A Comprehensive Set of lncRNAs on Porcine Chromosome X

Long non-coding RNAs (lncRNAs) are important players in the regulation of gene expression and therefore are involved in many cellular processes (e.g. embryonic stem cell (ESC) pluripotency, neurogenesis, cardiogenesis, and cell-cycle regulation) and pathologies (e.g. neurodegenerative disorders). Moreover, it has been shown that some lncRNA genes, which in cattle are expressed in muscles, are located within quantitative trait loci for meat quality traits. Thanks to GENCODE project, to date best annotation of lncRNAs is for the human genome. In contrast, the knowledge of lncRNAs in other mammals still requires substantial improvements. The analysis of lncRNAs conservation among species can be done at four different levels: sequence, secondary structure, and function homologies, as well as syntenic transcription. Our aim is to identify tissue-specific pig lncRNAs in newly assembled porcine X chromosome (Wellcome Trust Sanger Institute) using 18 RNA-seq data sets derived from eight different tissues. All assembled novel transcripts were assessed for their protein-coding potential using both bioinformatic and manual curation strategies in order to define a set of lncRNAs candidates. A further set of potential lncRNAs was retrieved using secondary structure homology to known lncRNAs in other species. Moreover, we are looking for lncRNAs transcribed from genomic blocks syntenic across pig, human, and mouse, as well as for conserved splice sites. At the PAG XXV I will present the most recent results of our lncRNA prediction analysis.