |
| title_full | Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle |
| title_fullStr | Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle |
| title_full_unstemmed | Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle |
| title_short | Identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle |
| title_sort | identification of enhancers responsible for the coordinated expression of myosin heavy chain isoforms in skeletal muscle |
| topic | Myh genes Chromatin interaction 4C-seq Enhancer |
| url | https://doi.org/10.1186/s12864-022-08737-9 |
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