The study characterizes the chloroplast‑localized protein AT4G33780 in Arabidopsis thaliana using CRISPR/Cas9 knockout and overexpression lines, revealing tissue‑specific expression and context‑dependent effects on seed germination, seedling growth, vegetative development, and root responses to nickel stress. Integrated transcriptomic (RNA‑seq) and untargeted metabolomic analyses show extensive transcriptional reprogramming—especially of cell‑wall genes—and altered central energy metabolism, indicating AT4G33780 coordinates metabolic state with developmental regulation rather than controlling single pathways.

The study used CRISPR/Cas9 to edit the downstream region of the Arabidopsis thaliana FLOWERING LOCUS T (FT) gene, identifying a 2.3‑kb segment containing the Block E enhancer as crucial for normal FT expression and flowering. Fine‑scale deletions pinpointed a 63‑bp core module with CCAAT‑ and G‑boxes, and revealed a cryptic CCAAT‑box that becomes active when repositioned, highlighting the importance of local chromatin context and motif arrangement for enhancer function.

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 applied a progressive, sublethal drought treatment to Arabidopsis thaliana, collecting time‑resolved phenotypic and transcriptomic data. Machine‑learning analysis revealed distinct drought stages driven by multiple overlapping transcriptional programs that intersect with plant aging, and identified high‑explanatory‑power transcripts as biomarkers rather than causal agents.

The study shows that inoculating Arabidopsis thaliana with the plant‑growth‑promoting bacterium Enterobacter sp. SA187 markedly boosts root and shoot biomass under elevated CO₂, accompanied by altered nitrogen and carbon content and reshaped phytohormone signaling. Transcriptomic and metabolomic analyses reveal activation of salicylic acid, jasmonic acid, and ethylene pathways and enhanced primary metabolism, while the ethylene‑insensitive ein2‑1 mutant demonstrates that the growth benefits are ethylene‑dependent.

The study combined cell biology, transcriptomics, and ionomics to reveal that zinc deficiency reduces root apical meristem size while preserving meristematic activity and local Zn levels, leading to enhanced cell elongation and differentiation in Arabidopsis thaliana. ZIP12 was identified as a highly induced gene in the zinc‑deficient root tip, and zip12 mutants displayed impaired root growth, altered RAM structure, disrupted Zn‑responsive gene expression, and abnormal metal partitioning, highlighting ZIP12’s role in maintaining Zn homeostasis and meristem function.

The study introduces a CRISPR/Cas9‑based restoration system (CiRBS) that reactivates a disabled luciferase reporter (LUC40Ins26bp) in transgenic Arabidopsis, enabling long‑term single‑cell bioluminescence monitoring. Restoration occurs within 24 h after particle‑bombardment‑mediated CRISPR delivery, with ~7 % of cells regaining luminescence and most restored cells carrying a single correctly edited chromosome, facilitating reliable analysis of cellular gene‑expression heterogeneity.

The study used Arabidopsis thaliana mutants with low (vtc2, vtc4) and high (vtc2/OE-VTC2) ascorbate levels to examine how ascorbate concentration affects gene expression and cellular homeostasis. Transcriptomic analysis revealed that altered ascorbate levels modulate defense and stress pathways, and that TAA1/TAR2‑mediated auxin biosynthesis is required for coping with elevated ascorbate in a light‑dependent manner.

The study compares transcriptional, proteomic, and metabolomic responses of wild‑type Arabidopsis and a cyp71A27 mutant to a plant‑growth‑promoting Pseudomonas fluorescens strain and a pathogenic Burkholderia glumeae strain, revealing distinct reprogramming and an unexpected signaling role for the non‑canonical P450 CYP71A27. Mutant analysis showed that loss of CYP71A27 alters gene and protein regulation, especially during interaction with the PGP bacterium, while having limited impact on root metabolites and exudates.

The study applied a CRISPR/Cas9 multiplex guide RNA strategy to delete entire open reading frames of four reproductive genes in Arabidopsis thaliana, achieving homozygous deletions already in the T1 generation with rates of 8.3–30%. Deletion efficiencies correlated with DeepSpCas9 prediction scores, and phenotypic analyses revealed unexpected effects of residual gene fragments on fertilization and seed development.