Abf1 and Rap1 are general regulatory factors (GRFs) that contribute to transcriptional activation of a large number of genes, as well as to replication, silencing and telomere structure in yeast. In spite of their widespread roles in transcription, the scope of their functional targets genome-wide has not been previously determined. Here, we use microarrays to examine the contribution of these essential GRFs to transcription genome-wide, by using ts mutants that dissociate from their binding sites at 37°C. We then combine this data with published ChIP-chip studies and motif analysis to identify probable direct targets for Abf1 and Rap1. We also identify a substantial number of genes likely to bind Rap1 or Abf1, but not affected by loss of GRF binding. Interestingly, the results strongly suggest that Rap1 can contribute to gene activation from farther upstream than can Abf1. Also, consistent with previous work, more genes that bind Abf1 are unaffected by loss of binding than those that bind Rap1. Finally, we show for several such genes that the Abf1 C-terminal region, which contains the putative activation domain, is not needed to confer this peculiar ‘memory effect’ that allows continued transcription after loss of Abf1 binding.

Autonomously replicating sequence binding factor 1 (ABF1) and repressor/activator protein 1 (RAP1) from budding yeast are multifunctional, site-specific DNA-binding proteins, with roles in gene activation and repression, replication, and telomere structure and function. Previously we have shown that RAP1 can prevent nucleosome positioning in the vicinity of its binding site and have provided evidence that this ability to create a local region of "open" chromatin contributes to RAP1 function at the HIS4 promoter by facilitating binding and activation by GCN4. Here we examine and directly compare to that of RAP1 the ability of ABF1 to create a region of open chromatin near its binding site and to contribute to activated transcription at the HIS4, ADE5,7, and HIS7 promoters. ABF1 behaves similarly to RAP1 in these assays, but it shows some subtle differences from RAP1 in the character of the open chromatin region near its binding site. Furthermore, although the two factors can similarly enhance activated transcription at the promoters tested, RAP1 binding is continuously required for this enhancement, but ABF1 binding is not. These results indicate that ABF1 and RAP1 achieve functional similarity in part via mechanistically distinct pathways.Autonomously replicating sequence (ARS) binding factor 1 (ABF1) and repressor/activator protein 1 (RAP1) are multifunctional proteins expressed in the budding yeast Saccharomyces cerevisiae that have both been categorized as general regulatory factors (GRFs) (3). Both proteins play important roles in transcriptional activation and repression, gene silencing, recombination, and telomere structure, and both are abundant and essential for cell growth (12,39,45). Binding sites for both proteins are present in the promoter regions of numerous yeast genes, and ABF1 and RAP1 have been shown to contribute to transcriptional activation of genes involved in carbon source regulation, sporulation, amino acid biosynthesis, and ribosomal functions (21,32,33,45). ABF1 and RAP1 act in concert to prevent gene expression at the silenced mating-type loci (7). ABF1 has also been implicated in gene silencing within subtelomeric regions (35) and nucleotide excision repair of silenced chromosomal regions (36), whereas RAP1 binds directly to telomere repeats to initiate formation of heterochromatin-like telomere structures (11).Given their overlapping functions, it is not surprising that in several specific instances ABF1 and RAP1 have been found to be directly interchangeable. Both RAP1 and ABF1 can synergize with T-rich elements present in the rpS33 and rpL45 promoters to activate transcription (8), and they have also been reported to be interchangeable at the TRP3 promoter (23). Both RAP1 and ABF1 binding sites in ribosomal protein gene promoters are associated with recruitment of Esa1p and concomitant histone acetylation, as well as with recruitment of TFIID (24, 37). Furthermore, binding sites for RAP1 and ABF1 support ARS1 replication origin function equally well in a plasmid stability assay (22...