RESUMO
AIM: To find out common transcription factor binding sites in the promoter regions of the encoding genes of the co-expressive proteins induced by N-methyl-N'-nitro-N- nitrosoguanidine (MNNG). METHODS: Using phylogenetic footprinting and TRANSFAC position weight matrix (PWM) searching program to predict the common transcription factor binding sites among the promoter regions of the genes encoding the co-expressive proteins. The predictive results were validated with electrophoresis mobility shift assay (EMSA). RESULTS: Eleven common transcription factor binding sites were predicted in the promoters of the co-expressive proteins, among them, besides the activator protein 1(AP1) which was previously identified to be activated in MNNG pretreated cells in this laboratory, the nuclear factor Y (NFY) and GATA binding factor (GATA) consensus oligonucleotides binding activity were found being increased in the nuclear extract of cells pre-treated with MNNG as demonstrated by EMSA. CONCLUSION: Phylogenetic footprinting can effectively decrease the false positive rate in predicting transcription factor binding sites. It is possible that NFY and GATA transcription factor binding sites are involved in the co-regulation of the MNNG induced co- expressive proteins. [
RESUMO
Gene transcriptional regulation research is one of the major challenges in the post-genome era. Bioinformatics has become more important with the rapid accumulation of complete genome sequences and the advances of computational methods and related databases. The current computational approaches in promoter prediction, transcription factor binding site identification, composite elements prediction, co-regulation of gene expression analysis and phylogenetic footprinting in the regulatory region analysis are discussed in this review.