Identification of Specific Long Noncoding RNA Profiles in Chicken with Different Susceptibility to Marek's Disease

Marek’s disease (MD) is an avian herpesvirus-induced lymphoma in chicken, which causes more than $1 billion economic loss in poultry industry worldwide. Breeding of genetically resistant chicken lines has become an important measure in MD control to augment vaccination. Evidently, a better understanding in the mechanism of genetic resistant to MD could empower the breeding for resistance. Long noncoding RNAs (lncRNAs) are a group of RNAs that are not protein-coding and are longer than 200 nucleotide (nt). Although only about 100 lncRNAs have been functionally annotated, they were found functionally involved in gene expression, chromatin structure regulation, and in various disease development in mammals. To study the potential functionality of lncRNA in MD resistance, we performed genome-wide transcriptome analysis of CD4⁺ T cells from two chicken lines either resistant or susceptible to MD on Illumina Hi-Seq 2000. After mapping the sequence reads back to the chicken genome by TopHat, we assembled the transcripts by Cufflinks. The assembled transcripts were then compared with the known transcripts in public databases including Ensembl and GenBank to identify novel transcripts. The lncRNAs were then predicted from the novel transcripts by excluding those less than 200nt and also those having an open reading frame (ORF) longer than 180nt. Thus, a total of 2,626 lncRNAs were identified in our samples. Of which 1,177 lncRNAs were found only in the MD-resistant chickens and 1,048 lncRNAs were found only in the MD-susceptible chickens. The dramatic difference of lncRNA enrichment in the two chicken lines indicated that the lncRNAs may play a role in MD resistance or susceptibility. Our research in lncRNAs provides useful information for further mechanism studies of disease resistance.