Impact of necrotic enteritis on long non-coding RNA expression in chicken

Abstract

<p>The poultry industry is globally affected by Necrotic enteritis (NE) due to the lack of effective preventive strategies, high mortality and reduced productivity in infected flocks. The extent to which long non-coding RNA (lncRNAs) are associated with the gene expression profile of sick chickens has yet to be understood. This study aimed to characterise the lncRNAs present in chicken and identify the cis- and trans-lncRNAs based on their location of action and association with other coding genes. Briefly, birds were inoculated with Eimeria species and Clostridium perfringens to induce NE. Tissue samples were obtained on day 16 from 12 chickens in a control group (n=6) and a challenge group (n=6). RNA sequences were obtained from the Illumina HiSeq2000 platform. The bioinformatics pipeline contemplated cleaning the sequences, aligning to the Gallus gallus reference genome (GRCg7b) with STAR, and merging the assemblies with cuffmerge from Cufflink. Transcripts were classified as lncRNAs if the length was greater than 200 bp, selected class code, lack of an open reading frame or a shorter one (< 300 nt), lack of coding potential, no miRNA precursor, more than one exon present and an average expression (FRKM) > 0.1. In total, 679 transcripts were identified as lncRNAs distributed across the genome. From these lncRNAs, 193 transcripts were classified as cis-acting due to their proximity to 359 coding genes, while the expression profile of 81 trans-acting lncRNA was associated with 219 genes. Our results provide an overview of the lncRNAs and target genes in chickens infected with NE.</p>