AUTHOR=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 

TITLE=Profiling of H3K4me3 and H3K27me3 and Their Roles in Gene Subfunctionalization in Allotetraploid Cotton

JOURNAL=Frontiers in Plant Science

VOLUME=Volume 12 - 2021

YEAR=2021

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2021.761059

DOI=10.3389/fpls.2021.761059

ISSN=1664-462X

ABSTRACT=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 subgenome 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 expression of genes between A and D subgenome, respectively. More importantly, H3K4me3 exhibited enrichment levels, positioning and distance-related effects on expression levels of related genes. Distinct GO term enrichment occurred between A and D-specific genes and homeologous genes with broad H3K4me3 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 of homeologous genes was more pronounced in A subgenome relative to D subgenome, reflecting distinct enrichment of H3K27me3 in homeologous genes between A and D subgenome. In addition, H3K4me3, H3K27me3 marks can indirectly influence gene expression through TF-mediated regulatory networks. Thus, our study provides detailed insights in functions of H3K4me3 and H3K27me3 in regulating differential gene expression and subfuncationalization of homeologous genes, therefore serving a driving force for polyploidization and domestication in cotton.