Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain

Long non-coding RNAs (lncRNAs) are the master regulators of numerous biological processes. Hypoxia causes oxidative stress with severe and detrimental effects on brain function and acts as a critical initiating factor in the pathogenesis of Alzheimer9s disease (AD). However, no data are available on the roles of lncRNAs and their target genes under hypoxia in the zebrafish brain. From the RNA-Seq in the forebrain (Fb), midbrain (Mb), and hindbrain (Hb) regions of hypoxic and normoxic zebrafish, we identified 8114, 7775, and 7816 novel lncRNA transcripts in the Fb, Mb, and Hb regions, respectively. In comparison to the normoxic group, hypoxic fish showed differential expression of 357, 553, and 786 novel lncRNA genes in the Fb, Mb, and Hb regions, respectively. Co-expression network analysis identified a series of lncRNA-mRNA pairs in all the regions, which were enriched for AD. In conclusion, functional annotation of lncRNAs induced by hypoxia provided knowledge on potential regulators for genes participating in AD pathogenesis.