Integrative transcriptome analysis reveals alternative polyadenylation potentially contributes to GCRV early infection

Sheng Tan; Jie Zhang; Yonglin Peng; Wenfei Du; Jingxuan Yan; Qin Fang

doi:10.3389/fmicb.2023.1269164

Integrative transcriptome analysis reveals alternative polyadenylation potentially contributes to GCRV early infection

Front Microbiol. 2023 Nov 3:14:1269164. doi: 10.3389/fmicb.2023.1269164. eCollection 2023.

Authors

Sheng Tan^#¹, Jie Zhang^#^{2

3}, Yonglin Peng^#¹, Wenfei Du¹, Jingxuan Yan⁴, Qin Fang²

Affiliations

¹ Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai, Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
² State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.
³ Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.
⁴ Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.

^# Contributed equally.

Abstract

Introduction: Grass carp reovirus (GCRV), a member of the Aquareovirus genus in the Reoviridae family, is considered to be the most pathogenic aquareovirus. Productive viral infection requires extensive interactions between viruses and host cells. However, the molecular mechanisms underlying GCRV early infection remains elusive.

Methods: In this study we performed transcriptome and DNA methylome analyses with Ctenopharyngodon idellus kidney (CIK) cells infected with GCRV at 0, 4, and 8 h post infection (hpi), respectively.

Results: We found that at early infection stage the differentially expressed genes related to defense response and immune response in CIK cells are activated. Although DNA methylation pattern of CIK cells 8 hpi is similar to mock-infected cells, we identified a considerable number of genes that selectively utilize alternative polyadenylation sites. Particularly, we found that biological processes of cytoskeleton organization and regulation of microtubule polymerization are statistically enriched in the genes with altered 3'UTRs.

Discussion: Our results suggest that alternative polyadenylation potentially contributes to GCRV early infection.

Keywords: Aquareovirus genus; Ctenopharyngodon idellus; DNA methylation; alternative polyadenylation; grass carp reovirus.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was supported by the National Natural Science Foundation of China grant (31972838 and 82173231).