Identification of long noncoding RNAs involved in adaptability to chronic hypoxic by whole transcriptome sequencing

Hypoxia has an important impact on the physiological changes of cells and organisms. Tibetan chickens have adapted to the low oxygen environment in the plateau due to long-term evolution, whereas the mechanism of hypoxia adaptation is unknown. In this study, we aimed to identify the long noncoding RNA (lncRNA) involved in hypoxia adaptation for providing insights into hypoxia-induced diseases. The heart tissues from four Tibetan chickens and four Daheng broilers were served as materials and used to RNA sequencing. The functional and pathway enrichment were used to analyze the differentially expressed lncRNA (DElncRNA). The ceRNA network was used to analyze the regulatory relationship and visualized by Cytoscape. The quantitative reverse transcription PCR (qRT-PCR) was used to test the expression of lncRNA. A total of 5504 lncRNAs and 16779 microRNAs (mRNAs) were obtained, and 70 up-regulated and 113 down-regulated lncRNAs in Tibetan chickens were identified. The DElncRNAs enriched in GO term of the protein complex localization, followed by small molecule metabolic process and RNA splicing. KEGG pathway showed that DElncRNAs were mainly enriched in pathways of regulating cell junctions and intercellular spaces, oxygen or energy metabolism for participating in hypoxic adaption. Moreover, the ceRNA network with five DElncRNAs interacted with three miRNAs acted on 42 pathways through 19 target genes. The qRT-PCR verified the expression of ENSGALG00000008047, ENSGALG00000050044, and ENSGALG00000053982 were significantly lower in Tibetan chickens. The lncRNA expression profiles of heart tissue from Tibetan chicken was obtained for the first time and provides new ideas for future research on biological adaptation to hypoxic stress.