Zhou Zhimin, Zhu Yaling, Zhang Zhen, Jiang Tao, Ling Ziqi, Yang Bin, Li Wanbo
State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
Laboratory Animal Research Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, China.
Front Genet. 2021 Jul 23;12:697994. doi: 10.3389/fgene.2021.697994. eCollection 2021.
The epigenetic regulation of gene expression is implicated in complex diseases in humans and various phenotypes in other species. There has been little exploration of regulatory elements in the pig. Here, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to profile histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 27 acetylation (H3K27ac) in the pituitary gland of adult Bama Xiang and Large White pigs, which have divergent evolutionary histories and large phenotypic differences. We identified a total of 65,044 non-redundant regulatory regions, including 23,680 H3K4me3 peaks and 61,791 H3K27ac peaks (12,318 proximal and 49,473 distal), augmenting the catalog of pituitary regulatory elements in pigs. We found 793 H3K4me3 and 3,602 H3K27ac peaks that show differential activity between the two breeds, overlapping with genes involved in the Notch signaling pathway, response to growth hormone (GH), thyroid hormone signaling pathway, and immune system, and enriched for binding motifs of transcription factors (TFs), including JunB, ATF3, FRA1, and BATF. We further identified 2,025 non-redundant super enhancers from H3K27ac ChIP-seq data, among which 302 were shared in all samples of cover genes enriched for biological processes related to pituitary function. This study generated a valuable dataset of H3K4me3 and H3K27ac regions in porcine pituitary glands and revealed H3K4me3 and H3K27ac peaks with differential activity between Bama Xiang and Large White pigs.
基因表达的表观遗传调控与人类复杂疾病以及其他物种的各种表型有关。猪体内调控元件的研究较少。在此，我们进行了染色质免疫沉淀结合高通量测序（ChIP-Seq），以分析成年巴马香猪和大白猪垂体中组蛋白H3赖氨酸4三甲基化（H3K4me3）和组蛋白H3赖氨酸27乙酰化（H3K27ac）情况，这两个品种具有不同的进化历史和较大的表型差异。我们共鉴定出65,044个非冗余调控区域，包括23,680个H3K4me3峰和61,791个H3K27ac峰（12,318个近端峰和49,473个远端峰），扩充了猪垂体调控元件的目录。我们发现793个H3K4me3峰和3,602个H3K27ac峰在两个品种间表现出差异活性，这些峰与参与Notch信号通路、对生长激素（GH）的反应、甲状腺激素信号通路和免疫系统的基因重叠，并富含转录因子（TFs）的结合基序，包括JunB、ATF3、FRA1和BATF。我们进一步从H3K27ac ChIP-seq数据中鉴定出2,025个非冗余超级增强子，其中302个在所有覆盖与垂体功能相关生物过程的基因样本中共享。本研究生成了一份有价值的猪垂体中H3K4me3和H3K27ac区域数据集，并揭示了巴马香猪和大白猪之间具有差异活性的H3K4me3和H3K27ac峰。
