Zhang Aicen, Wei Yangyang, Shi Yining, Deng Xiaojuan, Gao Jingjing, Feng Yilong, Zheng Dongyang, Cheng Xuejiao, Li Zhaoguo, Wang Tao, Wang Kunbo, Liu Fang, Peng Renhai, Zhang Wenli
State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, Nanjing, China.
Biological and Food Engineering, Anyang Institute of Technology, Anyang, China.
Front Plant Sci. 2021 Dec 15;12:761059. doi: 10.3389/fpls.2021.761059. eCollection 2021.
Cotton is an excellent model for studying crop polyploidization and domestication. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenomes in allotetraploid cotton. However, the detailed profiling and functional characterization of broad H3K4me3 and H3K27me3 are still understudied in cotton. In this study, we conducted H3K4me3- and H3K27me3-related ChIP-seq followed by comprehensively characterizing their roles in regulating gene transcription in cotton. We found that H3K4me3 and H3K27me3 exhibited active and repressive roles in regulating the expression of genes between A and D subgenomes, respectively. More importantly, H3K4me3 exhibited enrichment level-, position-, and distance-related impacts on expression levels of related genes. Distinct GO term enrichment occurred between A/D-specific and homeologous genes with broad H3K4me3 enrichment in promoters and gene bodies, suggesting that broad H3K4me3-marked genes might have some unique biological functions between A and D subgenome. An anticorrelation between H3K27me3 enrichment and expression levels of homeologous genes was more pronounced in the A subgenome relative to the D subgenome, reflecting distinct enrichment of H3K27me3 in homeologous genes between A and D subgenome. In addition, H3K4me3 and H3K27me3 marks can indirectly influence gene expression through regulatory networks with TF mediation. Thus, our study provides detailed insights into functions of H3K4me3 and H3K27me3 in regulating differential gene expression and subfunctionalization of homeologous genes, therefore serving as a driving force for polyploidization and domestication in cotton.
棉花是研究作物多倍体化和驯化的优秀模式植物。染色质分析有助于揭示组蛋白修饰如何参与调控异源四倍体棉花A和D亚基因组之间的差异基因表达。然而，在棉花中，广泛的H3K4me3和H3K27me3的详细分析和功能表征仍未得到充分研究。在本研究中，我们进行了与H3K4me3和H3K27me3相关的染色质免疫沉淀测序（ChIP-seq），随后全面表征了它们在调控棉花基因转录中的作用。我们发现，H3K4me3和H3K27me3分别在调控A和D亚基因组之间基因的表达中发挥激活和抑制作用。更重要的是，H3K4me3对相关基因的表达水平表现出与富集水平、位置和距离相关的影响。在启动子和基因体中具有广泛H3K4me3富集的A/D特异性基因和同源基因之间出现了不同的基因本体（GO）术语富集，这表明具有广泛H3K4me3标记的基因在A和D亚基因组之间可能具有一些独特的生物学功能。相对于D亚基因组，H3K27me3富集与同源基因表达水平之间的负相关在A亚基因组中更为明显，这反映了A和D亚基因组之间同源基因中H3K27me3的不同富集情况。此外，H3K4me3和H3K27me3标记可通过转录因子（TF）介导的调控网络间接影响基因表达。因此，我们的研究为H3K4me3和H3K27me3在调控差异基因表达和同源基因亚功能化中的作用提供了详细的见解，从而成为棉花多倍体化和驯化的驱动力。
