The long non-coding RNA LNC_000397 negatively regulates PRRSV replication through induction of interferon-stimulated genes

Jing Zhang; Lipeng Gan; Pu Sun; Jian Wang; Dong Li; Yimei Cao; Yuanfang Fu; Pinghua Li; Xingwen Bai; Kun Li; Xueqing Ma; Huifang Bao; Yingli Chen; Jie Zhang; Zaixin Liu; Zengjun Lu

doi:10.1186/s12985-022-01761-x

The long non-coding RNA LNC_000397 negatively regulates PRRSV replication through induction of interferon-stimulated genes

Virol J. 2022 Mar 5;19(1):40. doi: 10.1186/s12985-022-01761-x.

Authors

Jing Zhang¹, Lipeng Gan², Pu Sun², Jian Wang², Dong Li², Yimei Cao², Yuanfang Fu², Pinghua Li², Xingwen Bai², Kun Li², Xueqing Ma², Huifang Bao², Yingli Chen², Jie Zhang², Zaixin Liu³, Zengjun Lu⁴

Affiliations

¹ State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot-and-Mouth Disease Reference Laboratory of China, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping No.1, Yanchangpu, Lanzhou, 730046, Gansu, China. zhangjing@caas.cn.
² State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot-and-Mouth Disease Reference Laboratory of China, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping No.1, Yanchangpu, Lanzhou, 730046, Gansu, China.
³ State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot-and-Mouth Disease Reference Laboratory of China, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping No.1, Yanchangpu, Lanzhou, 730046, Gansu, China. liuzaixin@caas.cn.
⁴ State Key Laboratory of Veterinary Etiological Biology, OIE/National Foot-and-Mouth Disease Reference Laboratory of China, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xujiaping No.1, Yanchangpu, Lanzhou, 730046, Gansu, China. luzengjun@caas.cn.

Abstract

Background: Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most significant threats to the global swine industry. It is of great importance to understand viral-host interactions to develop novel antiviral strategies. Long non-coding RNAs (lncRNAs) have emerged as critical factors regulating host antiviral immune responses. However, lncRNAs participating in virus-host interactions during PRRSV infection remain largely unexplored.

Method: RNA transcripts of porcine alveolar macrophages (PAMs) infected with two different PRRSV strains, GSWW/2015 and VR2332, at 24 h post-infection were sequenced by high-throughput sequencing. Four programs namely, CNCI, CPC, PFAM, and phyloCSF, were utilized to predict the coding potential of transcripts. mRNAs co-localized or co-expressed with differentially expressed lncRNAs were considered as their targets. Fuction of lncRNAs was predicted by GO and KEGG analysis of their target mRNAs. The effect of LNC_000397 on PRRSV replication was validated by knockdown its expression using siRNA. Target genes of LNC_000397 were identified by RNA-Sequencing and validated by RT-qPCR.

Result: In this study, we analyzed lncRNA and mRNA expression profiles of PRRSV GSWW/2015 and VR2332 infected porcine alveolar macrophages. A total of 1,147 novel lncRNAs were characterized, and 293 lncRNAs were differentially expressed. mRNAs co-localized and co-expressed with lncRNAs were enriched in pathogen-infection-related biological processes such as Influenza A and Herpes simplex infection. Functional analysis revealed the lncRNA, LNC_000397, which was up-regulated by PRRSV infection, negatively regulated PRRSV replication. Knockdown of LNC_000397 significantly impaired expression of antiviral ISGs such as MX dynamin-like GTPase 1 (MX1), ISG15 Ubiquitin-like modifier (ISG15), and radical S-adenosyl methionine domain containing 2 (RSAD2).

Conclusions: LNC_000397 negatively regulated PRRSV replication by inducing interferon-stimulated genes (ISGs) expression. Our study is the first report unveiling the role of host lncRNA in regulating PRRSV replication, which might be beneficial for the development of novel antiviral therapeutics.

Keywords: Antiviral; Interferon; PRRSV; RNA-Sequencing; lncRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Antiviral Agents / metabolism
Interferons / metabolism
Macrophages, Alveolar
Porcine Reproductive and Respiratory Syndrome* / genetics
Porcine respiratory and reproductive syndrome virus* / genetics
Porcine respiratory and reproductive syndrome virus* / metabolism
RNA, Long Noncoding* / genetics
RNA, Long Noncoding* / metabolism
Swine
Virus Replication

Substances

Antiviral Agents
RNA, Long Noncoding
Interferons