Abstract
Histone modification is an important epigenetic modification that controls gene transcriptional regulation in eukaryotes. Histone methylation is accomplished by histone methyltransferase and can occur on two amino acid residues, arginine and lysine. JumonjiC (JmjC) domain-containing histone demethylase regulates gene transcription and chromatin structure by changing the methylation state of the lysine residue site and plays an important role in plant growth and development. In this study, we carried out genome-wide identification and comprehensive analysis of JmjC genes in the allotetraploid cotton species Gossypium hirsutum. In total, 50 JmjC genes were identified and in G. hirsutum, and 25 JmjC genes were identified in its two diploid progenitors, G. arboreum and G. raimondii, respectively. Phylogenetic analysis divided these JmjC genes into five subfamilies. A collinearity analysis of the two subgenomes of G. hirsutum and the genomes of G. arboreum and G. raimondii uncovered a one-to-one relationship between homologous genes of the JmjC gene family. Most homologs in the JmjC gene family between A and D subgenomes of G. hirsutum have similar exon-intron structures, which indicated that JmjC family genes were conserved after the polyploidization. All G. hirsutum JmjC genes were found to have a typical JmjC domain, and some genes also possess other special domains important for their function. Analysis of promoter regions revealed that cis-acting elements, such as those related to hormone and abiotic stress response, were enriched in G. hirsutum JmjC genes. According to a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, most G. hirsutum JmjC genes had high abundance expression at developmental stages of fibers, suggesting that they might participate in cotton fiber development. In addition, some G. hirsutum JmjC genes were found to have different degrees of response to cold or osmotic stress, thus indicating their potential role in these types of abiotic stress response. Our results provide useful information for understanding the evolutionary history and biological function of JmjC genes in cotton.
Highlights
Epigenetics is the study of changes in gene expression that can be inherited without changes in the DNA sequence [1]
To better understand the evolutionary history of G. hirsutum JmjC genes, we searched for JmjC genes in the other two diploid cotton species, G. arboreum and G. raimondii, using the same method
We identified 25 G. arboreum and 25 G. raimondii JmjC genes, exactly half the number found in G. hirsutum
Summary
Epigenetics is the study of changes in gene expression that can be inherited without changes in the DNA sequence [1]. Gene expression is controlled through epigenetic regulation, which mainly includes. DNA methylation, histone modification, chromatin remodeling and non-coding RNA regulation [2]. Post-translational covalent modification of histones is an important mode of epigenetic regulation that regulates gene expression and other processes by affecting the state of chromatin [4]. The N-terminal amino acid tails of histones are often covalently modified, mainly through acetylation, methylation, ubiquitination, phosphorylation, glycosylation, ADP-ribosylation and SUMOylation [5]. Different covalent modifications occur at different sites of histones. Histone methylation has important effects on gene transcription and chromatin structure that vary according to the location and degree of methylation. Histone methylation occurs mainly at the N-terminal arginine (R) and lysine (K) sites of histones H3 and H4, including K4, K9, K27, K36 of H3 and K20 for H4.
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