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

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

Genomic and epigenomic insights into the mechanism of cold response in upland cotton (Gossypium hirsutum)

“…They revealed genome-wide histone H3K4me3 modi cation patterns and found that the CUT&Tag procedure was faster and had a higher pro ling resolution with a lower background signal than ChIP-seq. In this paper, we adopted CUT&Tag to investigate the region and alternation of H3K4me3 and H3K9ac modi cation patterns genome-wide, indicating major genic region deposition, which was in line with previous reports by ChIP-seq(Wang et al 2017;Zhang et al 2021). Afterward, the relationship between DMGs and their corresponding gene differential expression was revealed, indicating that it is informative to study abiotic stress response .3 Dynamic changes in histone modi cation state function in regulating the transcription of cold-responsive genes Chromatin structure serves as a direct template for the binding and recruitment of proteins that are involved in the regulation of transcription factor binding, such as histone modi cations.…”

Epigenetic Regulation of Subgenomic Gene Expression in Allotetraploid Brassica napus

“…Histone modification is involved in regulating differential gene expression in rice under salt stress [ 37 ]. In allotetraploid cotton leaf tissue, H3K4me3 and H3K27me3 had both direct and indirect impacts on the differential transcription of genes or homologous gene pairs between subgenomes [ 38 ]. The expression of low-temperature-stress-related genes can be regulated by the antagonistic relationship between H3K27ac and H3K27me3 in rice [ 39 ].…”

Network and epigenetic characterization of subsets of genes specifically expressed in maize bundle sheath cells

“…6 E), which may maintain the transcription consistency [48] . Genes with broad H3K4me3 has been found to be involved in several important biological processes including cell identity, expression of tumor-suppressor genes, maternal-to-zygotic cell transition in humans and mammals [48] , [49] , [50] , [51] , [52] , and in photosynthesis and flower development in plants [39] , [53] . It is worth noting that this study used TF related ChIP-seq from M cells to indicate the potential binding of some of TFs in BS cells due to lack of related data in BS cells.…”