Jul 2026· Journal of Applied Genetics· 0 citations· 11 references
Medicine
TL;DR
It is demonstrated that impairment of the strigolactone pathway is consistently associated with selective CHH hypermethylation rather than global methylation changes, which is consistent with altered RdDM-associated regulation.
Abstract
Strigolactones are plant hormones that regulate diverse developmental processes and stress responses, but their potential role in epigenetic regulation remains poorly understood. Previous transcriptomic analyses of strigolactone mutants in various species revealed extensive transcriptional reprogramming, suggesting destabilisation of higher-order regulatory mechanisms rather than changes in discrete gene networks. Here, we investigated whether disruption in strigolactone biosynthesis or perception is associated with altered DNA methylation patterns. Whole-genome bisulfite sequencing was performed on 7-day-old seedlings of Arabidopsis thaliana wild-type and the strigolactone biosynthesis mutant max3 and the perception mutant d14. A comparative analysis identified differentially methylated regions in CG, CHG, and CHH sequence contexts. While CG methylation changes showed no directional bias, non-CG contexts exhibited a pronounced enrichment of hypermethylated regions in both mutants, with the strongest effect observed in the CHH context. CHH hypermethylation was preferentially enriched at promoter-associated regions, primarily overlapping non-coding and pseudogene loci and showed substantial overlap between max3 and d14, indicating a shared epigenetic response in both mutants. Gene-body-associated regions displayed a similar but weaker pattern. These results demonstrate that impairment of the strigolactone pathway is consistently associated with selective CHH hypermethylation rather than global methylation changes. Because CHH methylation in plants is commonly associated with RNA-directed DNA methylation, the observed pattern is consistent with altered RdDM-associated regulation; however, direct involvement of the RdDM machinery remains to be established. This study provides a genome-wide framework for exploring how strigolactones may be associated with epigenetic regulation in plants.
Chromatin remodeling plays a central role in regulating plant development and physiology by shaping the gene expression patterns that drive biological processes. Among epigenetic modifications, histone acetylation is particularly relevant as it alters chromatin structure and influences transcriptional activity. MYST-type histone acetyltransferases (HAT) are evolutionarily conserved components of the Nucleosome Acetyltransferase of histone H4 (NuA4) complex, a key regulator that acetylates histones H4, H2A, and the histone variant H2A.Z. Growing evidence supports the presence of a canonical NuA4-C in plants, similar to that described in yeast. In this review, we summarize recent studies that have begun to uncover its broad role in plant biology, highlighting its involvement in diverse processes such as the skoto- to photomorphogenesis switch, chloroplast development, shade avoidance responses, thermomorphogenesis, the vegetative-to-reproductive transition, plant growth, reproduction and hormonal signalling. In addition, we discuss recent advances in understanding the crosstalk of NuA4-C-mediated H4ac and H2A.Z deposition with other chromatin remodeling complexes in plants. Although significant progress has been made, a full understanding of the complex functions remains unavailable. Current evidence indicates that NuA4-C in yeast and TIP60 in humans are central regulators of transcription, acting not only through histone acetylation but also by influencing transcription elongation and RNA splicing, although direct evidence for similar functions in plant NuA4-C still remains limited. This regulatory role might be critical for integrating developmental programs with environmental signalling pathways. While initial insights into the recruitment of NuA4-C to target genes have emerged, further research is needed to clarify how its activity is controlled and modulated in different biological contexts.
María Guillem-Bernal, J. Barrero-Gil, J. A. Jarillo et al.· Journal of Experimental Bota...· 0 citations
Pectin acetylesterase (PAE) regulates pectin acetylation, which affects plant growth, development, and stress tolerance. While their functions are well-defined in models like Arabidopsis, we still know surprisingly little about how they operate in tomatoes (Solanum lycopersicum). We identified 17 SlPAE genes using tomato genome-wide analysis. These genes were classified phylogenetically into three conserved subfamilies, with branch members sharing domain architectures, motifs, and genomic structure. Promoter cis-element analysis identified multiple motifs related to hormone signaling, light response, and stress response. Spatiotemporal expression patterns obtained via qRT-PCR revealed the functional roles of SlPAE genes. Notably, silencing SlPAE16 effectively retarded pedicel abscission, a process mediated by the inhibition of TAPG1/2/4 expression. These findings clarify the functional diversity within the PAE gene family, providing a much-needed framework for future research into their specific biological roles in tomatoes.
Ruizhen Li, Lin Shen, Jianzhong Tie et al.· BMC Plant Biology· 0 citations
ELONGATED HYPOCOTYL5 (HY5), a bZIP transcription factor, is a central regulator of light signalling and secondary metabolism, yet its role in coordinating primary metabolism with plant stress responses remains unclear. Here, we investigated HY5 function in Nicotiana tabacum using wild-type, HY5-overexpressing (NtHY5OX), and CRISPR/Cas9-generated HY5 knockout (NtHY5CR) lines. Integrated transcriptomic analyses of leaves and roots, combined with LC/MS- and GC/MS-based metabolite profiling, revealed that HY5 overexpression promotes a broad metabolic reprogramming characterised by enhanced expression of genes associated with the Calvin cycle, tricarboxylic acid (TCA) cycle, flavonoid biosynthesis, and nicotine metabolism. These transcriptional changes were accompanied by increased accumulation of phenolic compounds and alkaloids, indicating a shift in metabolic reprogramming toward defence-related specialised metabolism. In contrast, NtHY5CR mutants accumulated higher levels of amino acids, lipids, and organic acids, consistent with prioritisation of growth-associated primary metabolism at the expense of protective secondary metabolite production. Pathway enrichment analyses identified HY5 as a key regulatory node integrating central carbon metabolism with specialised metabolite biosynthesis. Functionally, this HY5-dependent metabolic configuration enhanced resistance to Alternaria solani and improved tolerance to salt stress, demonstrating that HY5-mediated metabolic plasticity underpins adaptive stress responses in tobacco. Together, these findings establish HY5 as a critical coordinator of metabolic and defence networks, providing mechanistic insight into how light-responsive transcriptional regulation shapes plant stress resilience and offering targets for engineering stress-tolerant crops.
