Wei Zhou

Background: Su(var)3-9 SET genes encode key histone methyltransferases that catalyze H3K9 methylation, a modification generally associated with heterochromatin formation and transcriptional repression. Methods: We identified 23 GmSu(var)3-9 SETs and systematically characterized their tissue-specific epigenetic modifications as well as their phylogenetic relationships, chromosomal distributions, conserved domains, gene structures, GO annotations, collinearity, cis-regulatory elements, and expression profiles across diverse tissues and under salt stress. Results: These genes were divided into seven groups, exhibiting diverse structures and uneven distribution on chromosomes. Gene structure and conserved motif analyses revealed high structural diversity among family members, with variations in intron–exon distribution, conserved motifs, and functional domains. Promoter analysis detected multiple cis elements responsive to light, hormones, and abiotic stresses. Most genes showed preferential expression in meristems, roots, and leaves, and responded to salt stress. Co-expression network analysis revealed that these genes were co-expressed with stress- and development-related genes. GmSUVH12 histone modifications exhibited obvious tissue specificity. Conclusions: Overall, these results provided insights into the evolutionary and functional roles of GmSu(var)3-9 SETs in soybean.

The AT-hook motif nuclear localized (AHL) gene family encodes transcription factors pivotal in regulating plant growth, development, and responses to abiotic stimuli, including low temperature, salinity, darkness, and drought. In this study, we systematically identified 21 BpAHL genes in birch and characterized their sequence features, evolutionary relationships, and expression dynamics. Phylogenetic analysis classified BpAHLs into two clades (Clade-A and Clade-B) and three types (Type-I, -II, and -III), based on PPC domain and AT-hook motifs. Chromosomal mapping revealed an even distribution across nine chromosomes and one contig, with dispersed duplication events recognized as the major driver of BpAHL family expansion. Tissue-specific expression profiling uncovered striking divergence: Type-I BpAHLs displayed root-predominant expression, whereas Type-II/III BpAHLs were highly expressed in plant flowers and leaves. Notably, Type-II/III BpAHL genes in leaves showed distinct expression patterns in response to cold and heat stresses, while Type-I BpAHLs in roots were down-regulated under salt stress. This study provides a comprehensive phylogenomic and functional analysis of the AHLs in birch, providing insights into their roles in enhancing abiotic stress resilience in forest trees.

Since the last glacial maximum, the Earth has experienced drastic climate changes. However, with the advent of the Industrial Revolution, human activities have abruptly intensified, altering the planet’s climate patterns. Climate models predict that over the next hundred years, the globe will experience even more drastic changes than those observed in the past 20,000 years. Understanding how plants adapt to environmental changes has thus become a critical research priority. Currently, evidence suggests that plants adapt to environmental changes primarily through two distinct pathways: one mediated by genetic variation and the other involving the direct or indirect participation of epigenetic modifications. Given the unprecedented rate of contemporary climate change, epigenetic mechanisms may exert a more immediate and flexible influence than genetic modifications. Epigenetics, including DNA methylation, histone modification, and non-coding RNA, plays an important role in the post-transcriptional regulation process and affects the growth and development of plants, as well as their responses to environmental changes. In this review, we synthesize current knowledge on the epigenetic mechanisms underlying plant responses to environmental changes and examine the dynamic interplay between epigenetic regulation and environmental stimuli, aiming to provide insights into enhancing the tolerance of plants to environmental stress factors.

CRISPR/dCas9 is an important DNA modification tool in which a disarmed Cas9 protein with no nuclease activity is fused with a specific DNA modifying enzyme. A previous study reported that overexpression of the TET1 catalytic domain (TET1cd) reduces genome-wide methylation in Arabidopsis. A spontaneous naturally occurring methylation region (NMR19-4) was identified in the promoter region of the PPH (Pheophytin Pheophorbide Hydrolase) gene, which encodes an enzyme that can degrade chlorophyll and accelerate leaf senescence. The methylation status of NMR19-4 is associated with PPH expression and leaf senescence in Arabidopsis natural accessions. In this study, we show that the CRISPR/dCas9-TET1cd system can be used to target the methylation of hypermethylated NMR19-4 region to reduce the level of methylation, thereby increasing the expression of PPH and accelerating leaf senescence. Furthermore, hybridization between transgenic demethylated plants and hypermethylated ecotypes showed that the demethylation status of edited NMR19-4, along with the enhanced PPH expression and accelerated leaf senescence, showed Mendelian inheritance in F1 and F2 progeny, indicating that spontaneous epialleles are stably transmitted trans-generationally after demethylation editing. Our results provide a rational approach for future editing of spontaneously mutated epialleles and provide insights into the epigenetic mechanisms that control plant leaf senescence.