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Dissecting chromatin accessibility profiles of anatomically distinct skeletal muscles and different breeds in pigs at single-nucleus resolution

Yiwu Chen 1*, Yundi Zheng 1*, Ziyu Chen 1*, Geng Zhang 1, Chuang Tang 1, Fuwen Wang 1,2, Can Liu 1, Mingzhou Li 1#, Long Jin 1#

1 State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 625041, China

Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.

 Highlight 

1. Constructed the chromatin accessibility landscape of pig skeletal muscle at a single nucleus resolution;

2. Dissected regulatory divergences between oxidative and glycolytic myofibers, identifying DARs and TF networks;

3. Revealed breed-specific DARs in myofibers and displayed the dynamic chromatin remodeling during myogenesis.

1. Constructed the chromatin accessibility landscape of pig skeletal muscle at a single nucleus resolution;

2. Dissected regulatory divergences between oxidative and glycolytic myofibers, identifying DARs and TF networks;

3. Revealed breed-specific DARs in myofibers and displayed the dynamic chromatin remodeling during myogenesis. -->

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摘要  

为了在单细胞核分辨率下解析猪骨骼肌的染色质可及性谱,我们对大白猪的背最长肌和腰大肌进行了单细胞核ATAC测序。数据质控后,26,225个细胞核基于snRNA-seq的转移注释被鉴定为七种主要细胞类型,包括肌纤维、肌肉干细胞和免疫细胞等。我们共鉴定到158,438个可及染色质区域,其中细胞类型特异的差异可及区域(DAR)参与细胞特异性功能调控。不同肌核亚型(I型、IIA型、IIB型)之间表现出不同的染色质可及性模式,例如我们在快速肌纤维(II 型)富集到SIX1和MAF转录因子结合基序。不同部位骨骼肌之间的差异分析表明,腰大肌含有更多的I型肌纤维是导致部位间染色质差异的主要原因。不同品种猪(大白猪 vs. 荣昌猪)的肌核中鉴定到的品种特异性DAR提示了MEF2可能介导肌纤维肥大的调控。拟时序分析展示成肌调控中的关键成肌基因(例如MYF5MYH1)的染色质可及性动态变化。这项研究揭示了猪肌纤维特化、组织异质性及品种特异性肌肉发育在细胞类型分辨下的染色质景观。



Abstract  

To dissect chromatin accessibility profiles in pig skeletal muscle at single-nucleus resolution, we performed single-nucleus ATAC-seq on longissimus dorsi and psoas major muscles of Large White pigs. After quality control, 26,225 nuclei were classified into seven major cell types, including myofibers, muscle stem cells, and immune cells, using snRNA-seq-based label transfer. We identified 158,438 accessible chromatin regions, with cell-type-specific differentially accessible regions (DAR) enriching for specific functions. Myonuclei subtypes (type I, IIA, IIB) showed distinct accessibility patterns, with SIX1 and MAF transcription factor motifs enriched in fast myofibers (type II). Comparative analysis between muscles revealed that myofiber composition drove chromatin differences, with psoas major featuring more type I myofibers. Cross-breed analysis (Rongchang vs. Large White) identified breed-specific DARs in myonuclei, linking MEF2-mediated regulation to myofiber hypertrophy. Pseudo-temporal analysis of myogenesis showed dynamic accessibility changes in key myogenic genes (e.g., MYF5, MYH1). This study unveils cell-type-resolved chromatin landscapes underlying myofiber specification, tissue heterogeneity, and breed-specific muscle development in pigs.

 

Keywords:  pig              pig skeletal muscle              cell heterogeneity              transcriptional regulation              epigenomic regulation  
Online: 13 November 2025  
Fund: 

This work was supported by the National Natural Science Foundation of China (32341050, 32272837, 32494802, 32421005 and 32225046), the National Key R & D Program of China (2021YFA0805903 and 2020YFA0509500 ), the Tackling Project for Agricultural Key Core Technologies of China (NK2022110602), the Sichuan Science and Technology Program (2021ZDZX0008 and 2021YFYZ0009), the Program for Pig Industry Technology System Innovation Team of Sichuan Province (sccxtd-2025-08).

About author:  Yiwu Chen, E-mail: chenywww@outlook.com; Yundi Zheng, E-mail: guanyi53473@163.com; Ziyu Chen , E-mail: chenziyu@stu.sicau.edu.cn; #Correspondence E-mail: mingzhou.li@sicau.edu.cn; longjin@sicau.edu.cn * These authors contributed equally to this work.

Cite this article: 

Yiwu Chen, Yundi Zheng, Ziyu Chen, Geng Zhang, Chuang Tang, Fuwen Wang, Can Liu, Mingzhou Li, Long Jin. 2025. Dissecting chromatin accessibility profiles of anatomically distinct skeletal muscles and different breeds in pigs at single-nucleus resolution. Journal of Integrative Agriculture, Doi:10.1016/j.jia.2025.11.016

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