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 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 examines how the SnRK1 catalytic subunit KIN10 integrates carbon availability with root growth regulation in Arabidopsis thaliana. Loss of KIN10 reduces glucose‑induced inhibition of root elongation and triggers widespread transcriptional reprogramming of metabolic and hormonal pathways, notably affecting auxin and jasmonate signaling under sucrose supplementation. These findings highlight KIN10 as a central hub linking energy status to developmental and environmental cues in roots.

The study used phospho‑proteomics to uncover rapid phosphorylation changes in Arabidopsis seedlings upon light or sucrose exposure, identifying RS41 as a hyperphosphorylated SR protein. By creating single and higher‑order mutants of four RS genes, the authors demonstrated that these RS proteins are essential for photomorphogenic development and regulate light‑dependent alternative splicing, with loss of all four causing sterility.

The study investigated how Arabidopsis thaliana SR protein kinases (AtSRPKs) regulate alternative RNA splicing by using chemical inhibitors of SRPK activity. Inhibition with SPHINX31 and SRPIN340 caused reduced root growth and loss of root hairs, accompanied by widespread changes in splicing and phosphorylation of genes linked to root development and other cellular processes. Multi‑omics analysis (transcriptomics and phosphoproteomics) revealed that AtSRPKs modulate diverse splicing factors and affect the splicing landscape of numerous pathways.

The study used TurboID-based proximity labeling coupled with mass spectrometry to map the Arabidopsis alternative splicing machinery centered on ACINUS, PININ, and SR45, identifying 298 high-confidence components and revealing that splicing is tightly linked to transcription and other RNA processing steps. Bioinformatic and genetic analyses, including O-glycosylation double mutants, demonstrated both conserved and plant‑specific regulatory networks and highlighted the role of sugar modifications in modulating splicing.

The study shows that silencing of NOR2 rRNA genes in Arabidopsis thaliana depends primarily on CHH-context cytosine methylation, particularly mediated by CMT2 and the chromatin remodeler DDM1, rather than CG or CHG methylation. Comparative promoter analysis revealed a prevalence of CHH sites in plant rDNA promoters, explaining why CHH methylation mutants disrupt NOR2 silencing more strongly, while NOR2 loci are hyper‑methylated and more condensed than NOR4.

The study demonstrates that abscisic acid (ABA) accumulates in darkness to suppress cotyledon opening during seedling deetiolation, and that light exposure lifts this repression, enabling cotyledon aperture. Genome‑wide transcriptional and alternative‑splicing changes accompany this process, and the light‑dependent regulation requires the splicing factors RS40 and RS41, whose activity is repressed in the dark.