Integrated ATAC‐seq and RNA‐seq data analysis identifies transcription factors related to rice stripe virus infection in Oryza sativa

Molecular Plant Pathology, Journal Year: 2024, Volume and Issue: 25(3)

Published: March 1, 2024

Abstract Animal studies have shown that virus infection causes changes in host chromatin accessibility, but little is known about accessibility of plants infected by viruses and its potential impact. Here, rice stripe (RSV) was used to investigate virus‐induced accessibility. Our analysis identified a total 6462 open‐ 3587 closed‐differentially accessible regions (DACRs) under RSV ATAC‐seq. Additionally, integrating ATAC‐seq RNA‐seq, 349 up‐regulated genes open‐DACRs 126 down‐regulated closed‐DACRs were identified, which 34 transcription factors (TFs) further search upstream motifs. Transcription levels eight these TFs validated reverse transcription‐PCR. Importantly, four (OsWRKY77, OsWRKY28, OsZFP12 OsERF91) interacted with proteins are therefore predicted play important roles infection. This the first application RNA‐seq techniques analyse caused Integrating provides new approach select candidate response

Language: Английский

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Chromatin accessibility and differentially expressed genes profiling in large yellow croaker (Larimichthys crocea) head kidney cells following iridovirus infection

Frontiers in Immunology, Journal Year: 2025, Volume and Issue: 16

Published: Jan. 30, 2025

Introduction The large yellow croaker iridovirus (LYCIV) poses a significant threat to the aquaculture industry of Larimichthys crocea . Understanding host defense response LYCIV infection is crucial for developing effective strategies mitigate its impact. Methods In this study, an epigenetic approach was employed investigate dynamic changes in chromatin accessibility using assay transposase-accessible with high-throughput sequencing (ATAC-seq). Additionally, RNA (RNA-seq) used analyze expression pattern immune genes upon infection. Results Substantial alterations were observed, particularly regulatory regions key immune-related genes. Significant AP-1 transcription factors, including Batf gene, noted. CUT&Tag results revealed that significantly enriched open cytokine genes, potentially regulating LIF and CLCF1 Discussion These findings suggest may play role against viral by modulating inflammatory cytokines contributing cellular responses. This study provides comprehensive analysis epigenomic landscape gene regulation during L. , offering valuable insights breeding programs aimed at combating infections.

Language: Английский

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Integration of biological and information technologies to enhance plant autoluminescence

The Plant Cell, Journal Year: 2024, Volume and Issue: 36(11), P. 4703 - 4715

Published: Aug. 21, 2024

Abstract Autoluminescent plants have been genetically modified to express the fungal bioluminescence pathway (FBP). However, a bottleneck in precursor production has limited brightness of these luminescent plants. Here, we demonstrate effectiveness utilizing computational model guide multiplex five-gene-silencing strategy by an artificial microRNA array enhance caffeic acid (CA) and hispidin levels By combining loss-of-function-directed metabolic flux with tyrosine-derived CA pathway, achieved substantially enhanced levels. We successfully generated eFBP2 that emit considerably brighter for naked-eye reading integrating all validated DNA modules. Our analysis revealed luminous energy conversion efficiency is currently very low, suggesting luminescence intensity can be improved future iterations. These findings highlight potential plant through integration biological information technologies.

Language: Английский

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Linkage: an interactive shiny app and R package for linking of DNA regulatory peaks to genes

Published: April 28, 2024

Abstract Summary Existing studies have demonstrated that the integration analysis of transcriptomic and epigenomic data can be used to better understand onset progression many diseases, as well identify new diagnostic prognostic biomarkers. However, such investigations on large-scale sequencing remain challenging for researchers or clinicians with limited bioinformatics knowledge. To facilitate interpretation gene regulatory landscape, we developed an R Shiny application package [ Link ing a tac-seq g ene e xpression (Linkage)] exploring visualizing potential cis-regulatory elements (CREs) genes based ATAC-seq RNA-seq data. Linkage offers six modules systematically identify, annotate, interpret from whole genome step by step. provide interactive visualization correlation between chromatin accessibility expression. More than that, identifies transcription factors (TFs) potentially drive changes through identifying TF binding motifs within CREs constructing trans-regulatory networks target set. This powerful tool enables conduct extensive multiomics generate visually appealing visualizations effectively highlight relationship corresponding elements. With Linkage, users obtain publishable results gain deeper insights into landscape. Availability implementation ‘Linkage’ is freely available web ( https://xulabgdpu.org.cn/linkage ) https://github.com/XuLab-GDPU/Linkage ). The documentation at https://aicplane.github.io/Linkage-tutorial/

Language: Английский

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Genome-wide chromatin accessibility profiles in spleen of GIFT strain of Nile tilapia (Oreochromis niloticus) in response to Streptococcus agalactiae infection as revealed by ATAC-seq and RNA-seq

Aquaculture, Journal Year: 2024, Volume and Issue: unknown, P. 742079 - 742079

Published: Dec. 1, 2024

Language: Английский

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