Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus
Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus
复制标题
亚基因组的不对称表观基因组图揭示了甘蓝型油菜的不平衡转录和独特的进化趋势
DOI：
10.1016/j.molp.2020.12.020
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发表时间：
2021-04-05
期刊：
影响因子：
27.5
通讯作者：
Shen, Jinxiong
中科院分区：
文献类型：
--
作者：
Zhang, Qing;Guan, Pengpeng;Shen, Jinxiong
在植物多倍化过程中，表观基因组景观和转录调控的复杂性显着增加，这推动了基因组进化，并有助于提高对不同环境的适应性。然而，一个全面的甘蓝型油菜表观基因组图谱仍然不可用。在这项研究中，我们进行了五个组蛋白修饰，RNA聚合酶II占有率，DNA甲基化和转录组在两个B的综合分析。以甘蓝型油菜品系（2063A和B409）为研究对象，建立了这两个品系4种组织类型（幼叶、花蕾、角果和根）全基因组（包括An和Cn亚基因组）调控元件、染色质状态及其动态的全局图谱。大约65.8%的基因组用不同的表观基因组信号注释。与Cn亚基因组相比，An亚基因组具有更高水平的活性表观遗传标记和更低水平的抑制表观遗传标记。来自亚基因组独特区域的基因促成了An和Cn亚基因组之间的主要差异。同源异型基因对之间的不对称组蛋白修饰反映了它们的偏向性表达模式。我们在B中鉴定了一种新的二价染色质状态（具有H3K4me1和H3K27me3）。与组织特异性基因表达相关的基因。此外，我们观察到不同类型的重复基因具有不同的组蛋白修饰模式和DNA甲基化水平。总的来说，我们的研究结果为异源多倍体植物提供了宝贵的表观遗传资源。
The complexity of the epigenome landscape and transcriptional regulation is significantly increased during plant polyploidization, which drives genome evolution and contributes to the increased adaptability to diverse environments. However, a comprehensive epigenome map of Brassica napus is still unavailable. In this study, we performed integrative analysis of five histone modifications, RNA polymerase II occupancy, DNA methylation, and transcriptomes in two B. napus lines (2063A and B409), and established global maps of regulatory elements, chromatin states, and their dynamics for the whole genome (including the An and Cn subgenomes) in four tissue types (young leaf, flower bud, silique, and root) of these two lines. Approximately 65.8% of the genome was annotated with different epigenomic signals. Compared with the Cn subgenome, the An subgenome possesses a higher level of active epigenetic marks and lower level of repressive epigenetic marks. Genes from subgenome-unique regions contribute to the major differences between the An and Cn subgenomes. Asymmetric histone modifications between homeologous gene pairs reflect their biased expression patterns. We identified a novel bivalent chromatin state (with H3K4me1 and H3K27me3) in B. napus that is associated with tissue-specific gene expression. Furthermore, we observed that different types of duplicated genes have discrepant patterns of histone modification and DNA methylation levels. Collectively, our findings provide a valuable epigenetic resource for allopolyploid plants.