Expression profile screening and bioinformatics analysis of CircRNA, LncRNA, and mRNA in HeLa cells infected with Chlamydia muridarum

We have previously shown that circRNAs in host cells are involved in the process of Chlamydia trachomatis infection. In this study we aimed to identify significantly altered circRNAs/lncRNAs/mRNAs in Chlamydia muridarum infected cells and investigate their biological functions in the interaction between Chlamydia muridarum and host cells. For this purpose, circRNA, lncRNA and mRNA expression profiles were screened and identified in HeLa cells with or without Chlamydia muridarum infection by microarray. Bioinformatics analyses including Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) analysis were then carried out and the circRNA-miRNA ceRNA network was constructed. The differentially expressed circRNAs and lncRNAs were selected for validation by RT-qPCR. The results shown that a total of 834 circRNAs, 2149 lncRNAs and 1283 mRNAs were found to be differentially expressed. Enrichment analysis of GO and KEGG showed that the dysregulated genes involved nuclear-transcribed mRNA catabolic process, protein binding, RNA catabolic process and translation, the MAPK signaling pathway, apoptosis, Toll-like receptor signaling pathway, cAMP signaling pathway and Notch signaling pathway may play important roles in Chlamydia infection. Our study provides a systematic outlook on the potential function of non-coding RNAs in the molecular basis of Chlamydia infection.