Genetius

The study examines how ectopic accumulation of methionine in Arabidopsis thaliana leaves, driven by a deregulated AtCGS transgene under a seed‑specific promoter, reshapes metabolism, gene expression, and DNA methylation. High‑methionine lines exhibit increased amino acids and sugars, activation of stress‑hormone pathways, and reduced expression of DNA methyltransferases, while low‑methionine lines show heightened non‑CG methylation without major transcriptional changes. Integrated transcriptomic and methylomic analyses reveal a feedback loop linking sulfur‑carbon metabolism, stress adaptation, and epigenetic regulation.

The study mapped the cis‑regulatory landscape of the winter rapeseed cultivar Express617, identifying thousands of novel regulatory elements and characterizing super‑enhancers that are asymmetrically enriched in the Cn subgenome of Brassica napus. An in‑silico pipeline combining population‑level expression data and machine‑learning models revealed that many SE‑associated genes are expressed above predicted levels, and structural variants disrupting SEs lead to reduced gene expression, highlighting their functional importance for gene regulation and breeding.

The study integrated 16 Arabidopsis thaliana whole‑genome bisulfite sequencing datasets from 13 stress experiments using a unified bioinformatic pipeline to map common and stress‑specific DNA methylation changes. Differentially methylated regions varied by stress type and methylation context, with CG DMRs enriched in gene bodies and CHG/CHH DMRs in transposable elements, some of which overlapped loci prone to stable epimutations. Gene ontology and TE enrichment analyses highlighted shared stress pathways and suggest environmental stress can generate heritable epigenetic variation.

The study demonstrates that a rapid increase in cytosolic Ca²⁺ is the primary and sufficient signal mediating auxin‑induced root growth inhibition in Arabidopsis. Using live imaging, microfluidics, and optogenetic control of Ca²⁺ influx, the authors show that blocking Ca²⁺ entry prevents growth responses, while light‑triggered Ca²⁺ influx from the apoplast or ER mimics inhibition, indicating that diverse stimuli converge on a Ca²⁺‑dependent mechanism.

The study examined short‑term and transannual drought memory in cambium tissues of two Populus genotypes and four epitypes with modified DNA‑methylation machinery, revealing persistent hormone, transcript, and methylation changes one week after stress relief. Trees previously stressed in Year 1 displayed distinct physiological and molecular responses to a second drought in Year 2, indicating long‑term memory linked to stable CG‑context DNA methylation, with genotype‑dependent differences in plasticity and stability. These findings position the cambium as a reservoir for epigenetic stress memory and suggest exploitable epigenetic variation for tree breeding under drought.

The study uses an optogenetic ChannelRhodopsin 2 variant (XXM2.0) to generate defined cytosolic Ca²⁺ transients in Arabidopsis root cells, revealing that these Ca²⁺ signatures suppress auxin‑induced membrane depolarization, Ca²⁺ spikes, and auxin‑responsive transcription, leading to reversible inhibition of cell division and elongation. This demonstrates that optogenetically imposed Ca²⁺ signals act as dynamic regulators of auxin sensitivity in roots.

Using genome‑wide association studies in Arabidopsis thaliana, the authors identified the chromatin‑associated protein CDCA7 as a trans‑regulator that specifically controls CG methylation (mCG) and TE silencing. CDCA7 and its paralog CDCA7β bind the remodeler DDM1, modulating its activity without broadly affecting non‑CG methylation or histone variant deposition, and natural variation in CDCA7 regulatory sequences correlates with local ecological adaptation.

The study investigates how auxin signaling influences aluminium tolerance using tomato mutants with altered auxin sensitivity, showing that the auxin‑hypersensitive entire mutant tolerates Al stress while the auxin‑reduced dgt mutant is more sensitive. Differences in reactive oxygen species accumulation and root transition‑zone cell differentiation correlate with distinct metabolic responses, suggesting that modifying auxin perception can enhance crop Al tolerance.

The study demonstrates that the chromatin remodeler DDM1 is essential for biomass heterosis in Arabidopsis thaliana hybrids, as loss of DDM1 function leads to reduced rosette growth and extensive genotype‑specific transcriptomic and DNA methylation changes. Whole‑genome bisulfite sequencing revealed widespread hypomethylation in ddm1 mutants, while salicylic acid levels were found unrelated to heterosis, indicating that epigenetic divergence, rather than SA signaling, underpins hybrid vigor.

The study examined molecular responses in grapevine leaves with and without esca symptoms, using metabolite profiling, RNA‑seq and whole‑genome bisulfite sequencing. Metabolic and transcriptomic changes were confined to symptomatic leaves and linked to local DNA‑methylation alterations, while asymptomatic leaves showed distinct but overlapping methylation patterns, some present before symptoms, indicating potential epigenetic biomarkers for early disease detection.