Novel genes that mediate nuclear respiratory factor 1-regualted neurite outgrowth in neuroblastoma IMR-32 cells

Nuclear respiratory factor-1 (NRF-1) is a transcription factor that functions in neurite outgrowth; however, the genes downstream from NRF-1 that mediate this function remain largely unknown. This study employs a genome-wide analysis approach to identify NRF-1-targeted genes in human neuroblastoma IMR-32 cells. A total of 916 human genes containing the putative NRF-1 response element (NRE) in their promoter regions were identified using a cutoff score determined by results from electrophoretic mobility shift assays (EMSA). Seventy-four NRF-1 target genes were listed according to the typical locations and high conservation of NREs. Fifteen genes, MAPRE3, NPDC1, RAB3IP, TRAPPC3, SMAD5, PIP5K1A, USP10, SPRY4, GTF2F2, NR1D1, SUV39H2, SKA3, RHOA, RAPGEF6, and SMAP1 were selected for biological confirmation. EMSA and chromatin immunoprecipitation confirmed that all NREs of these fifteen genes are critical for NRF-1 binding. Quantitative RT-PCR demonstrated that mRNA levels of 12 of these genes are regulated by NRF-1. Overexpression or knockdown of candidate genes demonstrated that MAPRE3, NPDC1, SMAD5, USP10, SPRY4, GTF2F2, SKA3, SMAP1 positively regulated, and RHOA and RAPGEF6 negatively regulated neurite outgrowth. Overall, our data showed that the combination of genome-wide bioinformatic analysis and biological experiments helps to identify the novel NRF-1-regulated genes, which play roles in differentiation of neuroblastoma cells.

► Genome-wide bioinformatic analysis identified that the novel NRE containing genes.
► Functional assays verified that these NRE containing genes are regulated by NRF-1.
► Neurite outgrowth (NOG) assay showed that these genes are involved in this process.
► This approach is an excellent combination to identify novel genes involved in NOG.
► This study will expand our knowledge on the diverse biological processes in NOG.