Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler
Skeletal muscle development and intramuscular fat (IMF) content, which positively contribute to meat production and quality, are regulated by precisely orchestrated processes. However, changes in three-dimensional chromatin structure and interaction, a newly emerged mediator of gene expression, duri...
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Frontiers Media S.A.
2021
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oai:doaj.org-article:b9fba340be7d472286b9a09d95e213b02021-12-01T13:38:54ZChromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler2296-634X10.3389/fcell.2021.782268https://doaj.org/article/b9fba340be7d472286b9a09d95e213b02021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fcell.2021.782268/fullhttps://doaj.org/toc/2296-634XSkeletal muscle development and intramuscular fat (IMF) content, which positively contribute to meat production and quality, are regulated by precisely orchestrated processes. However, changes in three-dimensional chromatin structure and interaction, a newly emerged mediator of gene expression, during the skeletal muscle development and IMF deposition have remained unclear. In the present study, we analyzed the differences in muscle development and IMF content between one-day-old commercial Arbor Acres broiler (AA) and Chinese indigenous Lushi blue-shelled-egg chicken (LS) and performed Hi-C analysis on their breast muscles. Our results indicated that significantly higher IMF content, however remarkably lower muscle fiber diameter was detected in breast muscle of LS chicken compared to that of AA broiler. The chromatin intra-interaction was prior to inter-interaction in both AA and LS chicken, and chromatin inter-interaction was heavily focused on the small and gene-rich chromosomes. For genomic compartmentalization, no significant difference in the number of B type compartments was found, but AA had more A type compartments versus LS. The A/B compartment switching of AA versus LS showed more A to B switching than B to A switching. There were no significant differences in the average sizes and distributions of topologically associating domains (TAD). Additionally, approximately 50% of TAD boundaries were overlapping. The reforming and disappearing events of TAD boundaries were identified between AA and LS chicken breast muscles. Among these, the HMGCR gene was located in the TAD-boundary regions in AA broilers, but in TAD-interior regions in LS chickens, and the IGF2BP3 gene was located in the AA-unique TAD boundaries. Both HMGCR and IGF2BP3 genes exhibited increased mRNA expression in one-day-old AA broiler breast muscles. It was demonstrated that the IGF2BP3 and HMGCR genes regulated by TAD boundary sliding were potential biomarkers for chicken breast muscle development and IMF deposition. Our data not only provide a valuable understanding of higher-order chromatin dynamics during muscle development and lipid accumulation but also reveal new insights into the regulatory mechanisms of muscle development and IMF deposition in chicken.Weihua TianZhang WangDandan WangYihao ZhiJiajia DongRuirui JiangRuirui JiangRuirui JiangRuili HanRuili HanRuili HanZhuanjian LiZhuanjian LiZhuanjian LiXiangtao KangXiangtao KangXiangtao KangHong LiHong LiHong LiXiaojun LiuXiaojun LiuXiaojun LiuFrontiers Media S.A.articleHi-CA/B compartmentTADmuscle developmentIMF depositionchickenBiology (General)QH301-705.5ENFrontiers in Cell and Developmental Biology, Vol 9 (2021) |
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Hi-C A/B compartment TAD muscle development IMF deposition chicken Biology (General) QH301-705.5 |
| spellingShingle |
Hi-C A/B compartment TAD muscle development IMF deposition chicken Biology (General) QH301-705.5 Weihua Tian Zhang Wang Dandan Wang Yihao Zhi Jiajia Dong Ruirui Jiang Ruirui Jiang Ruirui Jiang Ruili Han Ruili Han Ruili Han Zhuanjian Li Zhuanjian Li Zhuanjian Li Xiangtao Kang Xiangtao Kang Xiangtao Kang Hong Li Hong Li Hong Li Xiaojun Liu Xiaojun Liu Xiaojun Liu Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler |
| description |
Skeletal muscle development and intramuscular fat (IMF) content, which positively contribute to meat production and quality, are regulated by precisely orchestrated processes. However, changes in three-dimensional chromatin structure and interaction, a newly emerged mediator of gene expression, during the skeletal muscle development and IMF deposition have remained unclear. In the present study, we analyzed the differences in muscle development and IMF content between one-day-old commercial Arbor Acres broiler (AA) and Chinese indigenous Lushi blue-shelled-egg chicken (LS) and performed Hi-C analysis on their breast muscles. Our results indicated that significantly higher IMF content, however remarkably lower muscle fiber diameter was detected in breast muscle of LS chicken compared to that of AA broiler. The chromatin intra-interaction was prior to inter-interaction in both AA and LS chicken, and chromatin inter-interaction was heavily focused on the small and gene-rich chromosomes. For genomic compartmentalization, no significant difference in the number of B type compartments was found, but AA had more A type compartments versus LS. The A/B compartment switching of AA versus LS showed more A to B switching than B to A switching. There were no significant differences in the average sizes and distributions of topologically associating domains (TAD). Additionally, approximately 50% of TAD boundaries were overlapping. The reforming and disappearing events of TAD boundaries were identified between AA and LS chicken breast muscles. Among these, the HMGCR gene was located in the TAD-boundary regions in AA broilers, but in TAD-interior regions in LS chickens, and the IGF2BP3 gene was located in the AA-unique TAD boundaries. Both HMGCR and IGF2BP3 genes exhibited increased mRNA expression in one-day-old AA broiler breast muscles. It was demonstrated that the IGF2BP3 and HMGCR genes regulated by TAD boundary sliding were potential biomarkers for chicken breast muscle development and IMF deposition. Our data not only provide a valuable understanding of higher-order chromatin dynamics during muscle development and lipid accumulation but also reveal new insights into the regulatory mechanisms of muscle development and IMF deposition in chicken. |
| format |
article |
| author |
Weihua Tian Zhang Wang Dandan Wang Yihao Zhi Jiajia Dong Ruirui Jiang Ruirui Jiang Ruirui Jiang Ruili Han Ruili Han Ruili Han Zhuanjian Li Zhuanjian Li Zhuanjian Li Xiangtao Kang Xiangtao Kang Xiangtao Kang Hong Li Hong Li Hong Li Xiaojun Liu Xiaojun Liu Xiaojun Liu |
| author_facet |
Weihua Tian Zhang Wang Dandan Wang Yihao Zhi Jiajia Dong Ruirui Jiang Ruirui Jiang Ruirui Jiang Ruili Han Ruili Han Ruili Han Zhuanjian Li Zhuanjian Li Zhuanjian Li Xiangtao Kang Xiangtao Kang Xiangtao Kang Hong Li Hong Li Hong Li Xiaojun Liu Xiaojun Liu Xiaojun Liu |
| author_sort |
Weihua Tian |
| title |
Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler |
| title_short |
Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler |
| title_full |
Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler |
| title_fullStr |
Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler |
| title_full_unstemmed |
Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler |
| title_sort |
chromatin interaction responds to breast muscle development and intramuscular fat deposition between chinese indigenous chicken and fast-growing broiler |
| publisher |
Frontiers Media S.A. |
| publishDate |
2021 |
| url |
https://doaj.org/article/b9fba340be7d472286b9a09d95e213b0 |
| work_keys_str_mv |
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