Genome-wide identification of sites that transcription factor ABF1 binds in S. cerevisiae

Abstract

Gene regulation is a complex process. Numerous factors appear to be required for the accurate temporal and spatial regulation of each gene. ABF1 is a sequence-specific transcription factor that is involved in disparate processes in yeast. ABF1 also binds DNA sequences associated with several ARSs. We carried out a genome wide prediction of ABF1 binding sites. Formaldehyde cross-linking was used to rapidly fix in vivo protein-DNA complex to conserve and analyze native structures. Antibody was used to immunoprecipitate ABF1 from the whole-cell extract. This describes a simple and sensitive method to determine whether a known protein is associated with specific DNA sequences. After cloning immunoprecipitated DNA into plasmid vector, PCR analysis of the cloned plasmid confirmed specific association of ABF1 with known target promoters. Sequencing and data base search were carried out. 93 sites that may bind with ABF1 were predicted. Among the predicted 93 sites, 7 sites corresponded with known sites. These results suggest that ABF1 may regulate many sites widely as well as known binding sites.