{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Munissa Sadykova"],"organism":["Arabidopsis thaliana"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16096"],"description":["Stress priming is a critical adaptive mechanism that enables plants to enhance responses to recurring environmental stresses. While transcriptomic changes associated with cold stress priming have been reported, the underlying epigenetic mechanisms remain largely unknown. In this study, we investigated transcriptomic and DNA methylation dynamics in cold-primed and non-primed Arabidopsis thaliana plants. Cold stress induces distinct gene expression patterns between primed and non-primed plants, accompanied by DNA methylation changes across all cytosine contexts in both protein-coding genes and transposable elements (TEs). Notably, CHH methylation within gene bodies and TEs is markedly reduced in cold-primed plants, suggesting a role for DNA hypomethylation in establishing cold stress memory. This hypomethylation correlates with decreased expression of the CMT2 DNA methyltransferase and components of the RNA-directed DNA methylation (RdDM) pathway, indicating a passive demethylation process during cold treatment. Furthermore, DNA methylation mutants exhibit enhanced cold stress memory, highlighting the role of methylation in preventing spurious gene activation and maintaining priming specificity. Particularly, met1, deficient in CG methylation, shows reduced methylation at the CBF gene cluster, correlating with their overexpression and enhanced activation of downstream cold-responsive genes. Our findings show that DNA methylation modulates cold stress memory by shaping chromatin and ensuring transcriptional precision."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was extracted from 100 mg of frozen samples with the Maxwell® 16 LEV Plant RNA Kit (Promega Corporation, USA) following instructions from the manufacturer.","Growth Protocol - Plants were grown in 0.5x Murashige and Skoog (MS) media with 0.8% agar with 0.1% sucrose content at 22°C with a long day (16 h light / 8 h dark) for 9 days, then transferred to soil for stress treatment and until the sample collection.","Sequencing - Paired-end sequencing with NovaSeq 6000 (Illumina).","Library Construction - RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, USA).","Sample Collection - RNA-seq was performed for 25-days-old Arabidopsis thaliana plants grown in control conditions (22°C) (non-primed, C), plants primed with cold stress at 4°C for 3 days (Priming only, P), plants triggered with cold stress at 4°C for 3 days (Triggering only, T), and the primed and triggered plants (Priming and Triggering, PT). Leaf samples of the plants were collected."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - RNA-seq results were analyzed using the nf-core pipeline “rnaseq” (revision 3.10.1). In short, reads quality check was performed with FastQC (v. 0.11.9), and adapters were trimmed using Trim Galore! software (v. 0.6.7). Reads were mapped with STAR (v. 2.7.9a) and quantified with Salmon (v. 1.9.0). The output of Salmon (quant.sf) was used as processed files."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Arabidopsis thaliana"],"pubmed_authors":["Munissa Sadykova"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptome and epigenome dynamics of cold stress priming in Arabidopsis thaliana.","description":"Stress priming is a critical adaptive mechanism that enables plants to enhance responses to recurring environmental stresses. While transcriptomic changes associated with cold stress priming have been reported, the underlying epigenetic mechanisms remain largely unknown. In this study, we investigated transcriptomic and DNA methylation dynamics in cold-primed and non-primed Arabidopsis thaliana plants. Cold stress induces distinct gene expression patterns between primed and non-primed plants, accompanied by DNA methylation changes across all cytosine contexts in both protein-coding genes and transposable elements (TEs). Notably, CHH methylation within gene bodies and TEs is markedly reduced in cold-primed plants, suggesting a role for DNA hypomethylation in establishing cold stress memory. This hypomethylation correlates with decreased expression of the CMT2 DNA methyltransferase and components of the RNA-directed DNA methylation (RdDM) pathway, indicating a passive demethylation process during cold treatment. Furthermore, DNA methylation mutants exhibit enhanced cold stress memory, highlighting the role of methylation in preventing spurious gene activation and maintaining priming specificity. Particularly, met1, deficient in CG methylation, shows reduced methylation at the CBF gene cluster, correlating with their overexpression and enhanced activation of downstream cold-responsive genes. Our findings show that DNA methylation modulates cold stress memory by shaping chromatin and ensuring transcriptional precision.","dates":{"release":"2026-03-13T00:00:00Z","modification":"2026-03-13T02:02:32.677Z","creation":"2025-11-12T12:13:59.733Z"},"accession":"E-MTAB-16096","cross_references":{"ENA":["ERP184283"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0003789","EFO_0005518","EFO_0003816","EFO_0004184"]}}