ArticleBMC plant biology2024
Integrated analysis of DNA methylome and transcriptome revealing epigenetic regulation of CRIR1-promoted cold tolerance.
Article in BMC plant biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Splicing Factor SR45 Enhances Cold Tolerance in Cassava by Recruiting Nu4A Complex and Transcription Factors to Activate WRKY30.Plant, cell & environment · 2026Article
- Integrated Methylome and Transcriptome Analyses Reveal Methylation-Associated Cadmium Stress Responses inPlants (Basel, Switzerland) · 2026Article
- New insights into controlling horticultural crop quality deterioration caused by cold stress: epigenetic modification.Horticulture research · 2026Article
- Epigenetic modifications in plant abiotic stress adaptation: towards climate-resilient and sustainable crop improvement.Frontiers in plant science · 2026Review
- Review
- Integrated genomic and transcriptomic analysis reveals the mechanisms underlying leaf variegation in 'Gonggan' mandarin.BMC plant biology · 2025Article
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Authors and funding
9 authors.
Funding
Abstract
backgroundDNA methylation contributes to the epigenetic regulation of nuclear gene expression, and is associated with plant growth, development, and stress responses. Compelling evidence has emerged that long non-coding RNA (lncRNA) regulates DNA methylation. Previous genetic and physiological evidence indicates that lncRNA-CRIR1 plays a positive role in the responses of cassava plants to cold stress. However, it is unclear whether global DNA methylation changes with CRIR1-promoted cold tolerance.
resultsIn this study, a comprehensive comparative analysis of DNA methylation and transcriptome profiles was performed to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression. Compared with the wild-type plants, CRIR1-overexpressing plants present gained DNA methylation in over 37,000 genomic regions and lost DNA methylation in about 16,000 genomic regions, indicating a global decrease in DNA methylation after CRIR1 overexpression. Declining DNA methylation is not correlated with decreased/increased expression of the DNA methylase/demethylase genes, but is associated with increased transcripts of a few transcription factors, chlorophyll metabolism and photosynthesis-related genes, which could contribute to the CRIR1-promoted cold tolerance.
conclusionsIn summary, a first set of transcriptome and epigenome data was integrated in this study to reveal the gene expression and epigenetic dynamics after CRIR1 overexpression, with the identification of several TFs, chlorophyll metabolism and photosynthesis-related genes that may be involved in CRIR1-promoted cold tolerance. Therefore, our study has provided valuable data for the systematic study of molecular insights for plant cold stress response.
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