A Study of Pig Chromosome X lncRNA Expression

The advent of high-throughput sequencing technologies has revealed a wealth of long RNAs not encoding proteins, called long non coding RNAs (lncRNAs). In human, the number of lncRNA genes annotated by Gencode has kept increasing, and has now reached 15,000, a number very close to the one of protein coding genes (mRNA, 20,000). Although function is known for only a small fraction of them, the few well studied lncRNAs point to a wide variety of functions: transcriptional activators or repressors of mRNAs, miRNA blockers, or regulators of RNA degradation.

Here we present an expression study of lncRNAs in pig using RNA-seq from 8 tissues (liver, spleen, testis, brain frontal lobe, muscle, olfactory bulb, lung and lymph node) from 3 breeds (Duroc, Large White, Pietrain). After applying our standard pipeline, we restricted our expression analysis to the better assembled chromosome X from the Wellcome Trust Sanger Institute, and found 127 bona fide lncRNA genes. Of those, 88 are in the sense orientation compared to their partner mRNA (mostly intronic), and 39 are in the antisense orientation (mostly intergenic).

LncRNA gene expression analysis reveals 4 classes of genes: testis-specific, brain-specific, highly expressed in all tissues and lowly expressed in all tissues. Co-expression analysis of lncRNA genes with their partner mRNAs reveals 6 clusters of lncRNAs whose expression is either very anti-correlated or very correlated to their mRNA partner’s expression. An ubiquitous lncRNA underexpressed in liver and associated to the OTC liver specific gene seems particularly interesting, however additional data is needed to confirm the importance and function of these cases