Study Of Epigenome Maps And Subgenome Imbalance In Brassica Napus

Epigenetics refers to a discipline that regulates gene expression changes through various modification signals without changing the DNA sequence information.Different epigenetic signals have different regulatory effects on gene expression activity.The co-modification of different types of epigenetic marks together annotates the chromatin structure characteristics of specific locations in the nucleus,and they can regulate gene expression in the correct spatiotemporal environment.This combination of epigenetic modifications plays an indispensable role in the normal life activities of eukaryotes.Analyzing the combined characteristics of epigenetic modifications in the genome of a species plays an important role in understanding the regulation of gene expression,the distribution of functional regulatory elements,and the structural characteristics of the genome.Brassica napus is an important Brassica oil crop and the typical allopolyploid plant.Polima Cytoplasmic Male Sterile Line(pol CMS)is the first practically valuable and most widely used Brassica napus male sterile lines.However,the epigeneticsrelated research of Brassica napus is still in its infancy,and the difference in activity of the An and Cn subgenomes at the epigenetic level is still unclear.In this research,the excellent pol CMS line 2063 A and its restorer line B409 as experimental materials were used in this study.We have completed the ChIP-Seq data of five histone modifications and RNAPII in four tissues.Combining with the transcriptome and DNA methylation,we constructed the largest epigenomic datasets in Brassica napus to date.Based on the epigenetic datasets,the epigenome maps of Brassica napus was constructed in this study,as part of the ENCODE(Encyclopedia of DNA elements)project of this species,it has taken important first step.Brassica napus is a typical allopolyploid plant,and its genome has two different subgenomes,An and Cn.We analyzed the epigenetic differences between the subgenomes and found that the overall gene expression level and epigenetic signal activity on the An subgenome were significantly higher than the Cn subgenome.However,the DNA methylation levels of Cn subgenome are significantly higher than that of An subgenome.In the process of mapping the chromatin state between the Brassica napus subgenomes,we also found that the An subgenome has a significantly higher proportion of the genome in the active-related chromatin state than the Cn subgenome.In the analysis of the dynamic changes in the four tissues of Brassica napus,it was also found that the gene expression and epigenetic signals change frequency of the An subgenome was significantly higher than that of the Cn subgenome.Therefore,we believe that An is the dominant subgenome in Brassica napus.By analyzing the differences in gene expression levels and epigenetic activity of homologous gene pairs and subgenome-specific genes on the An and Cn subgenomes of Brassica napus,we found that the expression bias of homeologous gene pairs among Brassica napus subgenomes was comparable.And the activity of gene expression has a significant correlation with the activity of epigenetic signals.However,the gene expression and epigenetic activity of An subgenome-specific genes are significantly higher than that of Cn subgenome-specific genes.The dynamic change frequency of gene expression and epigenetic signals of An subgenome-specific genes in the four tissues was also significantly higher than that of Cn subgenome homologous genes.We believe that the imbalance of subgenome-specific genes is an important reason for the imbalance between the subgenomes of Brassica napus.The bivalent chromatin state refers to the presence of active-related and repressedrelated histone modifications at the position where histones bind to DNA.It plays an important role in regulating the tissue-specific expression of genes.We found an unreported bivalent chromatin state in Brassica napus,which is composed of active histone modification H3K4me1 and repressed histone modification H3K27me3.By analyzing the dynamic changes between the tissues,it is proved that this state plays an important role in the tissue-specific expression of regulatory genes in Brassica napus.ChIP-Seq is widely used in experiments which related to the interaction between DNA and target protein.We has developed a simple and efficient ChIP-Seq method in plants.We tested this method in different plant species,different tissue types,and low input,we had proved that this experimental method can be applied to mass production of ChIP-Seq related datasets in plant,and can be used in special tissues in plants.In summary,this project has produced the largest epigenetics datasets so far,drawing the epigenetic map of the Brassica napus,which provides data resource for the research on the functional genomics of Brassica napus.On the other hand,we found that the epigenetic activity of An subgenome-specific genes is higher than that of Cn subgenome,which is an important reason for the imbalance between Brassica napus subgenomes.We discovered an unreported new bivalent chromatin state in the chromatin state map,which deepened people's understanding of the epigenetics related knowledge of Brassica napus,and also provide new ideas for the research on subgenome imbalance of other allopolyploid plants.