基于ATAC-seq筛选调控肉牛肌肉发育的关键转录因子

doi:10.3864/j.issn.0578-1752.2026.16.015

摘要/Abstract

摘要：

【目的】牛作为反刍动物，肌肉生长发育周期长，但在牛背最长肌发育过程中，染色质可及性的调控机制尚未明确。通过探究安格斯牛和西门塔尔牛背最长肌中染色质可及性的差异，筛选影响牛肌肉生长的关键转录因子，进而构建TF-gene调控网络，为深入研究牛肌肉发育的表观遗传调控机制提供理论依据和新的分子靶点。【方法】采集饲养管理方式相同的24月龄安格斯牛和西门塔尔牛各3头的背最长肌组织，依据国家标准《食品中氨基酸的测定》（GB 5009.124-2016）进行氨基酸含量检测，利用SPSS 9.4软件通过t检验进行组间背最长肌氨基酸含量差异显著性分析；并将采集的背最长肌组织进行ATAC-seq测序，通过识别染色质开放区（peak），进行组间差异peak分析、GO/KEGG功能富集分析、转录因子结合位点（motif）富集分析；并结合前期的RNA-seq测序得到的差异表达基因（DEGs），基于GTRD数据库与基迪奥云平台构建转录因子-基因（TF-gene）调控网络。【结果】结果表明：（1）AGS组背最长肌中赖氨酸（Lys）、丝氨酸（Ser）、精氨酸（Arg）、组氨酸（His）、谷氨酸（Glu）含量显著高于XM组（P<0.05）；而脯氨酸（Pro）含量则相反（P<0.05），说明氨基酸代谢表型在两组间显著差异；（2）染色质可及性在两组间整体保守，共检测到安格斯牛29 140个peak，西门塔尔牛28 781个peak，两组间染色质开放区域主要分布在转录起始位点（TSS）±2 kb，且在内含子区、远端基因间区和启动子区占比超过84.57%。（3）在两组间鉴定出6 185个差异peak，其中5 030个上调，1 155个下调，将差异peak注释到相关基因后，进行GO/KEGG富集分析发现，差异peak相关基因主要富集在解剖结构形态发生、肌肉结构发育、肌动蛋白丝介导过程、Hippo信号通路、MAPK信号通路、钙信号通路、肌动蛋白细胞骨架调控等经典肌肉发育相关通路。（4）Motif富集分析显示，在显著富集的前20个转录因子结合基序中，排名前4位均属于MEF2转录家族，分别是MEF2C、MEF2A、MEF2D与MEF2B；进一步聚焦AGS特异性peak和前期RNA-seq测序得到的差异表达基因交集分析，发现MEF2B与MEF2D结合位点富集程度最高，成功构建以MEF2B与MEF2D为核心转录因子的TF-gene调控网络，共筛选到ACTA1、CKM、CLCN1、SLN、MYOZ3等13个参与肌肉发育调控的靶基因；并利用IGV可视化证实上述靶基因启动子区存在MEF2B和MEF2D结合基序，并与ATAC-seq开放区域高度重合。【结论】本研究通过ATAC-seq和RNA-seq数据联合分析，揭示了安格斯牛和西门塔尔牛在背最长肌发育过程中的染色质可及性差异，并筛选到MEF2B和MEF2D作为调控牛肌肉生长的关键转录因子（TFs），构建以MEF2B与MEF2D为核心转录因子的TF-gene调控网络，为深入解析肉牛肌肉发育表观遗传机制及CRISPR-Cas9功能验证提供了理论基础。

关键词: 染色质可及性, 肌肉发育, 背最长肌, 氨基酸, ATAC-seq

Abstract:

