title: NF-κB target microRNAs and their target genes in TNFα-stimulated HeLa cells.
abstract: As a transcription factor, NF-κB was demonstrated to regulate the expressions of miRNAs. However, only a few miRNAs have been identified as its targets so far. In this study, by using ChIP-Seq, Genechip and miRNA-Seq techniques, we identified 14 NF-κB target miRNAs in TNFα-stimulated HeLa Cells, including miR-1276, miR-1286, miR-125b-1-3p, miR-219-1-3p, miR-2467-5p, miR-3200-3p, miR-449c-5p, miR-502-5p, miR-548d-5p, miR-30b-3p, miR-3620-5p, miR-340-3p, miR-4454 and miR-4485. Of these miRNAs, 8 detected miRNAs were also NF-κB target misRNAs in TNFα-stimulated HepG2 cells. We also identified 16 target genes of 6 miRNAs including miR-125b-1-3p, miR-1286, miR-502-5p, miR-1276, miR-219-1-3p and miR-30b-3p, in TNFα-stimulated HeLa cells. Target genes of miR-125b-1-3p and miR-1276 were validated in HeLa and HepG2 cells by transfecting their expression plasmids and mimics. Bioinformatic analysis revealed that two potential target genes of miR-1276, BMP2 and CASP9, were enriched in disease phenotypes. The former is enriched in osteoarthritis, and the latter is enriched in Type 2 diabetes and lung cancer, respectively. These findings suggested that this little known miRNA might play roles in these diseases via its two target genes of BMP2 and CASP9. The expression of miR-125b-1 regulated by NF-κB has been reported in diverse cell types under various stimuli, this study found that its expression was also significantly regulated by NF-κB in TNFα-stimulated HeLa and HepG2 cells. Therefore, this miRNA was proposed as a central mediator of NF-κB pathway. These findings provide new insights into the functions of NF-κB in its target miRNA-related biological processes and the mechanisms underlying the regulation of these miRNAs.
authors.affiliation: The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China. Electronic address: zhoufei1200@163.com.
authors.forename: Fei
authors.initials: F
authors.lastname: Zhou
authors.affiliation: The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China. Electronic address: xiaojuhao_2001@163.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.affiliation: The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China; Institute of Food Safety and Detection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China. Electronic address: xingyj@seu.edu.cn.
authors.forename: Yujun
authors.initials: Y
authors.lastname: Xing
authors.affiliation: The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China. Electronic address: wtt19891202@163.com.
authors.forename: Tingting
authors.initials: T
authors.lastname: Wang
authors.affiliation: The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China. Electronic address: xxhghkk@163.com.
authors.forename: Xinhui
authors.initials: X
authors.lastname: Xu
authors.affiliation: The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China. Electronic address: wangjinke@seu.edu.cn.
authors.forename: Jinke
authors.initials: J
authors.lastname: Wang
mesh_terms: D015972:Gene Expression Regulation, Neoplastic; D006367:HeLa Cells; D056945:Hep G2 Cells; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000302:isolation & purification; D016328:NF-kappa B / Q000235:genetics* / Q000378:metabolism; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology; D014409:Tumor Necrosis Factor-alpha / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D016328:NF-kappa B; D014409:Tumor Necrosis Factor-alpha
keywords: HeLa cell; NF-κB; TNFα; Target gene; miRNA