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Integrated mRNA and microRNA Transcriptome Sequencing Characterizes Sequence Variants and mRNA-microRNA Regulatory Networks in Grass Carp Fibroblasts Infected with Virulent and Attenuated GCRV

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Abstract

Grass carp hemorrhagic disease is a fatal disease caused by the grass carp reovirus (GCRV). The aberrant regulation of transcripts has been implicated in many types of diseases. In the present study, we characterized mRNA and miRNA transcriptomes of different virulent GCRVs using RNA sequencing (RNA-Seq). One hundred eighteen miRNAs were identified as being differentially expressed between different virulent viruses in grass carp fibroblasts. Eight miRNAs were selected to verify the RNA-Seq results using RT-PCR and mRNA methods. In total, 996 differentially expressed mRNA genes were identified in grass carp fibroblasts, while 901 miRNA-mRNA target pairs were observed to be inversely regulated in grass carp fibroblasts. Integrated mRNA/miRNA expression profiling analysis results showed that the most influenced processes were the immune response and cell death. Three miRNAs were shown to exhibit the same expression patterns when two different methods were used and had important functions during viral infection. These results provide insights into the miRNA-mediated regulation of mRNA and valuable resources on transcript variation and regulation during GCRV infection, which are potentially useful for mechanistic and drug studies.

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Funding

This work was supported by the Innovation and Strengthening Project of Guangdong Ocean University (230419067), the Innovative Strong School Engineering Key Platform Projects by the Department of Education in Guangdong Province (Q2018302) and a PhD Start-up grant (521202292).

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Authors and Affiliations

  1. College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, People’s Republic of China

    Qiucheng Yao, Mengdi Zhang, Weitian Xie, Jinjun Chen, Zhibao Chen, Ye Ge & Zhihui Zhao

  2. Haikou Customs District P.R. China, Haikou, Hainan, China

    Shaopo Zu

  3. Nanchang Animal Disease Prevention and Control Center, Jiangxi, Nanchang, People’s Republic of China

    Hong Yang

  4. School of Life Science and Engineering, Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Foshan University, Foshan, 528231, China

    Weiwei Zeng

  5. Key Laboratory of Fishery Drug Development, Ministry of Agriculture, Key Laboratory of Aquatic Animal Immune Technology, Guangdong Province, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510380, People’s Republic of China

    Weiwei Zeng

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  1. Qiucheng Yao
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  2. Mengdi Zhang
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  3. Shaopo Zu
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  4. Hong Yang
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  5. Weitian Xie
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  6. Jinjun Chen
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  7. Zhibao Chen
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  8. Ye Ge
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  9. Weiwei Zeng
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  10. Zhihui Zhao
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Contributions

Ye Ge designed the experiments, wrote the manuscript, participated in obtaining funding. Mengdi Zhang performed the RT-qPCR experiment. Shaopo Zu and Hong Yang gave some suggestions in manuscript. Jinjun Chen and Zhibao Chen provided some suggestions regarding the experiments. Weitian Xie prepared the reagents used throughout the study. Qiucheng Yao revised the manuscript and participated in obtaining funding. Weiwei Zeng performed the infection experiment and support the infected place. Zhihui Zhao participated in obtaining funding.

Corresponding authors

Correspondence to Ye Ge, Weiwei Zeng or Zhihui Zhao.

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Yao, Q., Zhang, M., Zu, S. et al. Integrated mRNA and microRNA Transcriptome Sequencing Characterizes Sequence Variants and mRNA-microRNA Regulatory Networks in Grass Carp Fibroblasts Infected with Virulent and Attenuated GCRV. Mar Biotechnol 23, 342–355 (2021). https://doi.org/10.1007/s10126-021-10029-4

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  • DOI: https://doi.org/10.1007/s10126-021-10029-4

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