The conservation and signatures of lincRNAs in Marek’s disease of chicken

Abstract

Long intergenic non-coding RNAs (lincRNAs) associated with a number of cancers and other diseases have been identified in mammals, but they are still formidable to be comprehensively identified and characterized. Marek’s disease (MD) is a T cell lymphoma of chickens induced by Marek’s disease virus (MDV). Here, we used a MD chicken model to develop a precise pipeline for identifying lincRNAs and to determine the roles of lincRNAs in T cell tumorigenesis. More than 1,000 lincRNA loci were identified in chicken bursa. Computational analyses demonstrated that lincRNAs are conserved among different species such as human, mouse and chicken. The putative lincRNAs were found to be associated with a wide range of biological functions including immune responses. Interestingly, we observed distinct lincRNA expression signatures in bursa between MD resistant and susceptible lines of chickens. One of the candidate lincRNAs, termed linc-satb1, was found to play a crucial role in MD immune response by regulating a nearby protein-coding gene SATB1. Thus, our results manifested that lincRNAs may exert considerable influence on MDV-induced T cell tumorigenesis and provide a rich resource for hypothesis-driven functional studies to reveal genetic mechanisms underlying susceptibility to tumorigenesis.

Porcine endemic diarrhea virus infection regulates long noncoding RNA expression

“…These molecules can regulate gene expression much faster than proteins because the production of RNAs needs only transcription. A correlation of expression between lncRNAs and their neighboring protein-coding genes has been widely described in previous studies (Cabili et al, 2011;Guttman et al, 2011;He et al, 2015;Pauli et al, 2012;Peng et al, 2010) and observed in our study. The association of lncRNAs with chromatin-modifying complexes has been recognized as the reason for the coexpression (Khalil et al, 2009;Peng et al, 2010).…”

“…These lncRNAs were characterized by lower expression levels and shorter transcript lengths. These properties were also observed in other reported lncRNAs within the mammalian genome (Cabili et al, 2011;He et al, 2015;Peng et al, 2010;Ulitsky et al, 2011;Young et al, 2012;Boltana et al, 2016;Li et al, 2012a;Okazaki et al, 2002;Ulitsky et al, 2011). In addition, GO term enrichment analysis and KEGG pathway analysis indicated that various immune signaling pathways and antiviral responses may be regulated by cellular lncRNAs in response to PEDV infection.…”

“…It is of great interest to find that lncRNA 9606 was upregulated 400fold in the ileum and at least 300-fold in the IPEC-J2 cells during PEDV infection, which showed the highest upregulation among all identified lncRNAs in this study. Previous studies have shown that there are strong expression correlations between lncRNAs and neighboring protein-coding genes than for randomly selected protein-coding gene pairs (Cabili et al, 2011;Guttman et al, 2011;He et al, 2015;Pauli et al, 2012;Peng et al, 2010). We searched the neighboring coding transcript of lncRNA 9606 and found that the T cell receptor alpha chain V region was located within a 2 kb region from lncRNA 9606.…”

“…Previous studies have proven that there are strong expression correlations between lncRNAs and neighboring protein-coding genes than for randomly selected protein-coding gene pairs (Cabili et al, 2011;Guttman et al, 2011;He et al, 2015;Pauli et al, 2012;Peng et al, 2010). To test whether lncRNAs were preferentially located in the vicinity of protein-coding genes with specific functions, KEGG and Gene Ontology (GO) enrichment analyses were performed for the Fig.…”

“…A microarray analysis showed that the expression levels of more than 4800 lncRNAs were changed during enterovirus 71 (EV71) infection (Yin et al, 2013). Some researchers also reported the distinctive kinetics of lncRNA expression profiles during infectious bursal disease virus and Marek's disease virus infections in chicken (He et al, 2015). It was shown that lncRNAs were also involved in HIV and influenza virus infections (Rice, 2015;Trypsteen et al, 2016;Winterling et al, 2014).…”