Shambhavi Dwivedi, Deeksha Singh, Sanchita Gupta et al.· Plant, Cell and Environment· 0 citations
The m⁶A demethylase ALKBH10B emerges as a crucial post-transcriptional regulator of hormonal crosstalk, photosynthetic maintenance, and mitochondrial energy metabolism to fine-tune plant stress adaptation to drought. Epitranscriptomic N⁶-methyladenosine (m⁶A) mRNA modification has emerged as an important regulatory layer of gene expression and protein synthesis in plant stress adaptation. In this study, expression profiling revealed that drought stress induces a global reprogramming of the m6A machinery in Arabidopsis thaliana, with the m6A demethylase ALKBH10B exhibiting a more pronounced time-dependent response. ALKBH10B transcription is induced by ABA, most likely via ABRE and MYB cis-elements, whereas jasmonate alleviates this activation. Moreover, ALKBH10B overexpressing plants (OX-1) accumulated wild type (WT) levels of ABA under drought stress but displayed a markedly reduced content in jasmonic acid (JA) and jasmonoyl-isoleucine (JA-Ile). They furthermore exhibit enhanced stomatal closure, improved water-use efficiency, and thus an enhanced drought tolerance. Transcriptome analysis revealed that drought stress induces fewer transcriptional changes in OX-1 plants compared to WT and the drought-sensitive alkbh10b-1 mutant. Differential expression and GO enrichment analyses highlight that photosynthesis-related processes were most affected by ALKBH10B activity, correlating with a preserved chlorophyll content and PSII efficiency in OX-1. Analysis by m⁶A-IP-qPCR showed that ALKBH10B directly demethylates specific photosynthesis-related and drought-responsive genes, while other transcripts are indirectly regulated by ALKBH10B-dependent processes. Moreover, transcripts associated with respiration were enriched in OX-1, indicating that ALKBH10B also supports mitochondrial energy metabolism during drought. Together, our results suggest that ALKBH10B enhances drought tolerance by coordinating m⁶A-dependent transcriptional and post-transcriptional regulation to maintain photosynthetic capacity and mitochondrial energy metabolism, as well as fine-tuning ABA-jasmonate crosstalk.
The phosphatidylethanolamine-binding protein (PEBP) gene family plays essential roles in flowering regulation, plant development, and stress responses. However, its characteristics in Osmanthus fragrans remains largely unexplored. Here, a genome-wide analysis was conducted to comprehensively investigate the OfPEBP gene family. A total of 11 OfPEBP genes were identified and classified into three subgroups: FT-, TFL1-, and MFT-like. Genes within the same subgroup exhibited similar motif compositions and exon–intron structures. Promoter analysis revealed abundant light- and hormone-responsive cis-elements. Population genetic analyses identified significant differentiation in OfPEBP3, OfPEBP7, and OfPEBP8, with their single nucleotide polymorphisms (SNPs) and haplotypes closely associated with seasonal flowering phenotypes. DNA methylation profiling indicated that CpG and CHG methylation predominated across the OfPEBP family and remained relatively stable during flower development, whereas OfPEBP6, OfPEBP9, and OfPEBP10 displayed higher methylation levels. Segmental duplication was identified as the primary driver of family expansion, and duplicated gene pairs experienced strong purifying selection. Expression analyses revealed tissue-specific expression patterns and differential responses to temperature, ethylene, and DNA methylation inhibitor (Aza) treatments. These findings provide useful insights into the potential involvement of OfPEBP genes in seasonal flowering and offer candidate genetic resources for future functional studies and molecular breeding in O. fragrans.
Hui Xia, Yuanhang Wu, Jie Yang et al.· Horticulturae· 0 citations
High-temperature stress impairs plant growth and alters secondary metabolism. Polymethoxyflavones (PMFs) are citrus-specific flavonoids with important nutritional benefits; however, their transcriptional responses to heat stress remain poorly understood. Here, five-month-old ‘Ponkan’ citrus seedlings were exposed to 40 °C for 6, 11, and 21 days. HPLC analysis showed that the accumulation of four major PMFs (sinensetin, nobiletin, tangeretin, and 5-demethylnobiletin) was significantly reduced in leaves under heat stress. RNA-seq identified 3424 differentially expressed genes shared across all three time points, which were enriched in pathways associated with microtubule cytoskeleton organization, cell cycle regulation, and glyoxylate and dicarboxylate metabolism. Further analysis of the PMF biosynthetic pathway revealed that 14 of 18 key structural genes, including CHS, CHI, FNSII, and OMT family members, were downregulated by heat treatment. In addition, several bHLH, AP2/EREBP, and MYB transcription factors, known regulators of flavonoid biosynthesis, exhibited expression patterns closely associated with PMF accumulation. RT-qPCR analysis validated the transcriptome results. Collectively, these findings suggest that heat stress suppresses PMF accumulation through coordinated repression of PMF biosynthetic genes and their potential regulators. This study provides new insights into the molecular basis of heat-responsive PMF metabolism and offers potential targets for maintaining citrus nutritional quality under elevated temperatures.
Xiaojuan Liu, Zhenkun Liao, Honglu Hu et al.· Horticulturae· 0 citations