ArticleMolecular plant pathology2024
Integrated ATAC-seq and RNA-seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa.
Article in Molecular plant pathology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 15 citations in OpenAlex.
- Functional and regulatory complexity: challenges and prospects for understanding rice WRKY transcription factors.Journal of experimental botany · 2026Review
- Integration of ATAC-seq and RNA-seq reveals temperature-responsive regulatory regions in Plasmodium falciparum asexual stages.Parasites & vectors · 2026Article
- Chromatin accessibility dynamics and a hierarchical transcriptional regulatory network for shoot apex cold stress inForestry research · 2026Article
- Recent advances in methodologies of epigenomics.Epigenomics · 2026Review
- ATAC-Seq and RNA-Seq Integration Reveals Chromatin Accessibility and Transcriptional Dynamics During Fruit Color Development in Mulberry.International journal of molecular sciences · 2026Article
- Transcriptomics Analysis Reveals an Early Response GeneCurrent issues in molecular biology · 2025Article
- Linkage: an interactive web application for linking of DNA regulatory peaks to genes.BMC genomics · 2025Article
- Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Frontiers in immunology · 2025Article
- Integration of biological and information technologies to enhance plant autoluminescence.The Plant cell · 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
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
Animal studies have shown that virus infection causes changes in host chromatin accessibility, but little is known about changes in chromatin accessibility of plants infected by viruses and its potential impact. Here, rice infected by rice stripe virus (RSV) was used to investigate virus-induced changes in chromatin accessibility. Our analysis identified a total of 6462 open- and 3587 closed-differentially accessible chromatin regions (DACRs) in rice under RSV infection by ATAC-seq. Additionally, by integrating ATAC-seq and RNA-seq, 349 up-regulated genes in open-DACRs and 126 down-regulated genes in closed-DACRs were identified, of which 34 transcription factors (TFs) were further identified by search of upstream motifs. Transcription levels of eight of these TFs were validated by reverse transcription-PCR. Importantly, four of these TFs (OsWRKY77, OsWRKY28, OsZFP12 and OsERF91) interacted with RSV proteins and are therefore predicted to play important roles in RSV infection. This is the first application of ATAC-seq and RNA-seq techniques to analyse changes in rice chromatin accessibility caused by RSV infection. Integrating ATAC-seq and RNA-seq provides a new approach to select candidate TFs in response to virus infection.
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