Cheng Jie, Cao Xiukai, Wang Xiaogang, Wang Jian, Yue Binglin, Sun Wei, Huang Yongzhen, Lan Xianyong, Ren Gang, Lei Chuzhao, Chen Hong
College of Animal Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling district, Yangling, Shaanxi province, 712100, China.
Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
J Anim Sci Biotechnol. 2023 Apr 14;14(1):59. doi: 10.1186/s40104-023-00855-y.
Sharply increased beef consumption is propelling the genetic improvement projects of beef cattle in China. Three-dimensional genome structure is confirmed to be an important layer of transcription regulation. Although genome-wide interaction data of several livestock species have already been produced, the genome structure states and its regulatory rules in cattle muscle are still limited.
Here we present the first 3D genome data in Longissimus dorsi muscle of fetal and adult cattle (Bos taurus). We showed that compartments, topologically associating domains (TADs), and loop undergo re-organization and the structure dynamics were consistent with transcriptomic divergence during muscle development. Furthermore, we annotated cis-regulatory elements in cattle genome during myogenesis and demonstrated the enrichments of promoter and enhancer in selection sweeps. We further validated the regulatory function of one HMGA2 intronic enhancer near a strong sweep region on primary bovine myoblast proliferation.
Our data provide key insights of the regulatory function of high order chromatin structure and cattle myogenic biology, which will benefit the progress of genetic improvement of beef cattle.
牛肉消费量的急剧增加推动了中国肉牛的遗传改良项目。三维基因组结构被证实是转录调控的重要层面。尽管已经产生了几种家畜物种的全基因组相互作用数据，但牛肌肉中的基因组结构状态及其调控规则仍然有限。
在此，我们展示了胎儿和成年牛（Bos taurus）背最长肌中的首个三维基因组数据。我们表明，区室、拓扑相关结构域（TADs）和环发生了重组，并且结构动态与肌肉发育过程中的转录组差异一致。此外，我们注释了牛基因组在肌生成过程中的顺式调控元件，并证明了选择清除中启动子和增强子的富集。我们进一步验证了一个位于强选择清除区域附近的HMGA2内含子增强子对原代牛成肌细胞增殖的调控功能。
我们的数据提供了关于高阶染色质结构调控功能和牛肌生成生物学的关键见解，这将有利于肉牛遗传改良的进展。
