Abstract
BackgroundHistone methylation occurs primarily on lysine residues and requires a set of enzymes capable of reading, writing, and erasing to control its establishment and deletion, which is essential for maintaining chromatin structure and gene expression. Histone methylation and demethylation are contributed to plant growth and development, and are involved in adapting to environmental stresses. The JmjC domain-containing proteins are extensively studied for their function in histone lysine demethylation in plants, and play a critical role in sustaining histone methylation homeostasis.ResultsIn this study, a total of 21 JmjC domain-containing histone demethylase proteins (JHDMs) in birch were identified and classified into five subfamilies based on structural characteristics and phylogenetic relationships among Arabidopsis, rice, maize, and birch. Although the BpJMJ genes displayed significant schematic variation, their distribution on the chromosomes is relatively uniform. Additionally, the BpJMJ genes in birch have never experienced a tandem-duplication event proved by WGD analysis and were remaining underwent purifying selection (Ka/Ks < < 1). A typical JmjC domain was found in all BpJMJ genes, some of which have other essential domains for their functions. In the promoter regions of BpJMJ genes, cis-acting elements associated with hormone and abiotic stress responses were overrepresented. Under abiotic stresses, the transcriptome profile reveals two contrasting expression patterns within 21 BpJMJ genes. Furthermore, it was established that most BpJMJ genes had higher expression in young tissues under normal conditions, with BpJMJ06/16 having the highest expression in germinating seeds and participating in the regulation of BpGA3ox1/2 gene expression. Eventually, BpJMJ genes were found to directly interact with genes involved in the “intracellular membrane” in respond to cold stress.ConclusionsThe present study will provide a foundation for future experiments on histone demethylases in birch and a theoretical basis for epigenetic research on growth and development in response to abiotic stresses.
Highlights
Histone methylation occurs primarily on lysine residues and requires a set of enzymes capable of reading, writing, and erasing to control its establishment and deletion, which is essential for maintaining chromatin structure and gene expression
Identification and classification of the JmjC domain-containing histone demethylase proteins (JHDMs) gene family in brich In order to identify all possible homologs of the JHDM gene family in birch, the full-length amino acid sequences of the JHDM proteins determined in Arabidopsis, rice, and maize were performed to query the protein sequence database of the Betula pendula genome with blastp program
To examine the evolutionary history of these protein families in these four species and to establish the phylogenetic relationship among JHDM family genes, the phylogenetic tree was constructed with MEGA6.0 based on the neighbor-joining algorithm with full-length JHDM protein sequences of birch (21), Arabidopsis (21), rice (20), and maize (21) (Fig. 1)
Summary
Histone methylation occurs primarily on lysine residues and requires a set of enzymes capable of reading, writing, and erasing to control its establishment and deletion, which is essential for maintaining chromatin structure and gene expression. The protein family of SET or PRMT domains, which are primarily responsible for the methylation of histone lysine and arginine residues, has received considerable attention so far in plant histone methyltransferases studies [10]. The methylation of histones has different impacts on gene expression; for example, H3K9 (H3K9me2/3) and H3K27 (H3K27me3) methylation are associated with transcriptional inhibition, while H3K4 (H3K4me2/3) and H3K36 (H3K36me3) methylation are associated with transcriptional activation [12]. These modifications serve as a kind of “histone code” for chromatin functions and transcriptional activities [13, 14]. Histone alteration homeostasis is essential for plants’ normal growth and development [15]
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