鸡骨骼肌发育过程中的三维基因组变化

doi:10.1016/j.jia.2024.03.052

Journal of Integrative Agriculture ›› 2026, Vol. 25 ›› Issue (1): 207-226.DOI: 10.1016/j.jia.2024.03.052

鸡骨骼肌发育过程中的三维基因组变化

收稿日期:2023-10-08 修回日期:2024-03-16 接受日期:2024-02-01 出版日期:2026-01-20 发布日期:2025-12-09

3D genomic alterations during development of skeletal muscle in chicken

Zhongxian Xu^{1, 2, 3*}, Tao Wang^{2, 3*}, Wei Zhu^2*, Maosen Yang², Dong Leng², Ziyu Li², Jiaman Zhang², Pengliang Liu², Zhoulin Wu⁴, Mengnan He⁵, Yan Li⁵, Hua Kui², Xue Bai², Bo Zeng², Yao Zhang², Qing Zhu², Xiaoling Zhao², Mingzhou Li^2#, Diyan Li^{2, 3#}

¹Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China
²Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
³Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610106, China
⁴Key Laboratory of Meat Processing of Sichuan, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
⁵Chengdu Research Base of Giant Panda Breeding, Chengdu 611081, China

Received:2023-10-08 Revised:2024-03-16 Accepted:2024-02-01 Online:2026-01-20 Published:2025-12-09
About author:Zhongxian Xu, E-mail: xu_zhongxian@cwnu.edu.cn; Tao Wang, E-mail: wanttao@hotmail.com; Wei Zhu, E-mail: 1424518023@qq.com; #Correspondence Diyan Li, E-mail: lidiyan@cdu.edu.cn; Mingzhou Li, E-mail: mingzhou.li@sicau.edu.cn * These authors contributed equally to this study.
Supported by:
This work was supported by the National Key R & D Program of China (2023YFD1300040 and 2022YFF1000100), the Sichuan Science and Technology Program, China (2022NSFSC0132, 2021YFYZ0009 and 2022JDJQ0054), the National Natural Science Foundation of China (32225046).

摘要/Abstract

摘要：

骨骼肌发育过程中包含了维持肌肉形态、收缩力、细胞增殖、分化、相互作用、迁移和死亡的基因。尽管肌细胞分化过程中的动态转录调控是研究最深入热点之一，但骨骼肌发育的三维染色质结构尚未得到深入研究。本文利用RNA-seq解析了鸡肌肉12个发育时间点的基因转录表达模式；并选择4个代表性时间点用Hi-C构建了骨骼肌发育中染色质三维构象，从染色质的3种不同层级结构（染色质区室、拓扑关联结构域、染色质环）探讨了染色质拓扑结构与基因表达调控之间的关系；还利用ChIP-seq定位了组蛋白H3K27ac和H3K4me3修饰的增强子和启动子位点。结果表明大部分基因组结构变化是单向的，并与复杂的基因表达开/关相耦合：在鸡骨骼肌发育过程中，有258.30 Mb在区室层面发生变化，大量与衰老相关的基因所在区室从抑制状态向活跃状态转变；316.57 Mb的TAD内部互作强度随着法与显著变化；一些肌肉相关基因的启动子在发育过程中与活性增强子互作，受活性增强子调控的基因数目随着发育逐渐降低，部分与肌肉疾病和衰老相关的基因在老年阶段被激活。研究结果可望从三维基因组视角解析几骨骼肌发育的分析机制，为分子遗传育种的实现提供理论指导，并将为日后筛选和鉴定农业动物重要数量性状的调控元件开辟新思路。

Abstract:

The development of skeletal muscle are complicated processes involving genes responsible for proper muscle morphology, contractility, cell proliferation, differentiation, interactions, migration, and death. The three-dimensional chromatin architecture of skeletal muscle development has not been studied intensively although dynamic transcriptional regulation during differentiation of muscle cells is one of the most deeply studied processes. The RNA-seq was used to analyze the transcriptome pattern during chicken muscle development across 12 stages. Hi-C was used to build chromatin architectures during four representative stages. ChIP-seq was conducted to identify enhancers and promoters in these four stages, which are occupied by histone H3K27ac and H3K4me3 peaks. Results show that large-scale genome architecture changes are mostly unidirectional, and coupled by complex on/off dynamic patterns of gene expression. Specifically, we observed 258.30 Mb of the genome undergoing A/B compartment switching. Notable alterations (316.57 Mb) of interaction frequencies within TADs were observed. Substantial aging-associated genes exhibited ascending connectivity with the compartment transition from repressive to active status during muscle development. Some muscle-related gene promoters that interacted with active enhancers during development, and some myopathy/aging-associated genes that were activated in aging muscle were founded. These results provide key insights into skeletal muscle development in vivo, and offer a valuable resource that allows in-depth functional characterization of candidate genes.

Key words: skeletal muscle , development , gene expression , chromatin architecture

Zhongxian Xu, Tao Wang, Wei Zhu, Maosen Yang, Dong Leng, Ziyu Li, Jiaman Zhang, Pengliang Liu, Zhoulin Wu, Mengnan He, Yan Li, Hua Kui, Xue Bai, Bo Zeng, Yao Zhang, Qing Zhu, Xiaoling Zhao, Mingzhou Li, Diyan Li. 鸡骨骼肌发育过程中的三维基因组变化[J]. Journal of Integrative Agriculture, 2026, 25(1): 207-226.

Zhongxian Xu, Tao Wang, Wei Zhu, Maosen Yang, Dong Leng, Ziyu Li, Jiaman Zhang, Pengliang Liu, Zhoulin Wu, Mengnan He, Yan Li, Hua Kui, Xue Bai, Bo Zeng, Yao Zhang, Qing Zhu, Xiaoling Zhao, Mingzhou Li, Diyan Li. 3D genomic alterations during development of skeletal muscle in chicken[J]. Journal of Integrative Agriculture, 2026, 25(1): 207-226.

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鸡骨骼肌发育过程中的三维基因组变化

3D genomic alterations during development of skeletal muscle in chicken

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