The Landscape of Accessible Chromatin during Yak Adipocyte Differentiation
Although significant advancement has been made in the study of adipogenesis, knowledge about how chromatin accessibility regulates yak adipogenesis is lacking. We here described genome-wide dynamic chromatin accessibility in preadipocytes and adipocytes by using the assay for transposase-accessible...
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MDPI AG
2022-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/17/9960 |
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| author | Zhilong Zhang Yongfeng Zhang Qi Bao Yarong Gu Chunnian Liang Min Chu Xian Guo Pengjia Bao Ping Yan |
| author_facet | Zhilong Zhang Yongfeng Zhang Qi Bao Yarong Gu Chunnian Liang Min Chu Xian Guo Pengjia Bao Ping Yan |
| author_sort | Zhilong Zhang |
| collection | DOAJ |
| description | Although significant advancement has been made in the study of adipogenesis, knowledge about how chromatin accessibility regulates yak adipogenesis is lacking. We here described genome-wide dynamic chromatin accessibility in preadipocytes and adipocytes by using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and thus revealed the unique characteristics of open chromatin during yak adipocyte differentiation. The chromatin accessibility of preadipocytes and adipocytes exhibited a similar genomic distribution, displaying a preferential location within the intergenic region, intron, and promoter. The pathway enrichment analysis identified that genes with differential chromatin accessibility were involved in adipogenic metabolism regulation pathways, such as the peroxisome proliferator activated receptor-γ (PPAR) signaling pathway, wingless-type MMTV integration site (Wnt) signaling pathway, and extracellular matrix-receptor (ECM–receptor) interaction. Integration of ATAC-seq and mRNA-seq revealed that genes with a high expression were associated with high levels of chromatin accessibility, especially within 1 kb upstream and downstream of the transcription start site. In addition, we identified a series of transcription factors (TFs) related to adipogenesis and created the TF regulatory network, providing the possible interactions between TFs during yak adipogenesis. This study is crucial for advancing the understanding of transcriptional regulatory mechanisms of adipogenesis and provides valuable information for understanding the adaptation of plateau species to high-altitude environments by maintaining whole body homeostasis through fat metabolism. |
| first_indexed | 2024-03-10T01:43:17Z |
| format | Article |
| id | doaj.art-6649957b20174ff8b6e9737ff2adfc93 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T01:43:17Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-6649957b20174ff8b6e9737ff2adfc932023-11-23T13:20:48ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-09-012317996010.3390/ijms23179960The Landscape of Accessible Chromatin during Yak Adipocyte DifferentiationZhilong Zhang0Yongfeng Zhang1Qi Bao2Yarong Gu3Chunnian Liang4Min Chu5Xian Guo6Pengjia Bao7Ping Yan8College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, ChinaKey Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaKey Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, ChinaCollege of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, ChinaAlthough significant advancement has been made in the study of adipogenesis, knowledge about how chromatin accessibility regulates yak adipogenesis is lacking. We here described genome-wide dynamic chromatin accessibility in preadipocytes and adipocytes by using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and thus revealed the unique characteristics of open chromatin during yak adipocyte differentiation. The chromatin accessibility of preadipocytes and adipocytes exhibited a similar genomic distribution, displaying a preferential location within the intergenic region, intron, and promoter. The pathway enrichment analysis identified that genes with differential chromatin accessibility were involved in adipogenic metabolism regulation pathways, such as the peroxisome proliferator activated receptor-γ (PPAR) signaling pathway, wingless-type MMTV integration site (Wnt) signaling pathway, and extracellular matrix-receptor (ECM–receptor) interaction. Integration of ATAC-seq and mRNA-seq revealed that genes with a high expression were associated with high levels of chromatin accessibility, especially within 1 kb upstream and downstream of the transcription start site. In addition, we identified a series of transcription factors (TFs) related to adipogenesis and created the TF regulatory network, providing the possible interactions between TFs during yak adipogenesis. This study is crucial for advancing the understanding of transcriptional regulatory mechanisms of adipogenesis and provides valuable information for understanding the adaptation of plateau species to high-altitude environments by maintaining whole body homeostasis through fat metabolism.https://www.mdpi.com/1422-0067/23/17/9960ATAC-seqchromatin accessibilityadipogenesisyak |
| spellingShingle | Zhilong Zhang Yongfeng Zhang Qi Bao Yarong Gu Chunnian Liang Min Chu Xian Guo Pengjia Bao Ping Yan The Landscape of Accessible Chromatin during Yak Adipocyte Differentiation International Journal of Molecular Sciences ATAC-seq chromatin accessibility adipogenesis yak |
| title | The Landscape of Accessible Chromatin during Yak Adipocyte Differentiation |
| title_full | The Landscape of Accessible Chromatin during Yak Adipocyte Differentiation |
| title_fullStr | The Landscape of Accessible Chromatin during Yak Adipocyte Differentiation |
| title_full_unstemmed | The Landscape of Accessible Chromatin during Yak Adipocyte Differentiation |
| title_short | The Landscape of Accessible Chromatin during Yak Adipocyte Differentiation |
| title_sort | landscape of accessible chromatin during yak adipocyte differentiation |
| topic | ATAC-seq chromatin accessibility adipogenesis yak |
| url | https://www.mdpi.com/1422-0067/23/17/9960 |
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