Long Noncoding RNAs Identified by RNAseq-Based Whole Transcriptome Analysis in the Jejunum of Pre-Weaned Calves

The functional annotation of the bovine genome is still incopmplete compared to that of model organisms or human. However, whole transcriptome sequencing (RNAseq) provides the tool for an accurate and holistic identification of novel, previously unknown functionally relevant loci in the genome. Particularly, long noncoding RNAs (lncRNAs) are emerging as important regulatory component of mechanisms involved in chromatin modification or epigenetic regulation. Our study monitored the whole transcriptome of the jejunum in male German Holstein calves fed two different diets (6 animals per group). The calves were slaughtered at about 81 days after birth and epithelial sections of the jejunum were collected and snap frozen in liquid nitrogen. Total RNA isolated from jejunum samples was used to prepare indexed, stranded sequencing libraries. After paired-end sequencing (2x 80 bp, Illumina HiSeq2500) and quality control of the sequencing data the reads were aligned to the bovine genome. The transcripts were assembled with an annotation-guided approach enabling discovery of yet unannotated genes and transcripts. About 88% of reads (from an average of 56.8 million paired-end reads obtained per sample) mapped to the bovine genome. In addition to known protein coding genes varying between 18,395 and 20,904 per sample, 16,378 novel transcripts were identified in the jejunal transcriptomes of the calves. To annotate lncRNAs from unknown RNAseq-assembled transcripts, the bioinformatic tool FEELnc is applied, which identifies novel lncRNAs and mRNA isoforms and also classifies lncRNAs into intergenic lncRNAs (lincRNAs) and genic sense or antisense lncRNAs.