The differential binding of E2F and CDF repressor complexes contributes to the timing of cell cycle-regulated transcription

B-myb and cdc25C exemplify different groups of genes whose transcription is consecutively up-regulated during the cell cycle, Both promoters are controlled by transcriptional repression via modules consisting of an E2F binding site (E2FBS) or the related CDE plus a contiguous CHR co-repressor element, We now show that the B-myb repressor module, which is derepressed early (mid G(1)), is preferentially recognized by E2F-DP complexes and that a mutation selectively abolishing E2F binding impairs regulation, In contrast, the cdc25C repressor module, which is derepressed late (S/G(2)), interacts selectively with CDE-CHR binding factor-1 (CDF-1), E2F binding, but not CDF-1 binding, requires specific nucleotides flanking the E2FBS/CDE core, while CDF-1 binding, but not E2F binding, depends on specific nucleotides in the CHR. Swapping these nucleotides between the two promoters profoundly changes protein binding patterns and alters expression kinetics, Thus predominant CDF-1 binding leads to derepression in late S, predominant E2F binding results in up-regulation in rate G(1), while promoters binding both E2F and CDF-1 with high efficiency show intermediate kinetics, Our results support a model where the differential binding of E2F and CDF-1 repressor complexes contributes to the timing of promoter activity during the cell cycle.