title: Novel genes that mediate nuclear respiratory factor 1-regualted neurite outgrowth in neuroblastoma IMR-32 cells.
abstract: 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.
authors.affiliation: Department of Physiology, National Cheng Kung University, College of Medicine, Tainan, Taiwan.
authors.forename: Chih-Wei
authors.initials: CW
authors.lastname: Tong
authors.forename: Jen-Ling
authors.initials: JL
authors.lastname: Wang
authors.forename: Mei-Sian
authors.initials: MS
authors.lastname: Jiang
authors.forename: Chia-Hao
authors.initials: CH
authors.lastname: Hsu
authors.forename: Wen-Teng
authors.initials: WT
authors.lastname: Chang
authors.forename: A-Min
authors.initials: AM
authors.lastname: Huang
mesh_terms: D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D055785:Gene Knockdown Techniques; D006801:Humans; D051265:NF-E2-Related Factor 1 / Q000378:metabolism*; D016501:Neurites / Q000378:metabolism*; D009447:Neuroblastoma / Q000235:genetics* / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D020218:Response Elements; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D051265:NF-E2-Related Factor 1; D012333:RNA, Messenger; D014157:Transcription Factors