On December 29, 2020, Molecular Plant published an online publication entitled”Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus” research paper. The study constructed the largest brassica napus epigenetics related data set so far, drawn its epigenetic reference genome map, explained the epigenetic basis of the imbalance between the Brassica napus subgenome, and identified plants A new bivalent chromatin state (H3K4me1-H3K27me3) in the medium, provides an important resource for epigenetic research on Brassica napus and other polyploid plants.
Epigenetics plays a vital role in plant growth and development. It regulates in different types of cells without changing DNA genetic information Constitutive and specific expression of genes. Brassica napus is an important allotetraploid crop with complex genomic information, but its epigenetic research is still in its infancy. The study used two parents of Huayouza 62 widely grown in China and neighboring countries as experimental materials, and used five histone modifications (H3K4me3, H3K27ac, H3K4me3, H3K27ac) of their four tissues (young leaves, roots, flower buds and siliques). H3K4me1, H3K27me3 and H3K9me2) and RNAPII ChIP-Seq data, as well as the corresponding RNA-Seq and DNA methylation data, constructed the largest epigenetic data set in Brassica napus so far, and based on this A comprehensive and systematic mapping of the epigenome of Brassica napus, annotated functional DNA elements covering 65.8%of its genome. This research has taken an important first step as part of the ENCODE project for Brassica napus.
Researchers conducted a systematic analysis of the epigenetic modifications between the two subgenomes of allopolyploid Brassica napus An and Cn, and found that The expression bias of homologous gene pairs between genomes is balanced, and homologous genes with higher expression levels have higher active related epigenetic modifications. However, the overall expression and epigenetic activity levels of genes specific to the An subgenome are much higher than those of the Cn subgenome. It is speculated that the specific genes of the subgenome are one of the important reasons for the imbalance between the Brassica napus subgenome.
The author of defined 15 chromatin states in the Brassica napus epigenome map, and observed that the active chromatin state in the An subgenome requires genome coverage Higher than the Cn subgenome, and the heterochromatin state in the Cn subgenome has a higher genome coverage than the An subgenome. In addition, through the verification of the ChIP-reChIP experiment, the author identified a new H3K4me1-H3K27me3 bivalent chromatin state. This chromatin state generally exists in the gene body, is related to the tissue-specific expression of the Brassica napus gene, and plays an important role in its growth and development. However, its specific biological functions need to be further studied.
This study provides a comprehensive overview of the epigenome map of Brassica napus, the epigenetic basis of the imbalance between An and Cn subgenomes, and the differences in different types of repetitive genes. Epigenetic differences and the newly identified bivalent chromatin status play an important role in the tissue-specific expression of genes in Brassica napus. These data provide an important resource for the comprehensive analysis of the genome of allotetraploid Brassica napus.
Huazhong Agricultural University Professor Shen Jinxiong, Professor Li Xingwang, and Professor Li Guoliang are the corresponding authors. PhD students Zhang Qing, Guan Pengpeng and postdoctoral fellow Zhao Lun are the joint firsts of this article Author.
original link:https://www.cell.com/molecular-plant/fulltext/S1674-2052(20)30451-2 div>