【Objective】 As a ruminant animal, cattle has a long muscle growth and development cycle. However, the regulatory mechanism of chromatin accessibility on bovine longissimus dorsi is not clear during the development of longissimus dorsi. This study aimed to explore the differential chromatin accessibility of the longissimus dorsi muscle of Angus cattle and Simmental cattle, screen the key transcription factors affecting bovine muscle growth, and then construct the TF-gene regulatory network, so as to provides the theoretical basis and new molecular target for further study of the epigenetic regulation mechanism of bovine muscle development.【Method】 The longissimus dorsi muscle tissues of 24-month-old Angus cattle (AGS) and Simmental cattle (XM) with the same feeding and management methods were collected, and the amino acid content was detected according to the national standard Determination of amino acids in food (GB 5009.124-2016). SPSS 9.4 software was used to analyze the significant difference of amino acid content in longissimus dorsi muscle between groups by t test. The collected longissimus dorsi muscle tissue was subjected to ATAC-seq sequencing. By identifying the chromatin open area (peak), peak analysis, GO/KEGG functional enrichment analysis, and transcription factor binding site (motif) enrichment analysis were performed. Combined with the differentially expressed genes (DEGs) obtained from the previous RNA-seq sequencing, a transcription factor-gene (TF-gene) regulatory network was constructed based on the GTRD database and the OmicShare Tools.【Result】 The results showed as follows：(1) The content of lysine (Lys), serine (Ser), arginine (Arg), histidine (His) and glutamic acid (Glu) in longissimus dorsi muscle of AGS group were significantly higher than those of XM group (P < 0.05); the content of proline (Pro) was the opposite (P < 0.05), indicating that the amino acid metabolic phenotype was significantly different between the two groups. (2) Chromatin accessibility was generally conserved between the two groups. A total of 29 140 peaks were detected in Angus cattle and 28 781 peaks were detected in Simmental cattle. The chromatin open regions between the two groups were mainly distributed at the transcription start site (TSS) ± 2 kb, and accounted for more than 84.57 % in the intron region, distal intergenic region and promoter region. (3) A total of 6 185 differential peaks were identified between the two groups, of which 5 030 peaks were up-regulated and 1155 were down-regulated. After the differential peak were annotated to related genes, GO/KEGG enrichment analysis showed that the differential peak-related genes were mainly enriched in classical muscle development-related pathways, such as anatomical morphogenesis, muscle structure development, actin filament-mediated, Hippo signaling pathway, MAPK signaling pathway, calcium signaling pathway, and actin cytoskeleton regulation. (4) Motif enrichment analysis showed that among the top 20 transcription factor binding motifs, the top four belonged to the MEF2 transcription family, which were MEF2C, MEF2A, MEF2D, and MEF2B, respectively. Further focusing on the intersection analysis of AGS-specific peak and differentially expressed genes obtained by previous RNA-seq sequencing, it was found that the binding sites of MEF2B and MEF2D were the most enriched, and the TF-gene regulatory network with MEF2B and MEF2D as the core transcription factors was successfully constructed. A total of 13 target genes involved in muscle development regulation were screened, including ACTA1, CKM, CLCN1, SLN, and MYOZ3. IGV visualization confirmed the presence of MEF2B and MEF2D binding motifs in the promoter region of the above target genes, and highly overlapped with the open region of ATAC-seq.【Conclusion】 In this study, the combined analysis of ATAC-seq and RNA-seq data revealed the differences in chromatin accessibility between Angus cattle and Simmental cattle during the development of longissimus dorsi muscle, and screened MEF2B and MEF2D as key transcription factors (TFs) regulating bovine muscle growth. The TF-gene regulatory network with MEF2B and MEF2D as core transcription factors was constructed, which provided a theoretical basis for further analysis of the epigenetic mechanism of muscle development in beef cattle and functional verification of CRISPR-Cas9.

Key words: chromatin accessibility, muscle development, longissimus dorsi, amino acids, ATAC-seq

楚洪恩, 刘源, 白雪, 杨梦丽, 刘涛, 李芬, 李兰兰, 马云. 基于ATAC-seq筛选调控肉牛肌肉发育的关键转录因子[J]. 中国农业科学, 2026, 59(16): 3687-3698.

CHU HongEn, LIU Yuan, BAI Xue, YANG MengLi, LIU Tao, LI Fen, LI LanLan, MA Yun. The Key Transcription Factors Regulating Beef Cattle Muscle Development Screened by ATAC-seq[J]. Scientia Agricultura Sinica, 2026, 59(16): 3687-3698.

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必需氨基酸 EAA(μg·g^-1 FW)	安格斯牛 AGS	西门塔尔牛 XM	非必需氨基酸 NEAA(μg·g^-1 FW)	安格斯牛 AGS	西门塔尔牛 XM
甲硫氨酸Met	10.89±1.85	9.49±0.22	甘氨酸Gly	77.44±2.88	70.17±7.14
赖氨酸Lys	68.80±13.04a	28.12±6.85b	丙氨酸Ala	258.28±26.76	281.53±24.40
苯丙氨酸Phe	19.67±4.45	17.53±1.42	丝氨酸Ser	127.76±3.62a	95.19±8.68b
色氨酸Trp	9.24±0.76	6.18±1.29	脯氨酸Pro	38.03±1.44b	46.59±1.83a
缬氨酸Val	35.45±6.92	30.50±6.58	酪氨酸Tyr	25.64±3.68	22.47±4.76
苏氨酸Thr	37.63±4.74	27.88±0.31	精氨酸Arg	82.59±2.36a	38.97±2.27b
亮氨酸Leu	42.08±6.55	36.40±0.35	组氨酸His	102.6±2.29a	46.05±7.47b
异亮氨酸Ile	28.54±4.29	24.24±2.72	天冬氨酸Asp	7.24±1.1	5.85±0.91
异亮氨酸Ile	28.54±4.29	24.24±2.72	谷氨酸Glu	94.63±3.33a	34.67±3.46b

样品 Sample	下机数据碱基总数 Clean date (bp)	过滤后有效碱基总数 HQ clean date (bp)	唯一比对的reads数目 Unique mapped reads	唯一比对的reads比例 Unique mapped rate (%)
AGS-1	14541584400	10980107923	65580095	67.92
AGS-2	14919508800	11321472992	66649331	67.33
AGS-3	16304789400	12394515837	74550934	68.88
XM-1	17579211000	13510839920	80089254	68.68
XM-2	14105058600	11076552540	63286080	67.66
XM-3	15497562000	11696995991	68232416	66.33

序号 Rank	转录因子 TF	E值 E-value	序号 Rank	转录因子 TF	E值 E-value
1	MEF2C	3.10e-37	11	NR2F2	1.32e-4
2	MEF2A	7.04e-35	12	Nr1H2	1.34e-4
3	MEF2D	7.48e-19	13	SIX1	1.60e-4
4	MEF2B	2.19e-17	14	TBP	1.73e-4
5	NR4A1	3.80e-16	15	CDX1	1.86e-4
6	NR4A2	9.85e-16	16	PBX2	2.28e-4
7	SIX2	3.64e-11	17	HOXD12	2.74e-4
8	MEIS2	3.70E-6	18	NFIX	4.56e-4
9	Hmga1	4.75e-6	19	Ppara	2.41e-6
10	Nr1h3	5.35e-6	20	FOXL1	7.47e-4