ArticleInternational journal of molecular sciences2022
Integrating ATAC-seq and RNA-seq Reveals the Dynamics of Chromatin Accessibility and Gene Expression in Apple Response to Drought.
Article in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Increased chromatin accessibility following 1α,25-dihydroxyvitamin DToxicology and applied pharmacology · 2026Article
- Deep Learning for Deciphering the Plant Cis-Regulatory Code.Plants (Basel, Switzerland) · 2026Review
- Epigenetic Memory and Hormonal Crosstalk in Plant Drought Adaptation: Mechanisms, miRNAs, and Technological Advances.Epigenomes · 2026Review
- Drought stress priming induces morphological adaptation and methylome changes in apple seedlings.BMC plant biology · 2026Article
- An integrative multi-omics analysis of histone modifications and DNA methylation reveals the epigenomic landscape in apple under drought stress.Plant biotechnology journal · 2025Article
- Redox-Epigenetic Crosstalk in Plant Stress Responses: The Roles of Reactive Oxygen and Nitrogen Species in Modulating Chromatin Dynamics.International journal of molecular sciences · 2025Review
- ISDH-seq: a robust methodology for profiling and characterization of open chromatin.Plant biotechnology journal · 2025Article
- Integration of ATAC-seq and RNA-seq reveals the dynamics of chromatin accessibility and gene expression in zoysiagrass response to drought.Plant cell reports · 2025Article
- CRISPR/dCas13(Rx) Derived RNA NAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Epigenetic Modifications of Hormonal Signaling Pathways in Plant Drought Response and Tolerance for Sustainable Food Security.International journal of molecular sciences · 2024Review
- Phenomics and transcriptomic profiling of fruit development in distinct apple varieties.Scientific data · 2024Article
- Integrated ATAC-seq and RNA-seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa.Molecular plant pathology · 2024Article
- Dynamics of chromatin accessibility and genome wide control of desiccation tolerance in the resurrection plant Haberlea rhodopensis.BMC plant biology · 2023Article
- Review
- Integrated ATAC-Seq and RNA-Seq Data Analysis to RevealInternational journal of molecular sciences · 2023Article
- Chromatin dynamics associated with seed desiccation tolerance/sensitivity at early germination inFrontiers in plant science · 2022Article
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10 authors.
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Abstract
Drought resistance in plants is influenced by multiple signaling pathways that involve various transcription factors, many target genes, and multiple types of epigenetic modifications. Studies on epigenetic modifications of drought focus on DNA methylation and histone modifications, with fewer on chromatin remodeling. Changes in chromatin accessibility can play an important role in abiotic stress in plants by affecting RNA polymerase binding and various regulatory factors. However, the changes in chromatin accessibility during drought in apples are not well understood. In this study, the landscape of chromatin accessibility associated with the gene expression of apple (GL3) under drought conditions was analyzed by Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq. Differential analysis between drought treatment and control identified 23,466 peaks of upregulated chromatin accessibility and 2447 peaks of downregulated accessibility. The drought-induced chromatin accessibility changed genes were mainly enriched in metabolism, stimulus, and binding pathways. By combining results from differential analysis of RNA-seq and ATAC-seq, we identified 240 genes with higher chromatin accessibility and increased gene expression under drought conditions that may play important functions in the drought response process. Among them, a total of nine transcription factor genes were identified, including ATHB7, HAT5, and WRKY26. These transcription factor genes are differentially expressed with different chromatin accessibility motif binding loci that may participate in apple response to drought by regulating downstream genes. Our study provides a reference for chromatin accessibility under drought stress in apples and the results will facilitate subsequent studies on chromatin remodelers and transcription factors.
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