Short communication MicroRNA profile analysis of Epithelioma papulosum cyprini cell line before and after SVCV infection Shusheng Wu a,b,c , Liyue Liu a,b,c , Ali Zohaib d , Li Lin a,b,c , Junfa Yuan a,b,c , Min Wang a , Xueqin Liu a,b,c, * a Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China b Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Wuhan 430070, China c Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan 430070, China d State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Hubei, Wuhan 430070, China ARTICLE INFO Article history: Received 9 July 2014 Revised 29 September 2014 Accepted 30 September 2014 Available online 5 October 2014 Keywords: Spring viremia of carp virus EPC cell miRNA Solexa sequencing A B ST R AC T MicroRNAs (miRNAs) play significant roles in regulating almost all of the biological processes in eukary- otes. An accumulating body of evidence shows that miRNAs are associated with cellular changes following viral infection. Spring viremia of carp virus (SVCV) is the pathogen of Spring viremia of carp (SVC), which results in heavy losses in the cultured common carp (Cyprinus carpio) industry in many countries. To study the involvement of miRNAs during SVCV infection, we adopted the Solexa sequencing technology to se- quence small RNA libraries from the Epithelioma papulosum cyprini (EPC) cell line before and after infection with SVCV. In this study, a total of 161 conserved and 26 novel miRNAs were identified. Subsequently, the expression patterns of these miRNAs were compared between the uninfected (control library, M) and SVCV-infected (infection library, E) libraries. In addition, to verify the Solexa sequencing results, the ex- pression patterns of 14 randomly selected miRNAs were validated by qRT-PCR. The targets of the significantly differentially expressed miRNAs were then predicted, and the miRNAs that could directly target the SVCV genome were also predicted. No miRNA encoded by SVCV itself was detected. To the best of our knowl- edge, this study presents the first miRNA profiling assessment in association with fish rhabdovirus infection, and the data presented lay a foundation for further investigations to determine the roles of miRNAs in regulating the molecular mechanism during SVCV infection. © 2014 Elsevier Ltd. All rights reserved. 1. Introduction miRNAs are small (~22 bp), endogenous non-coding RNAs (Bartel, 2007) that regulate gene expression through their sequence- specific binding to their target genes, particularly by targeting the 3′UTR of mRNAs, to cause transcript degradation or translational repression (Sontheimer and Carthew, 2005). These miRNAs are in- volved in almost all of the biological processes that occur in eukaryotes, such as apoptosis (Xu et al., 2003), cell differentiation and proliferation (Xiao et al., 2007), DNA repair (Adenovirus, 2010), innate and adaptive immunity (Ou et al., 2012) and stress re- sponses (Brzuzana et al., 2012; Yan B et al., 2012). Recent studies have also unveiled the role of miRNAs in modulating host–virus in- teractions (Scaria et al., 2006). Because the propagation of a virus relies highly on the host cell, the complex cellular regulatory network can have a major effect on viral replication (Sun et al., 2014). As cel- lular regulators, miRNAs play a role in the self-protection process (Lagos et al., 2010). To combat these, some viruses hijack the miRNA– mRNA cross-talk function (Grey et al., 2010). Therefore, the study of miRNA-mediated host–virus interactions may contribute to a deeper understanding of the mechanisms of virus infection and host counteraction. Spring viremia of carp virus (SVCV) is the pathogen of Spring viremia of carp (SVC), which results in heavy losses to the cul- tured common carp (Cyprinus carpio) industry in many countries (Ahne et al., 2002; Dikkeboom et al., 2004; Garver et al., 2007; Liu et al., 2004). It is a single-stranded negative-sense RNA virus of the genus Vesiculovirus with a genome approximately 11 kb in length that encodes five structural proteins: nucleoprotein (N), phospho- protein (P), matrix protein (M), glycoprotein (G), and RNA-dependent polymerase (L) (Fauquet et al., 2005; Liu et al., 2013; Teng et al., 2007). At present, the pathogenic mechanism of SVCV infection is poorly understood. To date, the involvement of miRNAs during SVCV infection has not been reported. Based on this information, we aimed to determine the repertoire of miRNAs expressed in the EPC cell line and to use this repertoire to study the responses of this cell line to * Corresponding author. College of Fisheries, Huazhong Agricultural University, Wuhan Agricultural University, Shizishan Street No. 1, Wuhan 430070, China. Tel.: +86 27 87282113; fax: 027-87282113. E-mail address: xueqinliu@mail.hzau.edu.cn (X. Liu). http://dx.doi.org/10.1016/j.dci.2014.09.012 0145-305X/© 2014 Elsevier Ltd. All rights reserved. Developmental and Comparative Immunology 48 (2015) 124–128 Contents lists available at ScienceDirect Developmental and Comparative Immunology journal homepage: www.elsevier.com/locate/dci