Long non-coding RNA expression profiling of macrophage line RAW264.7 infected by Mycobacterium tuberculosis

Long non-coding RNAs (lncRNAs) have been implicated in regulation of biological processes. The role of lncRNAs in macrophages in response to Mycobacterium tuberculosis infection has not been explored. We used high throughput lncRNA microarray analysis to detect differentially expressed lncRNAs and mRNAs in RAW264.7 macrophages with or without M. tuberculosis infection. Quantitative real-time PCR (qRT-PCR) was used to verify the microarray results. Bioinformatics analysis (GO and KEGG) were used to explore the function of significantly dysregulated genes. Microarray results indicated that 1,487 lncRNAs (791 up and 696 down) and 910 mRNAs (536 up and 374 down) were expressed differentially in RAW264.7 macrophages with M. tuberculosis infection compared to controls. GO and pathway analysis revealed that up-regulated mRNAs were involved in immune response, immune system process, system development or TNF signaling pathway, and antigen processing and presentation. To the contrary, down-regulated mRNAs participated in system development, regulation of biological processes and peroxisome proliferator-activated receptor (PPAR) signaling pathway. qRT-PCR results of 10 lncRNAs and mRNAs were consistent with the microarray data. M. tuberculosis infection of macrophages caused enhanced expression of lncRNA AK151345 in a time- and dose-dependent manner. We determined comprehensive expression profiles of differentially expressed lncRNAs in RAW264.7 macrophages infected by M. tuberculosis.