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

Author:

Li Miaomiao12,Li Jing12,Zhang Yan2,Zhai Yushan2,Chen Yi2,Lin Lin2,Peng Jiejun2,Zheng Hongying2,Chen Jianping12,Yan Fei2,Lu Yuwen2ORCID

Affiliation:

1. College of Agriculture and Biotechnology Zhejiang University Hangzhou China

2. State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products, Institute of Plant Virology Ningbo University Ningbo China

Abstract

AbstractAnimal 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.

Funder

National Natural Science Foundation of China

Natural Science Foundation of Ningbo

Publisher

Wiley

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