National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, Jiujiang, 332900, Jiangxi, China.
BMC Biol. 2023 Oct 31;21(1):241. doi: 10.1186/s12915-023-01735-7.
Epigenetic modifications that exhibit circadian oscillations also promote circadian oscillations of gene expression. Brassica napus is a heterozygous polyploid species that has undergone distant hybridization and genome doubling events and has a young and distinct species origin. Studies incorporating circadian rhythm analysis of epigenetic modifications can offer new insights into differences in diurnal oscillation behavior among subgenomes and the regulation of diverse expressions of homologous gene rhythms in biological clocks.
In this study, we created a high-resolution and multioscillatory gene expression dataset, active histone modification (H3K4me3, H3K9ac), and RNAPII recruitment in Brassica napus. We also conducted the pioneering characterization of the diurnal rhythm of transcription and epigenetic modifications in an allopolyploid species. We compared the evolution of diurnal rhythms between subgenomes and observed that the Cn subgenome had higher diurnal oscillation activity in both transcription and active histone modifications than the An subgenome. Compared to the A subgenome in Brassica rapa, the An subgenome of Brassica napus displayed significant changes in diurnal oscillation characteristics of transcription. Homologous gene pairs exhibited a higher proportion of diurnal oscillation in transcription than subgenome-specific genes, attributed to higher chromatin accessibility and abundance of active epigenetic modification types. We found that the diurnal expression of homologous genes displayed diversity, and the redundancy of the circadian system resulted in extensive changes in the diurnal rhythm characteristics of clock genes after distant hybridization and genome duplication events. Epigenetic modifications influenced the differences in the diurnal rhythm of homologous gene expression, and the diurnal oscillation of homologous gene expression was affected by the combination of multiple histone modifications.
Herein, we presented, for the first time, a characterization of the diurnal rhythm characteristics of gene expression and its epigenetic modifications in an allopolyploid species. Our discoveries shed light on the epigenetic factors responsible for the diurnal oscillation activity imbalance between subgenomes and homologous genes' rhythmic expression differences. The comprehensive time-series dataset we generated for gene expression and epigenetic modifications provides a valuable resource for future investigations into the regulatory mechanisms of protein-coding genes in Brassica napus.
表现出昼夜节律振荡的表观遗传修饰也促进了基因表达的昼夜节律振荡。油菜是一种异源多倍体物种，经历了远缘杂交和基因组加倍事件，具有年轻而独特的物种起源。结合对表观遗传修饰昼夜节律的研究可以为亚基因组之间昼夜振荡行为的差异以及生物钟中同源基因节律的多样化表达的调控提供新的见解。
在这项研究中，我们创建了一个高分辨率和多振荡的基因表达数据集，包括油菜中活跃的组蛋白修饰（H3K4me3、H3K9ac）和 RNA 聚合酶 II 的募集。我们还开创性地描述了异源多倍体物种中转录和表观遗传修饰的昼夜节律。我们比较了亚基因组之间昼夜节律的演化，发现 Cn 亚基因组在转录和活跃组蛋白修饰方面的昼夜振荡活性都高于 An 亚基因组。与拟南芥 Brassica rapa 的 A 亚基因组相比，油菜 Brassica napus 的 An 亚基因组的转录昼夜振荡特征发生了显著变化。同源基因对的转录昼夜振荡比例高于亚基因组特异性基因，这归因于更高的染色质可及性和活跃的表观遗传修饰类型的丰度。我们发现，同源基因的昼夜表达表现出多样性，并且在远缘杂交和基因组加倍事件后，生物钟基因的昼夜节律特征发生了广泛的变化，导致了生物钟系统的冗余。表观遗传修饰影响了同源基因表达昼夜节律的差异，并且同源基因表达的昼夜振荡受到多种组蛋白修饰的组合影响。
本文首次描述了异源多倍体物种中基因表达及其表观遗传修饰的昼夜节律特征。我们的发现揭示了导致亚基因组和同源基因节律表达差异的昼夜振荡活性失衡的表观遗传因素。我们生成的关于基因表达和表观遗传修饰的综合时间序列数据集为未来研究油菜中蛋白质编码基因的调控机制提供了有价值的资源。
