Analysis of long non-coding RNA expression profiles in neonatal rats with hypoxic-ischemic brain damage

Hypoxic-ischemic brain damage (HIBD) which is a common cause of acute mortality and neurological dysfunction in neonates still lacks effective therapeutic methods. Long noncoding RNAs (lncRNAs) were demonstrated to play a crucial role in many diseases. To give a foundation for subsequent functional studies of lncRNAs in HIBD, we investigated the profiling of lncRNAs and messenger RNAs (mRNAs) using neonatal HIBD rat model. Six neonatal rats were divided into sham-operated group (n = 3) and HIBD group (n = 3) randomly. Deep RNA sequencing was implemented to find out the meaningful lncRNAs and mRNAs. Quantitative realtime PCR was used to validate expressions of lncRNAs and mRNAs. The Gene Ontology (GO) and kyoto encyclopedia of genes a genomes (KEGG) database were used to predict functions of lncRNAs. A total of 328 differentially expressed lncRNAs (177 down-regulated vs 151 up-regulated) and 7157 differentially expressed mRNAs (2552 down-regulated vs 4605 up-regulated) were identified. The Quantitative realtime PCR results showed significant differential expressions of five lncRNAs and five mRNAs which were consistent with the RNA-Seq data. Gene ontology and KEGG analysis showed these lncRNAs and their expression-correlated mRNAs were closely related to the Janus tyrosine kinasesignal transducer and activator of transcription (JAK-STAT) signaling pathway, NF-kappa B signaling pathway, Toll-like receptor signaling pathway, calcium signaling pathway, Notch signaling pathway, mitogen activated protein kinase signaling pathway, neuroactive ligand-receptor interaction pathway and more. The results of our study identified the characterization and expression profiles of lncRNAs in neonatal HIBD and may be a basis for further therapeutic research.