Identifying Tissue Specific Long Noncoding RNAs in the Chicken Genome

Long noncoding RNAs (lncRNAs) are transcripts that lack protein coding capabilities. These transcripts have been previously found to exhibit cell and/or tissue-specific expression, in which they may regulate expression of nearby genes, whose functions might be essential for specific cells or tissues. Tissue-specific lncRNAs have been discovered in humans and mice, but nothing is currently known for the Gallus gallus genome. This study is part of the FAANG initiative, which is working towards functionally annotating farm animal genomes. The objective of this study was to identify and verify tissue-specific lncRNAs in the chicken. LncRNAs at each tissue were identified from about 290 million RNA-seq 100bp pair-end reads from two biological replicates across eight tissues: adipose, cerebellum, cortex, hypothalamus, liver, lung, muscle and spleen. DESeq 2 and Coding Potential Calculator were used to identify tissue-specific lncRNAs; we identified approximately 234 to 1014 tissue specific lncRNAs across all eight tissues. In order to validate these tissue-specific lncRNAs, three to six candidate lncRNAs were selected and primers were designed to amplify these candidate lncRNAs. The RT-PCR results indicate that two of three muscle, one of four adipose, one of three cerebellum, one adipose, one of four cortex, and two of four liver primers tested confirmed tissue-specific lncRNAs expressions. Further confirmation of tissue-specific lncRNAs in lung and hypothalamus is underway.