Identification of Bovine Long Noncoding RNA Using Single-Molecule Transcript Sequencing

Long noncoding RNAs (lncRNA) lack the ability to code for protein, but serve as key regulators of diverse biological processes and can, for example, alter chromatin structure and regulate gene expression at the transcriptional and post-transcriptional levels. Criteria for identifying lncRNA sequences include lack of coding potential, lack of similarity to other noncoding RNA classes, and usually at least 200 nucleotides in length. One challenge in lncRNA identification is that they often lack evolutionary sequence conservation. Identifying the full repertoire of lncRNA in bovine remains a computational and technological challenge.  We have used PacBio’s Iso-Seq RNA sequencing technology supplemented with short read RNAseq (Illumina 100bp single-end) to identify bovine lncRNA and determine their expression values for various tissues. The bovine genome and transcriptome are filled with repetitive elements, making it difficult to accurately align short RNAseq reads to the genome. Some advantages of Iso-Seq are that long read lengths allow us to identify lncRNA that have repeats and to avoid splitting of predicted lncRNA into fragments, and the high proportion of sense strand reads in Iso-Seq provides confidence for the prediction of single exon lncRNA. This study adds to the growing list of lncRNA identified in the bovine genome.