Genome-Wide DNA Methylation Analysis of Soybean Curled-Cotyledons Mutant and Functional Evaluation of a Homeodomain-Leucine Zipper (HD-Zip) I Gene GmHDZ20

Abstract

DNA methylation is a major, conserved epigenetic modification that influences many biological processes. Cotyledons are specialized tissues that provide nutrition for seedlings at the early developmental stage. To investigate the patterns of genomic DNA methylation of germinated cotyledons in soybean (Glycine max) and its effect on cotyledon development, we performed a genome-wide comparative analysis of DNA methylation between the soybean curled-cotyledons (cco) mutant, which has abnormal cotyledons, and its corresponding wild type (WT) by whole-genome bisulfite sequencing. The cco mutant was methylated at more sites but at a slightly lower level overall than the WT on the whole-genome level. A total of 46 CG-, 92 CHG-, and 9723 CHH- (H = A, C, or T) differentially methylated genes (DMGs) were identified in cotyledons. Notably, hypomethylated CHH-DMGs were enriched in the gene ontology term “sequence-specific DNA binding transcription factor activity.” We selected a DMG encoding a homeodomain-leucine zipper (HD-Zip) I subgroup transcription factor (GmHDZ20) for further functional characterization. GmHDZ20 localized to the nucleus and was highly expressed in leaf and cotyledon tissues. Constitutive expression of GmHDZ20 in Arabidopsis thaliana led to serrated rosette leaves, shorter siliques, and reduced seed number per silique. A yeast two-hybrid assay revealed that GmHDZ20 physically interacted with three proteins associated with multiple aspects of plant growth. Collectively, our results provide a comprehensive study of soybean DNA methylation in normal and aberrant cotyledons, which will be useful for the identification of specific DMGs that participate in cotyledon development, and also provide a foundation for future in-depth functional study of GmHDZ20 in soybean.

G9a promotes inflammation in Streptococcus pneumoniae induced pneumonia mice by stimulating M1 macrophage polarization and H3K9me2 methylation in FOXP1 promoter region

“…Epigenetic changes such as DNA methylation and histone modification are known to modulate gene expression changes and impact cellular function (28,29). As an epigenetic modifier, G9a has been documented to participate in many diseases (30,31) but its expression pattern and mechanism in Spn is largely unknown.…”

Beyond transcription factors: more regulatory layers affecting soybean gene expression under abiotic stress

“…The soybean ( Glycine max ) genome presents 28 HDAC genes that were identified and characterized based on sequence analysis, chromosomal location, subcellular localizations, tissue and organ-specific expression profile, and stress responsiveness ( Yang et al, 2018 ). Phylogenetic analysis shows that soybean has HDACs that belong to the three families: 18 members of RPD3/HDA1 family, named GmHDA1 to GmHDA18 according to their coordinates on soybean chromosome, four members of SIR2 family with highly conserved Sir2 domains, and six plant-specific HDACs (HD2 family) displaying the conserved amino-terminal conserved motif ( Yang et al , 2018 ). HDAC genes in soybean outnumber Arabidopsis , rice, and tomato deacetylase orthologs ( Pandey et al, 2002 ; Fu et al, 2007 ; Zhao et al, 2014 ).…”

A tomato HD-zip I transcription factor, VAHOX1, acts as a negative regulator of fruit ripening

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