Long Non-Coding RNA (lncRNA) Is Abundantly Expressed in the Gastro Intestinal Tract of Calves

Long non-coding RNA (lncRNA) constitutes the largest portion of the mammalian non-coding transcriptome and information on its regulation of gene expression and involvement in many biological processes is beginning to emerge.  While relatively more is known about occurrence and functions of lncRNA in the human genome, little information exist on bovine. To gain insights into the occurrence, expression pattern and possible functions of lncRNA in the gastro-intestinal-tract of calves, rumen and ileum tissue samples from 32 calves were subjected to next-generation RNA sequencing (RNA-Seq). Calves were managed following standard procedures. Sixteen calves were humanely euthanized at 33 days of age (pre-weaning) and another sixteen at 96 days of age (post-weaning) for collection of ileum and rumen tissue samples. Total RNA from tissues were subjected to 100 bp paired end RNA-Seq. Sequencing generated 1,919,500,055 unique reads corresponding to approximately 79% of the total after alignment against the bovine genome (UMD3.1). Reads were assembled into transcripts using Cufflinks v2.2.1. Transcripts ≥180 nt were retained and those that matched to small ncRNA, tRNA, rRNA and mRNA were removed. Coding potential of transcripts were assessed using Coding-Non-Coding Index and Coding Potential Assessment Tool programs and only transcripts that were considered by both softwares as non-coding were kept. Finally, transcripts with no hit in Swiss-Prot database were retained. Using NONCODE data base as a reference, a total of 715 and 631 known and 37687 and 25682 novel lncRNAs were identified respectively in ileum and colon tissues. This number is higher than the number of bovine lncRNAs deposited in NONCODE data base. In Rumen, more lncRNAs were identified on day 33 as compared to day 96. Majority of identified lncRNAs are located within intergenic regions followed by intronic regions. Furthermore, more than half of identified lncRNAs are composed of one exon followed by two and three exons. Some lncRNAs had >7 exons. Our data suggest that lncRNAs may play roles in the development of the gastro-intestinal tract and that they are widely distributed in the bovine genome. Computational challenges in managing lncRNA data abound and no unified system of nomenclature exist.